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Replication initiation: Implications in genome integrity. DNA Repair (Amst) 2021; 103:103131. [PMID: 33992866 DOI: 10.1016/j.dnarep.2021.103131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 02/01/2023]
Abstract
In every cell cycle, billions of nucleotides need to be duplicated within hours, with extraordinary precision and accuracy. The molecular mechanism by which cells regulate the replication event is very complicated, and the entire process begins way before the onset of S phase. During the G1 phase of the cell cycle, cells prepare by assembling essential replication factors to establish the pre-replicative complex at origins, sites that dictate where replication would initiate during S phase. During S phase, the replication process is tightly coupled with the DNA repair system to ensure the fidelity of replication. Defects in replication and any error must be recognized by DNA damage response and checkpoint signaling pathways in order to halt the cell cycle before cells are allowed to divide. The coordination of these processes throughout the cell cycle is therefore critical to achieve genomic integrity and prevent diseases. In this review, we focus on the current understanding of how the replication initiation events are regulated to achieve genome stability.
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Ma S, Cao C, Che S, Wang Y, Su D, Liu S, Gong W, Liu L, Sun J, Zhao J, Wang Q, Song N, Ge T, Guo Q, Tian S, Chen CD, Zhang T, Wang J, Ding X, Yang F, Ying G, Yang J, Zhang K, Zhu Y, Yao Z, Yang N, Shi L. PHF8-promoted TOPBP1 demethylation drives ATR activation and preserves genome stability. SCIENCE ADVANCES 2021; 7:7/19/eabf7684. [PMID: 33952527 PMCID: PMC8099190 DOI: 10.1126/sciadv.abf7684] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 03/16/2021] [Indexed: 05/03/2023]
Abstract
The checkpoint kinase ATR [ATM (ataxia-telangiectasia mutated) and rad3-related] is a master regulator of DNA damage response. Yet, how ATR activity is regulated remains to be investigated. We report here that histone demethylase PHF8 (plant homeodomain finger protein 8) plays a key role in ATR activation and replication stress response. Mechanistically, PHF8 interacts with and demethylates TOPBP1 (DNA topoisomerase 2-binding protein 1), an essential allosteric activator of ATR, under unperturbed conditions, but replication stress results in PHF8 phosphorylation and dissociation from TOPBP1. Consequently, hypomethylated TOPBP1 facilitates RAD9 (RADiation sensitive 9) binding and chromatin loading of the TOPBP1-RAD9 complex to fully activate ATR and thus safeguard the genome and protect cells against replication stress. Our study uncovers a demethylation and phosphorylation code that controls the assembly of TOPBP1-scaffolded protein complex, and provides molecular insight into non-histone methylation switch in ATR activation.
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Affiliation(s)
- Shuai Ma
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Cheng Cao
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Shiyou Che
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, 300353 Tianjin, China
| | - Yuejiao Wang
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Dongxue Su
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Shuai Liu
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Wenchen Gong
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Ling Liu
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Jixue Sun
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, 300353 Tianjin, China
| | - Jiao Zhao
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Qian Wang
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Nan Song
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Tong Ge
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Qiushi Guo
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Shanshan Tian
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Charlie Degui Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Tao Zhang
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Ju Wang
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Xiang Ding
- Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Fuquan Yang
- Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Guoguang Ying
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Jie Yang
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Kai Zhang
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Yi Zhu
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Zhi Yao
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China.
| | - Na Yang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, 300353 Tianjin, China.
| | - Lei Shi
- State Key Laboratory of Experimental Hematology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China.
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Abstract
Frattini et al. (2021) demonstrate that TopBP1 forms phase-separated nuclear condensates to promote activation of ATR in cells experiencing genomic stress.
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54
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Cancer genome datamining and functional genetic analysis implicate mechanisms of ATM/ATR dysfunction underpinning carcinogenesis. Commun Biol 2021; 4:363. [PMID: 33742106 PMCID: PMC7979806 DOI: 10.1038/s42003-021-01884-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 02/17/2021] [Indexed: 12/16/2022] Open
Abstract
ATM and ATR are conserved regulators of the DNA damage response linked to cancer. Comprehensive DNA sequencing efforts identified ~4,000 cancer-associated mutations in ATM/ATR; however, their cancer implications remain largely unknown. To gain insights, we identify functionally important conserved residues in ATM, ATR and budding yeast Mec1ATR via cancer genome datamining and a functional genetic analysis, respectively. Surprisingly, only a small fraction of the critical residues is in the active site of the respective enzyme complexes, implying that loss of the intrinsic kinase activity is infrequent in carcinogenesis. A number of residues are solvent accessible, suggestive of their involvement in interacting with a protein-partner(s). The majority, buried inside the respective enzyme complexes, might play a structural or regulatory role. Together, these findings identify evolutionarily conserved ATM, ATR, and Mec1ATR residues involved in diverse aspects of the enzyme function and provide fresh insights into the elusive genotype-phenotype relationships in ATM/ATR and their cancer-associated variants. Waskiewicz et al. identify functionally important and evolutionarily conserved residues of ATM/ATR via data mining and a functional genetic analysis, finding that loss of the intrinsic kinase activity occurs infrequently in carcinogenesis. This study provides insights into the genotype-phenotype relationships in ATM/ATR and their cancer-associated variants.
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55
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ATM: Translating the DNA Damage Response to Adaptive Immunity. Trends Immunol 2021; 42:350-365. [PMID: 33663955 DOI: 10.1016/j.it.2021.02.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/22/2021] [Accepted: 02/01/2021] [Indexed: 12/20/2022]
Abstract
ATM is often dubbed the master regulator of the DNA double stranded break (DSB) response. Since proper induction and repair of DNA DSBs forms the core of immunological diversity, it is surprising that patients with ataxia telangiectasia generally have a mild immunodeficiency in contrast to other DSB repair syndromes. In this review, we address this discrepancy by delving into the functions of ATM in DSB repair and cell cycle control and translate these to adaptive immunity. We conclude that ATM, despite its myriad functions, is not an absolute requirement for acquiring sufficient levels of immunological diversity to prevent severe viral and opportunistic infections. There is, however, a more clinically pronounced antibody deficiency in ataxia telangiectasia due to disturbed class switch recombination.
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56
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Thada V, Cortez D. ATR activation is regulated by dimerization of ATR activating proteins. J Biol Chem 2021; 296:100455. [PMID: 33636182 PMCID: PMC7994790 DOI: 10.1016/j.jbc.2021.100455] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/17/2021] [Accepted: 02/22/2021] [Indexed: 02/06/2023] Open
Abstract
The checkpoint kinase ATR regulates DNA repair, cell cycle progression, and other DNA damage and replication stress responses. ATR signaling is stimulated by an ATR activating protein, and in metazoan cells, there are at least two ATR activators: TOPBP1 and ETAA1. Current evidence indicates TOPBP1 and ETAA1 activate ATR via the same biochemical mechanism, but several aspects of this mechanism remain undefined. For example, ATR and its obligate binding partner ATR interacting protein (ATRIP) form a tetrameric complex consisting of two ATR and two ATRIP molecules, but whether TOPBP1 or ETAA1 dimerization is similarly required for ATR function is unclear. Here, we show that fusion of the TOPBP1 and ETAA1 ATR activation domains (AADs) to dimeric tags makes them more potent activators of ATR in vitro. Furthermore, induced dimerization of both AADs using chemical dimerization of a modified FKBP tag enhances ATR kinase activation and signaling in cells. ETAA1 forms oligomeric complexes mediated by regions of the protein that are predicted to be intrinsically disordered. Induced dimerization of a “mini-ETAA1” protein that contains the AAD and Replication Protein A (RPA) interaction motifs enhances ATR signaling, rescues cellular hypersensitivity to DNA damaging agents, and suppresses micronuclei formation in ETAA1-deficient cells. Together, our results indicate that TOPBP1 and ETAA1 dimerization is important for optimal ATR signaling and genome stability.
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Affiliation(s)
- Vaughn Thada
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville Tennessee, USA
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville Tennessee, USA.
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57
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Control of replication stress and mitosis in colorectal cancer stem cells through the interplay of PARP1, MRE11 and RAD51. Cell Death Differ 2021; 28:2060-2082. [PMID: 33531658 PMCID: PMC8257675 DOI: 10.1038/s41418-020-00733-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/20/2020] [Accepted: 12/30/2020] [Indexed: 12/31/2022] Open
Abstract
Cancer stem cells (CSCs) are tumor subpopulations driving disease development, progression, relapse and therapy resistance, and their targeting ensures tumor eradication. CSCs display heterogeneous replication stress (RS), but the functionality/relevance of the RS response (RSR) centered on the ATR-CHK1 axis is debated. Here, we show that the RSR is efficient in primary CSCs from colorectal cancer (CRC-SCs), and describe unique roles for PARP1 and MRE11/RAD51. First, we demonstrated that PARP1 is upregulated in CRC-SCs resistant to several replication poisons and RSR inhibitors (RSRi). In these cells, PARP1 modulates replication fork speed resulting in low constitutive RS. Second, we showed that MRE11 and RAD51 cooperate in the genoprotection and mitosis execution of PARP1-upregulated CRC-SCs. These roles represent therapeutic vulnerabilities for CSCs. Indeed, PARP1i sensitized CRC-SCs to ATRi/CHK1i, inducing replication catastrophe, and prevented the development of resistance to CHK1i. Also, MRE11i + RAD51i selectively killed PARP1-upregulated CRC-SCs via mitotic catastrophe. These results provide the rationale for biomarker-driven clinical trials in CRC using distinct RSRi combinations.
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58
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Frattini C, Promonet A, Alghoul E, Vidal-Eychenie S, Lamarque M, Blanchard MP, Urbach S, Basbous J, Constantinou A. TopBP1 assembles nuclear condensates to switch on ATR signaling. Mol Cell 2021; 81:1231-1245.e8. [PMID: 33503405 DOI: 10.1016/j.molcel.2020.12.049] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 10/01/2020] [Accepted: 12/16/2020] [Indexed: 12/13/2022]
Abstract
ATR checkpoint signaling is crucial for cellular responses to DNA replication impediments. Using an optogenetic platform, we show that TopBP1, the main activator of ATR, self-assembles extensively to yield micrometer-sized condensates. These opto-TopBP1 condensates are functional entities organized in tightly packed clusters of spherical nano-particles. TopBP1 condensates are reversible, occasionally fuse, and co-localize with TopBP1 partner proteins. We provide evidence that TopBP1 condensation is a molecular switch that amplifies ATR activity to phosphorylate checkpoint kinase 1 (Chk1) and slow down replication forks. Single amino acid substitutions of key residues in the intrinsically disordered ATR activation domain disrupt TopBP1 condensation and consequently ATR/Chk1 signaling. In physiologic salt concentration and pH, purified TopBP1 undergoes liquid-liquid phase separation in vitro. We propose that the actuation mechanism of ATR signaling is the assembly of TopBP1 condensates driven by highly regulated multivalent and cooperative interactions.
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Affiliation(s)
- Camilla Frattini
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Alexy Promonet
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Emile Alghoul
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | | | - Marie Lamarque
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | | | - Serge Urbach
- Institut de Génomique Fonctionnelle, CNRS INSERM, Université de Montpellier, Montpellier, France
| | - Jihane Basbous
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France.
| | - Angelos Constantinou
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France.
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59
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Marin PA, Obonaga R, Pavani RS, da Silva MS, de Araujo CB, Lima AA, Avila CC, Cestari I, Machado CR, Elias MC. ATR Kinase Is a Crucial Player Mediating the DNA Damage Response in Trypanosoma brucei. Front Cell Dev Biol 2020; 8:602956. [PMID: 33415107 PMCID: PMC7783291 DOI: 10.3389/fcell.2020.602956] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/02/2020] [Indexed: 12/26/2022] Open
Abstract
DNA double-strand breaks (DSBs) are among the most deleterious lesions that threaten genome integrity. To address DSBs, eukaryotic cells of model organisms have evolved a complex network of cellular pathways that are able to detect DNA damage, activate a checkpoint response to delay cell cycle progression, recruit the proper repair machinery, and resume the cell cycle once the DNA damage is repaired. Cell cycle checkpoints are primarily regulated by the apical kinases ATR and ATM, which are conserved throughout the eukaryotic kingdom. Trypanosoma brucei is a divergent pathogenic protozoan parasite that causes human African trypanosomiasis (HAT), a neglected disease that can be fatal when left untreated. The proper signaling and accuracy of DNA repair is fundamental to T. brucei not only to ensure parasite survival after genotoxic stress but also because DSBs are involved in the process of generating antigenic variations used by this parasite to evade the host immune system. DSBs trigger a strong DNA damage response and efficient repair process in T. brucei, but it is unclear how these processes are coordinated. Here, by knocking down ATR in T. brucei using two different approaches (conditional RNAi and an ATR inhibitor), we show that ATR is required to mediate intra-S and partial G1/S checkpoint responses. ATR is also involved in replication fork stalling, is critical for H2A histone phosphorylation in a small group of cells and is necessary for the recruitment and upregulation of the HR-mediated DNA repair protein RAD51 after ionizing radiation (IR) induces DSBs. In summary, this work shows that apical ATR kinase plays a central role in signal transduction and is critical for orchestrating the DNA damage response in T. brucei.
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Affiliation(s)
- Paula Andrea Marin
- Laboratory of Cell Cycle (LCC), Center of Toxins, Immune Response and Cell Signaling (CETICs), Butantan Institute, São Paulo, Brazil
| | - Ricardo Obonaga
- Laboratory of Cell Cycle (LCC), Center of Toxins, Immune Response and Cell Signaling (CETICs), Butantan Institute, São Paulo, Brazil
| | - Raphael Souza Pavani
- Laboratory of Cell Cycle (LCC), Center of Toxins, Immune Response and Cell Signaling (CETICs), Butantan Institute, São Paulo, Brazil
| | - Marcelo Santos da Silva
- Laboratory of Cell Cycle (LCC), Center of Toxins, Immune Response and Cell Signaling (CETICs), Butantan Institute, São Paulo, Brazil
| | - Christiane Bezerra de Araujo
- Laboratory of Cell Cycle (LCC), Center of Toxins, Immune Response and Cell Signaling (CETICs), Butantan Institute, São Paulo, Brazil
| | - André Arruda Lima
- Laboratory of Cell Cycle (LCC), Center of Toxins, Immune Response and Cell Signaling (CETICs), Butantan Institute, São Paulo, Brazil
| | - Carla Cristi Avila
- Laboratory of Cell Cycle (LCC), Center of Toxins, Immune Response and Cell Signaling (CETICs), Butantan Institute, São Paulo, Brazil
| | - Igor Cestari
- Institute of Parasitology, McGill University, Montreal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Carlos Renato Machado
- Biochemical and Immunology Department, Institute of Biomedical Science, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Maria Carolina Elias
- Laboratory of Cell Cycle (LCC), Center of Toxins, Immune Response and Cell Signaling (CETICs), Butantan Institute, São Paulo, Brazil
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60
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Tannous EA, Yates LA, Zhang X, Burgers PM. Mechanism of auto-inhibition and activation of Mec1 ATR checkpoint kinase. Nat Struct Mol Biol 2020; 28:50-61. [PMID: 33169019 PMCID: PMC7855233 DOI: 10.1038/s41594-020-00522-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 09/24/2020] [Indexed: 01/01/2023]
Abstract
In response to DNA damage or replication fork stalling, the basal activity of Mec1ATR is stimulated in a cell-cycle-dependent manner, leading to cell-cycle arrest and the promotion of DNA repair. Mec1ATR dysfunction leads to cell death in yeast and causes chromosome instability and embryonic lethality in mammals. Thus, ATR is a major target for cancer therapies in homologous recombination-deficient cancers. Here we identify a single mutation in Mec1, conserved in ATR, that results in constitutive activity. Using cryo-electron microscopy, we determine the structures of this constitutively active form (Mec1(F2244L)-Ddc2) at 2.8 Å and the wild type at 3.8 Å, both in complex with Mg2+-AMP-PNP. These structures yield a near-complete atomic model for Mec1-Ddc2 and uncover the molecular basis for low basal activity and the conformational changes required for activation. Combined with biochemical and genetic data, we discover key regulatory regions and propose a Mec1 activation mechanism.
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Affiliation(s)
- Elias A Tannous
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO, USA
| | - Luke A Yates
- Section of Structural Biology, Department of Infectious Disease, Imperial College London, South Kensington, London, UK
| | - Xiaodong Zhang
- Section of Structural Biology, Department of Infectious Disease, Imperial College London, South Kensington, London, UK.
| | - Peter M Burgers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO, USA.
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61
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Lees-Miller JP, Cobban A, Katsonis P, Bacolla A, Tsutakawa SE, Hammel M, Meek K, Anderson DW, Lichtarge O, Tainer JA, Lees-Miller SP. Uncovering DNA-PKcs ancient phylogeny, unique sequence motifs and insights for human disease. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 163:87-108. [PMID: 33035590 PMCID: PMC8021618 DOI: 10.1016/j.pbiomolbio.2020.09.010] [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] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/12/2020] [Accepted: 09/29/2020] [Indexed: 01/26/2023]
Abstract
DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is a key member of the phosphatidylinositol-3 kinase-like (PIKK) family of protein kinases with critical roles in DNA-double strand break repair, transcription, metastasis, mitosis, RNA processing, and innate and adaptive immunity. The absence of DNA-PKcs from many model organisms has led to the assumption that DNA-PKcs is a vertebrate-specific PIKK. Here, we find that DNA-PKcs is widely distributed in invertebrates, fungi, plants, and protists, and that threonines 2609, 2638, and 2647 of the ABCDE cluster of phosphorylation sites are highly conserved amongst most Eukaryotes. Furthermore, we identify highly conserved amino acid sequence motifs and domains that are characteristic of DNA-PKcs relative to other PIKKs. These include residues in the Forehead domain and a novel motif we have termed YRPD, located in an α helix C-terminal to the ABCDE phosphorylation site loop. Combining sequence with biochemistry plus structural data on human DNA-PKcs unveils conserved sequence and conformational features with functional insights and implications. The defined generally progressive DNA-PKcs sequence diversification uncovers conserved functionality supported by Evolutionary Trace analysis, suggesting that for many organisms both functional sites and evolutionary pressures remain identical due to fundamental cell biology. The mining of cancer genomic data and germline mutations causing human inherited disease reveal that robust DNA-PKcs activity in tumors is detrimental to patient survival, whereas germline mutations compromising function are linked to severe immunodeficiency and neuronal degeneration. We anticipate that these collective results will enable ongoing DNA-PKcs functional analyses with biological and medical implications.
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Affiliation(s)
- James P Lees-Miller
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
| | - Alexander Cobban
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
| | - Panagiotis Katsonis
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Albino Bacolla
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA
| | - Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Katheryn Meek
- College of Veterinary Medicine, Department of Microbiology & Molecular Genetics, And Department of Pathobiology & Diagnostic Investigation, Michigan State University, East Lansing, MI, 48824, USA
| | - Dave W Anderson
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
| | - Olivier Lichtarge
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - John A Tainer
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Susan P Lees-Miller
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada.
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Nguyen DD, Kim EY, Sang PB, Chai W. Roles of OB-Fold Proteins in Replication Stress. Front Cell Dev Biol 2020; 8:574466. [PMID: 33043007 PMCID: PMC7517361 DOI: 10.3389/fcell.2020.574466] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/25/2020] [Indexed: 12/20/2022] Open
Abstract
Accurate DNA replication is essential for maintaining genome stability. However, this stability becomes vulnerable when replication fork progression is stalled or slowed - a condition known as replication stress. Prolonged fork stalling can cause DNA damage, leading to genome instabilities. Thus, cells have developed several pathways and a complex set of proteins to overcome the challenge at stalled replication forks. Oligonucleotide/oligosaccharide binding (OB)-fold containing proteins are a group of proteins that play a crucial role in fork protection and fork restart. These proteins bind to single-stranded DNA with high affinity and prevent premature annealing and unwanted nuclease digestion. Among these OB-fold containing proteins, the best studied in eukaryotic cells are replication protein A (RPA) and breast cancer susceptibility protein 2 (BRCA2). Recently, another RPA-like protein complex CTC1-STN1-TEN1 (CST) complex has been found to counter replication perturbation. In this review, we discuss the latest findings on how these OB-fold containing proteins (RPA, BRCA2, CST) cooperate to safeguard DNA replication and maintain genome stability.
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Affiliation(s)
| | | | | | - Weihang Chai
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, United States
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63
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Hiregange D, Naick H, Rao BJ. ATR signalling mediates the prosurvival function of phospho-NPM against PIDDosome mediated cell death. Cell Signal 2020; 71:109602. [DOI: 10.1016/j.cellsig.2020.109602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 03/14/2020] [Indexed: 12/14/2022]
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64
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Abstract
Cells confront DNA damage in every cell cycle. Among the most deleterious types of DNA damage are DNA double-strand breaks (DSBs), which can cause cell lethality if unrepaired or cancers if improperly repaired. In response to DNA DSBs, cells activate a complex DNA damage checkpoint (DDC) response that arrests the cell cycle, reprograms gene expression, and mobilizes DNA repair factors to prevent the inheritance of unrepaired and broken chromosomes. Here we examine the DDC, induced by DNA DSBs, in the budding yeast model system and in mammals.
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Affiliation(s)
- David P Waterman
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454, USA;
| | - James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454, USA;
| | - Marcus B Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA;
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65
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Dibitetto D, Sims JR, Ascenção CFR, Feng K, Kim D, Oberly S, Freire R, Smolka MB. Intrinsic ATR signaling shapes DNA end resection and suppresses toxic DNA-PKcs signaling. NAR Cancer 2020; 2:zcaa006. [PMID: 32743550 PMCID: PMC7380482 DOI: 10.1093/narcan/zcaa006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/08/2020] [Accepted: 04/16/2020] [Indexed: 12/13/2022] Open
Abstract
Most cancer cells experience oncogene-induced replication stress and, as a result, exhibit high intrinsic activation of the ATR kinase. Although cancer cells often become more dependent on ATR for survival, the precise mechanism by which ATR signaling ensures cancer cell fitness and viability remains incompletely understood. Here, we find that intrinsic ATR signaling is crucial for the ability of cancer cells to promote DNA end resection, the first step in homology-directed DNA repair. Inhibition of ATR over multiple cell division cycles depletes the pool of pro-resection factors and prevents the engagement of RAD51 as well as RAD52 at nuclear foci, leading to toxic DNA-PKcs signaling and hypersensitivity to PARP inhibitors. The effect is markedly distinct from acute ATR inhibition, which blocks RAD51-mediated repair but not resection and engagement of RAD52. Our findings reveal a key pro-resection function for ATR and define how ATR inhibitors can be used for effective manipulation of DNA end resection capacity and DNA repair outcomes in cancer cells.
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Affiliation(s)
- Diego Dibitetto
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jennie R Sims
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Carolline F R Ascenção
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Kevin Feng
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Dongsung Kim
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Susannah Oberly
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Raimundo Freire
- Unidad de Investigación, Hospital Universitario de Canarias, Ofra s/n, La Cuesta, 38320 La Laguna, Tenerife, Spain.,Instituto de Tecnologías Biomédicas, Universidad de La Laguna, 38200 La Laguna, Tenerife, Spain.,Universidad Fernando Pessoa Canarias, 35450 Las Palmas de Gran Canaria, Spain
| | - Marcus B Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
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66
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Makinwa Y, Musich PR, Zou Y. Phosphorylation-Dependent Pin1 Isomerization of ATR: Its Role in Regulating ATR's Anti-apoptotic Function at Mitochondria, and the Implications in Cancer. Front Cell Dev Biol 2020; 8:281. [PMID: 32426354 PMCID: PMC7203486 DOI: 10.3389/fcell.2020.00281] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/31/2020] [Indexed: 12/11/2022] Open
Abstract
Peptidyl-prolyl isomerization is an important post-translational modification of protein because proline is the only amino acid that can stably exist as cis and trans, while other amino acids are in the trans conformation in protein backbones. This makes prolyl isomerization a unique mechanism for cells to control many cellular processes. Isomerization is a rate-limiting process that requires a peptidyl-prolyl cis/trans isomerase (PPIase) to overcome the energy barrier between cis and trans isomeric forms. Pin1, a key PPIase in the cell, recognizes a phosphorylated Ser/Thr-Pro motif to catalyze peptidyl-prolyl isomerization in proteins. The significance of the phosphorylation-dependent Pin1 activity was recently highlighted for isomerization of ATR (ataxia telangiectasia- and Rad3-related). ATR, a PIKK protein kinase, plays a crucial role in DNA damage responses (DDR) by phosphorylating hundreds of proteins. ATR can form cis or trans isomers in the cytoplasm depending on Pin1 which isomerizes cis-ATR to trans-ATR. Trans-ATR functions primarily in the nucleus. The cis-ATR, containing an exposed BH3 domain, is anti-apoptotic at mitochondria by binding to tBid, preventing activation of pro-apoptotic Bax. Given the roles of apoptosis in many human diseases, particularly cancer, we propose that cytoplasmic cis-ATR enables cells to evade apoptosis, thus addicting cancer cells to cis-ATR formation for survival. But in normal DDR, a predominance of trans-ATR in the nucleus coordinates with a minimal level of cytoplasmic cis-ATR to promote DNA repair while preventing cell death; however, cells can die when DNA repair fails. Therefore, a delicate balance/equilibrium of the levels of cis- and trans-ATR is required to ensure the cellular homeostasis. In this review, we make a case that this anti-apoptotic role of cis-ATR supports oncogenesis, while Pin1 that drives the formation of trans-ATR suppresses tumor growth. We offer a potential, novel target that can be specifically targeted in cancer cells, without killing normal cells, to significantly reduce the adverse effects usually seen in cancer treatment. We also raise important issues regarding the roles of phosphorylation-dependent Pin1 isomerization of ATR in diseases and propose areas of future studies that would shed more understanding on this important cellular mechanism.
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Affiliation(s)
- Yetunde Makinwa
- Department of Cancer Biology, University of Toledo College of Medicine, Toledo, OH, United States
| | - Phillip R Musich
- Department of Biomedical Sciences, JH Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States
| | - Yue Zou
- Department of Cancer Biology, University of Toledo College of Medicine, Toledo, OH, United States.,Department of Biomedical Sciences, JH Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States
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67
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Colombo CV, Gnugnoli M, Gobbini E, Longhese MP. How do cells sense DNA lesions? Biochem Soc Trans 2020; 48:677-691. [PMID: 32219379 DOI: 10.1042/bst20191118] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/06/2020] [Accepted: 03/12/2020] [Indexed: 12/17/2023]
Abstract
DNA is exposed to both endogenous and exogenous DNA damaging agents that chemically modify it. To counteract the deleterious effects exerted by DNA lesions, eukaryotic cells have evolved a network of cellular pathways, termed DNA damage response (DDR). The DDR comprises both mechanisms devoted to repair DNA lesions and signal transduction pathways that sense DNA damage and transduce this information to specific cellular targets. These targets, in turn, impact a wide range of cellular processes including DNA replication, DNA repair and cell cycle transitions. The importance of the DDR is highlighted by the fact that DDR inactivation is commonly found in cancer and causes many different human diseases. The protein kinases ATM and ATR, as well as their budding yeast orthologs Tel1 and Mec1, act as master regulators of the DDR. The initiating events in the DDR entail both DNA lesion recognition and assembly of protein complexes at the damaged DNA sites. Here, we review what is known about the early steps of the DDR.
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Affiliation(s)
- Chiara Vittoria Colombo
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Marco Gnugnoli
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Elisa Gobbini
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
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68
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Gorecki L, Andrs M, Rezacova M, Korabecny J. Discovery of ATR kinase inhibitor berzosertib (VX-970, M6620): Clinical candidate for cancer therapy. Pharmacol Ther 2020; 210:107518. [PMID: 32109490 DOI: 10.1016/j.pharmthera.2020.107518] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/11/2020] [Indexed: 02/07/2023]
Abstract
Chemoresistance, radioresistance, and the challenge of achieving complete resection are major driving forces in the search for more robust and targeted anticancer therapies. Targeting the DNA damage response has recently attracted research interest, as these processes are enhanced in tumour cells. The major replication stress responder is ATM and Rad3-related (ATR) kinase, which is attracting attention worldwide with four drug candidates currently in phase I/II clinical trials. This review addresses a potent and selective small-molecule ATR inhibitor, which is known as VX-970 (also known as berzosertib or M6620), and summarizes the existing preclinical data to provide deep insight regarding its real potential. We also outline the transition from preclinical to clinical studies, as well as its relationships with other clinical candidates (AZD6738, VX-803 [M4344], and BAY1895344). The results suggest that VX-970 is indeed a promising anticancer drug that can be used both as monotherapy and in combination with either chemotherapy or radiotherapy strategies. Based on patient anamnesis and biomarker identification, VX-970 could become a valuable tool for oncologists in the fight against cancer.
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Affiliation(s)
- Lukas Gorecki
- Biomedical Research Center, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic
| | - Martin Andrs
- Biomedical Research Center, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic; Laboratory of Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Martina Rezacova
- Department of Medical Biochemistry, Faculty of Medicine in Hradec Kralove, Charles University, Simkova 870, 500 38 Hradec Kralove, Czech Republic
| | - Jan Korabecny
- Biomedical Research Center, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic.
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69
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Williams RM, Yates LA, Zhang X. Structures and regulations of ATM and ATR, master kinases in genome integrity. Curr Opin Struct Biol 2020; 61:98-105. [PMID: 31924595 DOI: 10.1016/j.sbi.2019.12.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/27/2019] [Accepted: 12/07/2019] [Indexed: 12/24/2022]
Abstract
Homologous recombination (HR) is a faithful repair mechanism for double stranded DNA breaks. Two highly homologous master kinases, the tumour suppressors ATM and ATR (Tel1 and Mec1 in yeast), coordinate cell cycle progression with repair during HR. Despite their importance, our molecular understanding of these apical coordinators has been limited, in part due to their large sizes. With the recent development in cryo-electron microscopy, significant advances have been made in structural characterisation of these proteins in the last two years. These structures, combined with new biochemical studies, now provide a more detailed understanding of how a low basal activity is maintained and how activation may occur. In this review, we summarize recent advances in the structural and molecular understanding of these key components in HR, compare the common and distinct features of these kinases and suggest aspects of structural components that are likely to be involved in regulating its activity.
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Affiliation(s)
- Rhys M Williams
- Section of Structural Biology, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Luke A Yates
- Section of Structural Biology, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Xiaodong Zhang
- Section of Structural Biology, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK.
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70
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Sun Y, McCorvie TJ, Yates LA, Zhang X. Structural basis of homologous recombination. Cell Mol Life Sci 2020; 77:3-18. [PMID: 31748913 PMCID: PMC6957567 DOI: 10.1007/s00018-019-03365-1] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 10/10/2019] [Accepted: 10/31/2019] [Indexed: 12/12/2022]
Abstract
Homologous recombination (HR) is a pathway to faithfully repair DNA double-strand breaks (DSBs). At the core of this pathway is a DNA recombinase, which, as a nucleoprotein filament on ssDNA, pairs with homologous DNA as a template to repair the damaged site. In eukaryotes Rad51 is the recombinase capable of carrying out essential steps including strand invasion, homology search on the sister chromatid and strand exchange. Importantly, a tightly regulated process involving many protein factors has evolved to ensure proper localisation of this DNA repair machinery and its correct timing within the cell cycle. Dysregulation of any of the proteins involved can result in unchecked DNA damage, leading to uncontrolled cell division and cancer. Indeed, many are tumour suppressors and are key targets in the development of new cancer therapies. Over the past 40 years, our structural and mechanistic understanding of homologous recombination has steadily increased with notable recent advancements due to the advances in single particle cryo electron microscopy. These have resulted in higher resolution structural models of the signalling proteins ATM (ataxia telangiectasia mutated), and ATR (ataxia telangiectasia and Rad3-related protein), along with various structures of Rad51. However, structural information of the other major players involved, such as BRCA1 (breast cancer type 1 susceptibility protein) and BRCA2 (breast cancer type 2 susceptibility protein), has been limited to crystal structures of isolated domains and low-resolution electron microscopy reconstructions of the full-length proteins. Here we summarise the current structural understanding of homologous recombination, focusing on key proteins in recruitment and signalling events as well as the mediators for the Rad51 recombinase.
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Affiliation(s)
- Yueru Sun
- Section of Structural Biology, Department of Infectious Diseases, Imperial College, London, SW7 2AZ, UK
| | - Thomas J McCorvie
- Section of Structural Biology, Department of Infectious Diseases, Imperial College, London, SW7 2AZ, UK
| | - Luke A Yates
- Section of Structural Biology, Department of Infectious Diseases, Imperial College, London, SW7 2AZ, UK
| | - Xiaodong Zhang
- Section of Structural Biology, Department of Infectious Diseases, Imperial College, London, SW7 2AZ, UK.
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71
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McGrail DJ, Lin CCJ, Dai H, Mo W, Li Y, Stephan C, Davies P, Lu Z, Mills GB, Lee JS, Lin SY. Defective Replication Stress Response Is Inherently Linked to the Cancer Stem Cell Phenotype. Cell Rep 2019; 23:2095-2106. [PMID: 29768207 DOI: 10.1016/j.celrep.2018.04.068] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 01/04/2018] [Accepted: 02/12/2018] [Indexed: 01/05/2023] Open
Abstract
Extensive spontaneous DNA damage from oncogene-induced replication stress is ubiquitous in precancerous lesions. While this damage induces differentiation, senescence, or apoptosis in normal cells, defects in DNA replication stress response (RSR) allow cells to continue proliferating, ultimately leading to early tumorigenesis. Using systems-level approaches, we developed a replication stress response defect gene signature that predicted risk of cancer development from hyperplastic lesions. Intriguingly, we found that replication stress response defects rewire non-malignant cells into a cancer stem cell (CSC)-like state, and analysis of CSCs indicated that they inherently harbor replication stress response defects. High-throughput drug screening to elucidate molecules required for survival of replication stress response defective cells identified a dependence on MEK/ERK signaling. Inhibition of this signaling cascade restored oncogene-induced senescence through a p53-independent MDM2/p21 axis. Moreover, MEK/ERK inhibition also depleted CSC populations. Together, these findings provide insights into the role of replication stress response defects in CSCs and an actionable pathway for therapeutic targeting.
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Affiliation(s)
- Daniel J McGrail
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Curtis Chun-Jen Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hui Dai
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wei Mo
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yang Li
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Clifford Stephan
- The Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Peter Davies
- The Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Zhimin Lu
- Brain Tumor Center and Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ju-Seog Lee
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shiaw-Yih Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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72
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Cryo-EM Structure of Nucleotide-Bound Tel1 ATM Unravels the Molecular Basis of Inhibition and Structural Rationale for Disease-Associated Mutations. Structure 2019; 28:96-104.e3. [PMID: 31740029 PMCID: PMC6945111 DOI: 10.1016/j.str.2019.10.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/05/2019] [Accepted: 10/18/2019] [Indexed: 01/20/2023]
Abstract
Yeast Tel1 and its highly conserved human ortholog ataxia-telangiectasia mutated (ATM) are large protein kinases central to the maintenance of genome integrity. Mutations in ATM are found in ataxia-telangiectasia (A-T) patients and ATM is one of the most frequently mutated genes in many cancers. Using cryoelectron microscopy, we present the structure of Tel1 in a nucleotide-bound state. Our structure reveals molecular details of key residues surrounding the nucleotide binding site and provides a structural and molecular basis for its intrinsically low basal activity. We show that the catalytic residues are in a productive conformation for catalysis, but the phosphatidylinositol 3-kinase-related kinase (PIKK) regulatory domain insert restricts peptide substrate access and the N-lobe is in an open conformation, thus explaining the requirement for Tel1 activation. Structural comparisons with other PIKKs suggest a conserved and common allosteric activation mechanism. Our work also provides a structural rationale for many mutations found in A-T and cancer.
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73
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Mota MBS, Carvalho MA, Monteiro ANA, Mesquita RD. DNA damage response and repair in perspective: Aedes aegypti, Drosophila melanogaster and Homo sapiens. Parasit Vectors 2019; 12:533. [PMID: 31711518 PMCID: PMC6849265 DOI: 10.1186/s13071-019-3792-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/05/2019] [Indexed: 01/18/2023] Open
Abstract
Background The maintenance of genomic integrity is the responsibility of a complex network, denominated the DNA damage response (DDR), which controls the lesion detection and DNA repair. The main repair pathways are base excision repair (BER), nucleotide excision repair (NER), mismatch repair (MMR), homologous recombination repair (HR) and non-homologous end joining repair (NHEJ). They correct double-strand breaks (DSB), single-strand breaks, mismatches and others, or when the damage is quite extensive and repair insufficient, apoptosis is activated. Methods In this study we used the BLAST reciprocal best-hit methodology to search for DDR orthologs proteins in Aedes aegypti. We also provided a comparison between Ae. aegypti, D. melanogaster and human DDR network. Results Our analysis revealed the presence of ATR and ATM signaling, including the H2AX ortholog, in Ae. aegypti. Key DDR proteins (orthologs to RAD51, Ku and MRN complexes, XP-components, MutS and MutL) were also identified in this insect. Other proteins were not identified in both Ae. aegypti and D. melanogaster, including BRCA1 and its partners from BRCA1-A complex, TP53BP1, PALB2, POLk, CSA, CSB and POLβ. In humans, their absence affects DSB signaling, HR and sub-pathways of NER and BER. Seven orthologs not known in D. melanogaster were found in Ae. aegypti (RNF168, RIF1, WRN, RAD54B, RMI1, DNAPKcs, ARTEMIS). Conclusions The presence of key DDR proteins in Ae. aegypti suggests that the main DDR pathways are functional in this insect, and the identification of proteins not known in D. melanogaster can help fill gaps in the DDR network. The mapping of the DDR network in Ae. aegypti can support mosquito biology studies and inform genetic manipulation approaches applied to this vector.
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Affiliation(s)
- Maria Beatriz S Mota
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Marcelo Alex Carvalho
- Instituto Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Câncer, Divisão de Pesquisa Clínica, Rio de Janeiro, RJ, Brazil
| | - Alvaro N A Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Rafael D Mesquita
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. .,Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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74
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Ma M, Rodriguez A, Sugimoto K. Activation of ATR-related protein kinase upon DNA damage recognition. Curr Genet 2019; 66:327-333. [PMID: 31624858 DOI: 10.1007/s00294-019-01039-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/08/2019] [Accepted: 10/10/2019] [Indexed: 12/20/2022]
Abstract
Chromosomes are constantly damaged by exogenous and endogenous factors. To cope with DNA damage, eukaryotic cells are equipped with three phosphatidylinositol 3-kinase-related kinases (PIKKs), such as ATM, ATR, and DNA-PK. PIKKs are structurally related to phosphatidylinositol 3-kinase (lipid kinase), however possess protein kinase activities. The Mre11-Rad50-Nbs1 and the Ku complex interact with and activate ATM and DNA-PKcs at double-stranded DNA breaks (DSBs), respectively. In contrast, ATR responds to various types of DNA lesions by interacting with replication protein A (RPA)-covered single-stranded DNA (ssDNA). Several lines of evidence have established a model in which ATR is activated by interacting with ATR activating proteins including TopBP1 and ETAA1 at DNA lesions in humans, yet the interaction of ATR with RPA-covered ssDNA does not result in ATR activation. In budding yeast, the Mec1-Ddc2 complex (Mec1-Ddc2) corresponds to ATR-ATRIP. Similar to ATR, Mec1 activation is accomplished by interactions with Mec1 activating proteins, which are Ddc1, Dpb11 (TopBP1 homolog) and Dna2. However, recent studies provide results supporting the idea that Mec1ATR is also activated by interacting with RPA-covered ssDNA tracts. These observations suggest that all the ATM, ATR, DNA-PK family proteins can be activated immediately upon DNA damage recognition.
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Affiliation(s)
- Minh Ma
- Department of Microbiology, Biochemistry and Molecular Genetics, International Center for Public Health, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA
| | - Anibian Rodriguez
- Department of Microbiology, Biochemistry and Molecular Genetics, International Center for Public Health, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA
| | - Katsunori Sugimoto
- Department of Microbiology, Biochemistry and Molecular Genetics, International Center for Public Health, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA.
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75
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Wu T, Zhang Z, Wang X. Preparation of endogenous TopBP1/Dpb11 and effect on central checkpoint kinase Mec1- Ddc2 (human ATR-ATRIP homolog). Biochem Biophys Res Commun 2019; 517:291-296. [PMID: 31349966 DOI: 10.1016/j.bbrc.2019.07.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 07/17/2019] [Indexed: 11/18/2022]
Abstract
The Saccharomyces cerevisiae Mec1 kinase, the mammalian ATR ortholog, is essential for sensing a variety of DNA lesions and initiating DNA damage response. The Dpb11, a homolog of human TopBP1, functions in activating the Mec1 upon DNA replication stress and DNA damages. Here, we report an affinity purification and ion exchange chromatography method to efficiently purify endogenous Dpb11 under normal expression level directly from yeast whole cell extraction. The final concentration of 5 μM of high purity and homogeneity biochemical preparation enables functional and structural characterization of the physical interaction between Dpb11 and Mec1-Ddc2 complex. The Dpb11 obtained by endogenous purification strongly stimulates the Mec1 kinase activity and promotes the changes in conformational distribution. This observation suggests the Dpb11 activates Mec1 kinase probably through modulation in the kinase conformations.
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Affiliation(s)
- Tengwei Wu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China and Hefei National Laboratory for Physical Sciences at Microscale, Hefei, 230026, Anhui, China
| | - Zhihui Zhang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China and Hefei National Laboratory for Physical Sciences at Microscale, Hefei, 230026, Anhui, China
| | - Xuejuan Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China and Hefei National Laboratory for Physical Sciences at Microscale, Hefei, 230026, Anhui, China.
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76
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Deshar R, Yoo W, Cho EB, Kim S, Yoon JB. RNF8 mediates NONO degradation following UV-induced DNA damage to properly terminate ATR-CHK1 checkpoint signaling. Nucleic Acids Res 2019; 47:762-778. [PMID: 30445466 PMCID: PMC6344893 DOI: 10.1093/nar/gky1166] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 11/02/2018] [Indexed: 12/26/2022] Open
Abstract
RNF8 plays a critical role in DNA damage response (DDR) to initiate ubiquitination-dependent signaling. To better characterize the role of RNF8 in UV-induced DDR, we searched for novel substrates of RNF8 and identified NONO as one intriguing substrate. We found that: (i) RNF8 ubiquitinates NONO and (ii) UV radiation triggers NONO ubiquitination and its subsequent degradation. Depletion of RNF8 inhibited UV-induced degradation of NONO, suggesting that RNF8 targets NONO for degradation in response to UV damage. In addition, we found that 3 NONO lysine residues (positions 279, 290 and 295) are important for conferring its instability in UV-DDR. Depletion of RNF8 or expression of NONO with lysine to arginine substitutions at positions 279, 290 and 295 prolonged CHK1 phosphorylation over an extended period of time. Furthermore, expression of the stable mutant, but not wild-type NONO, induced a prolonged S phase following UV exposure. Stable cell lines expressing the stable NONO mutant showed increased UV sensitivity in a clonogenic survival assay. Since RNF8 recruitment to the UV-damaged sites is dependent on ATR, we propose that RNF8-mediated NONO degradation and subsequent inhibition of NONO-dependent chromatin loading of TOPBP1, a key activator of ATR, function as a negative feedback loop critical for turning off ATR-CHK1 checkpoint signaling in UV-DDR.
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Affiliation(s)
- Rakesh Deshar
- Department of Medical Lifesciences, The Catholic University of Korea, Seoul 137-701, Korea
| | - Wonjin Yoo
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Eun-Bee Cho
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Sungjoo Kim
- Department of Medical Lifesciences, The Catholic University of Korea, Seoul 137-701, Korea
| | - Jong-Bok Yoon
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 120-749, Korea
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77
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Biswas H, Goto G, Wang W, Sung P, Sugimoto K. Ddc2ATRIP promotes Mec1ATR activation at RPA-ssDNA tracts. PLoS Genet 2019; 15:e1008294. [PMID: 31369547 PMCID: PMC6692047 DOI: 10.1371/journal.pgen.1008294] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 08/13/2019] [Accepted: 07/07/2019] [Indexed: 11/19/2022] Open
Abstract
The DNA damage checkpoint response is controlled by the phosphatidylinositol 3-kinase-related kinases (PIKK), including ataxia telangiectasia-mutated (ATM) and ATM and Rad3-related (ATR). ATR forms a complex with its partner ATRIP. In budding yeast, ATR and ATRIP correspond to Mec1 and Ddc2, respectively. ATRIP/Ddc2 interacts with replication protein A-bound single-stranded DNA (RPA-ssDNA) and recruits ATR/Mec1 to sites of DNA damage. Mec1 is stimulated by the canonical activators including Ddc1, Dpb11 and Dna2. We have characterized the ddc2-S4 mutation and shown that Ddc2 not only recruits Mec1 to sites of DNA damage but also stimulates Mec1 kinase activity. However, the underlying mechanism of Ddc2-dependent Mec1 activation remains to be elucidated. Here we show that Ddc2 promotes Mec1 activation independently of Ddc1/Dpb11/Dna2 function in vivo and through ssDNA recognition in vitro. The ddc2-S4 mutation diminishes damage-induced phosphorylation of the checkpoint mediators, Rad9 and Mrc1. Rad9 controls checkpoint throughout the cell-cycle whereas Mrc1 is specifically required for the S-phase checkpoint. Notably, S-phase checkpoint signaling is more defective in ddc2-S4 mutants than in cells where the Mec1 activators (Ddc1/Dpb11 and Dna2) are dysfunctional. To understand a role of Ddc2 in Mec1 activation, we reconstituted an in vitro assay using purified Mec1-Ddc2 complex, RPA and ssDNA. Whereas ssDNA stimulates kinase activity of the Mec1-Ddc2 complex, RPA does not. However, RPA can promote ssDNA-dependent Mec1 activation. Neither ssDNA nor RPA-ssDNA efficiently stimulates the Mec1-Ddc2 complex containing Ddc2-S4 mutant. Together, our data support a model in which Ddc2 promotes Mec1 activation at RPA-ssDNA tracts.
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Affiliation(s)
- Himadri Biswas
- Department of Microbiology, Biochemistry and Molecular Genetics, International Center for Public Health, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
| | - Greicy Goto
- Department of Microbiology, Biochemistry and Molecular Genetics, International Center for Public Health, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
| | - Weibin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Katsunori Sugimoto
- Department of Microbiology, Biochemistry and Molecular Genetics, International Center for Public Health, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
- * E-mail:
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78
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Rozpędek W, Pytel D, Nowak-Zduńczyk A, Lewko D, Wojtczak R, Diehl JA, Majsterek I. Breaking the DNA Damage Response via Serine/Threonine Kinase Inhibitors to Improve Cancer Treatment. Curr Med Chem 2019; 26:1425-1445. [PMID: 29345572 DOI: 10.2174/0929867325666180117102233] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/13/2017] [Accepted: 11/24/2017] [Indexed: 12/22/2022]
Abstract
Multiple, both endogenous and exogenous, sources may induce DNA damage and DNA replication stress. Cells have developed DNA damage response (DDR) signaling pathways to maintain genomic stability and effectively detect and repair DNA lesions. Serine/ threonine kinases such as Ataxia-telangiectasia mutated (ATM) and Ataxia-telangiectasia and Rad3-Related (ATR) are the major regulators of DDR, since after sensing stalled DNA replication forks, DNA double- or single-strand breaks, may directly phosphorylate and activate their downstream targets, that play a key role in DNA repair, cell cycle arrest and apoptotic cell death. Interestingly, key components of DDR signaling networks may constitute an attractive target for anti-cancer therapy through two distinct potential approaches: as chemoand radiosensitizers to enhance the effectiveness of currently used genotoxic treatment or as single agents to exploit defects in DDR in cancer cells via synthetic lethal approach. Moreover, the newest data reported that serine/threonine protein kinase R (PKR)-like endoplasmic reticulum kinase (PERK) is also closely associated with cancer development and progression. Thereby, utilization of small-molecule, serine/threonine kinase inhibitors may provide a novel, groundbreaking, anti-cancer treatment strategy. Currently, a range of potent, highlyselective toward ATM, ATR and PERK inhibitors has been discovered, but after foregoing study, additional investigations are necessary for their future clinical use.
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Affiliation(s)
- Wioletta Rozpędek
- Department of Clinical Chemistry and Biochemistry, Military-Medical Faculty, Medical University of Lodz, Lodz, Poland
| | - Dariusz Pytel
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, United States
| | - Alicja Nowak-Zduńczyk
- Department of Clinical Chemistry and Biochemistry, Military-Medical Faculty, Medical University of Lodz, Lodz, Poland
| | - Dawid Lewko
- Department of Clinical Chemistry and Biochemistry, Military-Medical Faculty, Medical University of Lodz, Lodz, Poland
| | - Radosław Wojtczak
- Department of Clinical Chemistry and Biochemistry, Military-Medical Faculty, Medical University of Lodz, Lodz, Poland
| | - J Alan Diehl
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, United States
| | - Ireneusz Majsterek
- Department of Clinical Chemistry and Biochemistry, Military-Medical Faculty, Medical University of Lodz, Lodz, Poland
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79
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Mladenov E, Fan X, Dueva R, Soni A, Iliakis G. Radiation-dose-dependent functional synergisms between ATM, ATR and DNA-PKcs in checkpoint control and resection in G 2-phase. Sci Rep 2019; 9:8255. [PMID: 31164689 PMCID: PMC6547644 DOI: 10.1038/s41598-019-44771-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/23/2019] [Indexed: 12/31/2022] Open
Abstract
Using data generated with cells exposed to ionizing-radiation (IR) in G2-phase of the cell cycle, we describe dose-dependent interactions between ATM, ATR and DNA-PKcs revealing unknown mechanistic underpinnings for two key facets of the DNA damage response: DSB end-resection and G2-checkpoint activation. At low IR-doses that induce low DSB-numbers in the genome, ATM and ATR regulate epistatically the G2-checkpoint, with ATR at the output-node, interfacing with the cell-cycle predominantly through Chk1. Strikingly, at low IR-doses, ATM and ATR epistatically regulate also resection, and inhibition of either activity fully suppresses resection. At high IR-doses that induce high DSB-numbers in the genome, the tight ATM/ATR coupling relaxes and independent outputs to G2-checkpoint and resection occur. Consequently, both kinases must be inhibited to fully suppress checkpoint activation and resection. DNA-PKcs integrates to the ATM/ATR module by regulating resection at all IR-doses, with defects in DNA-PKcs causing hyper-resection and G2-checkpoint hyper-activation. Notably, hyper-resection is absent from other c-NHEJ mutants. Thus, DNA-PKcs specifically regulates resection and adjusts the activation of the ATM/ATR module. We propose that selected DSBs are shepherd by DNA-PKcs from c-NHEJ to resection-dependent pathways for processing under the regulatory supervision of the ATM/ATR module.
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Affiliation(s)
- Emil Mladenov
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122, Essen, Germany
| | - Xiaoxiang Fan
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122, Essen, Germany
| | - Rositsa Dueva
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122, Essen, Germany
| | - Aashish Soni
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122, Essen, Germany
| | - George Iliakis
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122, Essen, Germany.
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80
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Abd Rahim MS, Cherniavskyi YK, Tieleman DP, Dames SA. NMR- and MD simulation-based structural characterization of the membrane-associating FATC domain of ataxia telangiectasia mutated. J Biol Chem 2019; 294:7098-7112. [PMID: 30867195 PMCID: PMC6497961 DOI: 10.1074/jbc.ra119.007653] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/08/2019] [Indexed: 12/26/2022] Open
Abstract
The Ser/Thr protein kinase ataxia telangiectasia mutated (ATM) plays an important role in the DNA damage response, signaling in response to redox signals, the control of metabolic processes, and mitochondrial homeostasis. ATM localizes to the nucleus and at the plasma membrane, mitochondria, peroxisomes, and other cytoplasmic vesicular structures. It has been shown that the C-terminal FATC domain of human ATM (hATMfatc) can interact with a range of membrane mimetics and may thereby act as a membrane-anchoring unit. Here, NMR structural and 15N relaxation data, NMR data using spin-labeled micelles, and MD simulations of micelle-associated hATMfatc revealed that it binds the micelle by a dynamic assembly of three helices with many residues of hATMfatc located in the headgroup region. We observed that none of the three helices penetrates the micelle deeply or makes significant tertiary contacts to the other helices. NMR-monitored interaction experiments with hATMfatc variants in which two conserved aromatic residues (Phe3049 and Trp3052) were either individually or both replaced by alanine disclosed that the double substitution does not abrogate the interaction with micelles and bicelles at the high concentrations at which these aggregates are typically used, but impairs interactions with small unilamellar vesicles, usually used at much lower lipid concentrations and considered a better mimetic for natural membranes. We conclude that the observed dynamic structure of micelle-associated hATMfatc may enable it to interact with differently composed membranes or membrane-associated interaction partners and thereby regulate ATM's kinase activity. Moreover, the FATC domain of ATM may function as a membrane-anchoring unit for other biomolecules.
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Affiliation(s)
- Munirah S Abd Rahim
- From the Chair of Biomolecular NMR Spectroscopy, Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Yevhen K Cherniavskyi
- the Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Calgary, Alberta T2N 1N4, Canada, and
| | - D Peter Tieleman
- the Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Calgary, Alberta T2N 1N4, Canada, and
| | - Sonja A Dames
- From the Chair of Biomolecular NMR Spectroscopy, Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany,
- the Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
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81
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Abstract
Besides TopBP1, ETAA1 has been identified more recently as an activator of the ATR-ATRIP complex in human cells. We have examined the role of ETAA1 in the Xenopus egg-extract system, which has been instrumental in the study of ATR-ATRIP. Depletion of ETAA1 from egg extracts did not noticeably reduce the activation of ATR-ATRIP in response to replication stress, as monitored by the ATR-dependent phosphorylation of Chk1 and RPA. Moreover, lack of ETAA1 did not appear to affect DNA replication during an unperturbed S-phase. Significantly, we find that TopBP1 is considerably more abundant than ETAA1 in egg extracts. We proceeded to show that ETAA1 could support the activation of ATR-ATRIP in response to replication stress if we increased its concentration in egg extracts by adding extra full-length recombinant ETAA1. Thus, TopBP1 appears to be the predominant activator of ATR-ATRIP in response to replication stress in this system. We have also explored the biochemical mechanism by which ETAA1 activates ATR-ATRIP. We have developed an in vitro system in which full-length recombinant ETAA1 supports activation of ATR-ATRIP in the presence of defined components. We find that binding of ETAA1 to RPA associated with single-stranded DNA (ssDNA) greatly stimulates its ability to activate ATR-ATRIP. Thus, RPA-coated ssDNA serves as a direct positive effector in the ETAA1-mediated activation of ATR-ATRIP.
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Affiliation(s)
- Ke Lyu
- a Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , CA , USA
| | - Akiko Kumagai
- a Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , CA , USA
| | - William G Dunphy
- a Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , CA , USA
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82
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Thada V, Cortez D. Common motifs in ETAA1 and TOPBP1 required for ATR kinase activation. J Biol Chem 2019; 294:8395-8402. [PMID: 30940728 DOI: 10.1074/jbc.ra119.008154] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/29/2019] [Indexed: 01/12/2023] Open
Abstract
DNA damage response Ser/Thr kinases, including ataxia telangiectasia-mutated (ATM) and Rad3-related (ATR), control cell cycle progression, DNA repair, and apoptosis. ATR is activated by ETAA1 activator of ATR kinase (ETAA1) or DNA topoisomerase II binding protein 1 (TOPBP1). Both ETAA1 and TOPBP1 contain experimentally defined ATR activation domains (AADs) that are mostly unstructured and have minimal sequence similarity. A tryptophan residue in both AADs is required for ATR activation, but the other features of these domains and the mechanism by which they activate ATR are unknown. In this study, using bioinformatic analyses, kinase assays, co-immunoprecipitation, and immunofluorescence measures of signaling, we more specifically defined the TOPBP1 and ETAA1 AADs and identified additional features of the AADs needed for ATR activation. We found that both ETAA1 and TOPBP1 contain a predicted coiled-coil motif that is required for ATR activation in vitro and in cells. Mutation of the predicted coiled coils does not alter AAD oligomerization but does impair binding of the AADs to ATR. These results suggest that TOPBP1 and ETAA1 activate ATR using similar motifs and mechanisms.
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Affiliation(s)
- Vaughn Thada
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232.
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83
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Day M, Rappas M, Ptasinska K, Boos D, Oliver AW, Pearl LH. BRCT domains of the DNA damage checkpoint proteins TOPBP1/Rad4 display distinct specificities for phosphopeptide ligands. eLife 2018; 7:e39979. [PMID: 30295604 PMCID: PMC6175577 DOI: 10.7554/elife.39979] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/24/2018] [Indexed: 12/28/2022] Open
Abstract
TOPBP1 and its fission yeast homologueRad4, are critical players in a range of DNA replication, repair and damage signalling processes. They are composed of multiple BRCT domains, some of which bind phosphorylated motifs in other proteins. They thus act as multi-point adaptors bringing proteins together into functional combinations, dependent on post-translational modifications downstream of cell cycle and DNA damage signals. We have now structurally and/or biochemically characterised a sufficient number of high-affinity complexes for the conserved N-terminal region of TOPBP1 and Rad4 with diverse phospho-ligands, including human RAD9 and Treslin, and Schizosaccharomyces pombe Crb2 and Sld3, to define the determinants of BRCT domain specificity. We use this to identify and characterise previously unknown phosphorylation-dependent TOPBP1/Rad4-binding motifs in human RHNO1 and the fission yeast homologue of MDC1, Mdb1. These results provide important insights into how multiple BRCT domains within TOPBP1/Rad4 achieve selective and combinatorial binding of their multiple partner proteins.
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Affiliation(s)
- Matthew Day
- Cancer Research UK DNA Repair Enzymes GroupGenome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Mathieu Rappas
- Cancer Research UK DNA Repair Enzymes GroupGenome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Katie Ptasinska
- Genome Damage and Stability CentreSchool of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Dominik Boos
- Fakultät für BiologieUniversität Duisburg-EssenGermanyUnited Kingdom
| | - Antony W Oliver
- Cancer Research UK DNA Repair Enzymes GroupGenome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Laurence H Pearl
- Cancer Research UK DNA Repair Enzymes GroupGenome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
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84
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Abstract
The chemical treatment of cancer started with the realization that DNA damaging agents such as mustard gas present notable antitumoural properties. Consequently, early drug development focused on genotoxic chemicals, some of which are still widely used in the clinic. However, the efficacy of such therapies is often limited by the side effects of these drugs on healthy cells. A refinement to this approach is to use compounds that can exploit the presence of DNA damage in cancer cells. Given that replication stress (RS) is a major source of genomic instability in cancer, targeting the RS-response kinase ataxia telangiectasia and Rad3-related protein (ATR) has emerged as a promising alternative. With ATR inhibitors now entering clinical trials, we here revisit the biology behind this strategy and discuss potential biomarkers that could be used for a better selection of patients who respond to therapy.
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Affiliation(s)
- Emilio Lecona
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Oscar Fernandez-Capetillo
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden.
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85
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Ohashi E, Tsurimoto T. Functions of Multiple Clamp and Clamp-Loader Complexes in Eukaryotic DNA Replication. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1042:135-162. [PMID: 29357057 DOI: 10.1007/978-981-10-6955-0_7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Proliferating cell nuclear antigen (PCNA) and replication factor C (RFC) were identified in the late 1980s as essential factors for replication of simian virus 40 DNA in human cells, by reconstitution of the reaction in vitro. Initially, they were only thought to be involved in the elongation stage of DNA replication. Subsequent studies have demonstrated that PCNA functions as more than a replication factor, through its involvement in multiple protein-protein interactions. PCNA appears as a functional hub on replicating and replicated chromosomal DNA and has an essential role in the maintenance genome integrity in proliferating cells.Eukaryotes have multiple paralogues of sliding clamp, PCNA and its loader, RFC. The PCNA paralogues, RAD9, HUS1, and RAD1 form the heterotrimeric 9-1-1 ring that is similar to the PCNA homotrimeric ring, and the 9-1-1 clamp complex is loaded onto sites of DNA damage by its specific loader RAD17-RFC. This alternative clamp-loader system transmits DNA-damage signals in genomic DNA to the checkpoint-activation network and the DNA-repair apparatus.Another two alternative loader complexes, CTF18-RFC and ELG1-RFC, have roles that are distinguishable from the role of the canonical loader, RFC. CTF18-RFC interacts with one of the replicative DNA polymerases, Polε, and loads PCNA onto leading-strand DNA, and ELG1-RFC unloads PCNA after ligation of lagging-strand DNA. In the progression of S phase, these alternative PCNA loaders maintain appropriate amounts of PCNA on the replicating sister DNAs to ensure that specific enzymes are tethered at specific chromosomal locations.
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Affiliation(s)
- Eiji Ohashi
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Toshiki Tsurimoto
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan.
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86
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Kumbhar R, Vidal-Eychenié S, Kontopoulos DG, Larroque M, Larroque C, Basbous J, Kossida S, Ribeyre C, Constantinou A. Recruitment of ubiquitin-activating enzyme UBA1 to DNA by poly(ADP-ribose) promotes ATR signalling. Life Sci Alliance 2018; 1:e201800096. [PMID: 30456359 PMCID: PMC6238597 DOI: 10.26508/lsa.201800096] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 06/14/2018] [Accepted: 06/14/2018] [Indexed: 01/23/2023] Open
Abstract
The DNA damage response (DDR) ensures cellular adaptation to genotoxic insults. In the crowded environment of the nucleus, the assembly of productive DDR complexes requires multiple protein modifications. How the apical E1 ubiquitin activation enzyme UBA1 integrates spatially and temporally in the DDR remains elusive. Using a human cell-free system, we show that poly(ADP-ribose) polymerase 1 promotes the recruitment of UBA1 to DNA. We find that the association of UBA1 with poly(ADP-ribosyl)ated protein-DNA complexes is necessary for the phosphorylation replication protein A and checkpoint kinase 1 by the serine/threonine protein kinase ataxia-telangiectasia and RAD3-related, a prototypal response to DNA damage. UBA1 interacts directly with poly(ADP-ribose) via a solvent-accessible and positively charged patch conserved in the Animalia kingdom but not in Fungi. Thus, ubiquitin activation can anchor to poly(ADP-ribose)-seeded protein assemblies, ensuring the formation of functional ataxia-telangiectasia mutated and RAD3-related-signalling complexes.
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Affiliation(s)
- Ramhari Kumbhar
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier, France
| | - Sophie Vidal-Eychenié
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier, France
| | | | | | - Christian Larroque
- Institut de Recherche en Cancérologie de Montpellier, Université de Montpellier, Institut National de la Santé et de la Recherche Médicale, Montpellier, France
| | - Jihane Basbous
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier, France
| | - Sofia Kossida
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier, France.,IMGT, The International ImMunoGeneTics Information System, Montpellier, France
| | - Cyril Ribeyre
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier, France
| | - Angelos Constantinou
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier, France
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87
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Lanz MC, Oberly S, Sanford EJ, Sharma S, Chabes A, Smolka MB. Separable roles for Mec1/ATR in genome maintenance, DNA replication, and checkpoint signaling. Genes Dev 2018; 32:822-835. [PMID: 29899143 PMCID: PMC6049512 DOI: 10.1101/gad.308148.117] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 04/27/2018] [Indexed: 02/02/2023]
Abstract
In this study, Lanz et al. investigated how the Mec1/ATR kinase functions in genome maintenance and replication and, using a novel genetic system to spatially manipulate Mec1 activation and action, show that the ability of Mec1 to suppress genomic instabilities is separate from a novel role in promoting DNA replication. These findings establish that the Mec1/ATR kinase initiates checkpoint signaling, promotes DNA replication, and maintains genetic stability through distinct modes of action. The Mec1/ATR kinase coordinates multiple cellular responses to replication stress. In addition to its canonical role in activating the checkpoint kinase Rad53, Mec1 also plays checkpoint-independent roles in genome maintenance that are not well understood. Here we used a combined genetic–phosphoproteomic approach to manipulate Mec1 activation and globally monitor Mec1 signaling, allowing us to delineate distinct checkpoint-independent modes of Mec1 action. Using cells in which endogenous Mec1 activators were genetically ablated, we found that expression of “free” Mec1 activation domains (MADs) can robustly activate Mec1 and rescue the severe DNA replication and growth defects of these cells back to wild-type levels. However, unlike the activation mediated by endogenous activator proteins, “free” MADs are unable to stimulate Mec1-mediated suppression of gross chromosomal rearrangements (GCRs), revealing that Mec1's role in genome maintenance is separable from a previously unappreciated proreplicative function. Both Mec1's functions in promoting replication and suppressing GCRs are independent of the downstream checkpoint kinases. Additionally, Mec1-dependent GCR suppression seems to require localized Mec1 action at DNA lesions, which correlates with the phosphorylation of activator-proximal substrates involved in homologous recombination-mediated DNA repair. These findings establish that Mec1 initiates checkpoint signaling, promotes DNA replication, and maintains genetic stability through distinct modes of action.
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Affiliation(s)
- Michael Charles Lanz
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
| | - Susannah Oberly
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
| | - Ethan James Sanford
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
| | - Sushma Sharma
- Department of Medical Biochemistry and Biophysics.,Laboratory for Molecular Infection Medicine (MIMS), Umeå University, Umeå SE 90187, Sweden
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics.,Laboratory for Molecular Infection Medicine (MIMS), Umeå University, Umeå SE 90187, Sweden
| | - Marcus Bustamante Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
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88
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Imseng S, Aylett CHS, Maier T. Architecture and activation of phosphatidylinositol 3-kinase related kinases. Curr Opin Struct Biol 2018; 49:177-189. [DOI: 10.1016/j.sbi.2018.03.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/02/2018] [Accepted: 03/08/2018] [Indexed: 12/23/2022]
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89
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Rahim MSA, Sommer LAM, Wacker A, Schaad M, Dames SA. 1H, 15N, and 13C chemical shift assignments of the micelle immersed FAT C-terminal (FATC) domains of the human protein kinases ataxia-telangiectasia mutated (ATM) and DNA-dependent protein kinase catalytic subunit (DNA-PKcs) fused to the B1 domain of streptococcal protein G (GB1). BIOMOLECULAR NMR ASSIGNMENTS 2018; 12:149-154. [PMID: 29349619 DOI: 10.1007/s12104-018-9798-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/01/2018] [Indexed: 06/07/2023]
Abstract
FAT C-terminal (FATC) is a circa 33 residue-long domain. It controls the kinase functionality in phosphatidylinositol-3 kinase-related kinases (PIKKs). Recent NMR- and CD-monitored interaction studies indicated that the FATC domains of all PIKKs can interact with membrane mimetics albeit with different preferences for membrane properties such as surface charge and curvature. Thus they may generally act as membrane anchoring unit. Here, we present the 1H, 15N, and 13C chemical shift assignments of the DPC micelle immersed FATC domains of the human PIKKs ataxia-telangiectasia mutated (ATM, residues 3024-3056) and DNA protein kinase catalytic subunit (DNA-PKcs, residues 4096-4128), both fused to the 56 residue long B1 domain of Streptococcal protein G (GB1). Each fusion protein is 100 amino acids long and contains in the linking region between the GB1 tag and the FATC region a thrombin (LVPRGS) and an enterokinase (DDDDK) protease site. The assignments pave the route for the detailed structural characterization of the membrane mimetic bound states, which will help to better understand the role of the proper cellular localization at membranes for the function and regulation of PIKKs. The chemical shift assignment of the GB1 tag is useful for NMR spectroscopists developing new experiments or using GB1 otherwise for case studies in the field of in-cell NMR spectroscopy or protein folding. Moreover it is often used as purification tag. Earlier we showed already that GB1 does not interact with membrane mimetics and thus does not disturb the NMR monitoring of membrane mimetic interactions of attached proteins.
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Affiliation(s)
- Munirah S Abd Rahim
- Department of Chemistry, Biomolecular NMR Spectroscopy, Technische Universität München, Lichtenbergstr. 4, 85747, Garching, Germany
| | - Lisa A M Sommer
- Department of Chemistry, Biomolecular NMR Spectroscopy, Technische Universität München, Lichtenbergstr. 4, 85747, Garching, Germany
- Roche Diagnostics GmbH, Centralised and Point of Care Solutions, Nonnenwald 2, 82377, Penzberg, Germany
| | - Anja Wacker
- Department of Chemistry, Biomolecular NMR Spectroscopy, Technische Universität München, Lichtenbergstr. 4, 85747, Garching, Germany
- Division of Radiopharmaceutical Chemistry, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Martin Schaad
- Quintiles AG, Hochstrasse 50, 4053, Basel, Switzerland
| | - Sonja A Dames
- Department of Chemistry, Biomolecular NMR Spectroscopy, Technische Universität München, Lichtenbergstr. 4, 85747, Garching, Germany.
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
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90
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Caridi CP, Delabaere L, Tjong H, Hopp H, Das D, Alber F, Chiolo I. Quantitative Methods to Investigate the 4D Dynamics of Heterochromatic Repair Sites in Drosophila Cells. Methods Enzymol 2018. [PMID: 29523239 DOI: 10.1016/bs.mie.2017.11.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Heterochromatin is mostly composed of long stretches of repeated DNA sequences prone to ectopic recombination during double-strand break (DSB) repair. In Drosophila, "safe" homologous recombination (HR) repair of heterochromatic DSBs relies on a striking relocalization of repair sites to the nuclear periphery. Central to understanding heterochromatin repair is the ability to investigate the 4D dynamics (movement in space and time) of repair sites. A specific challenge of these studies is preventing phototoxicity and photobleaching effects while imaging the sample over long periods of time, and with sufficient time points and Z-stacks to track repair foci over time. Here we describe an optimized approach for high-resolution live imaging of heterochromatic DSBs in Drosophila cells, with a specific emphasis on the fluorescent markers and imaging setup used to capture the motion of repair foci over long-time periods. We detail approaches that minimize photobleaching and phototoxicity with a DeltaVision widefield deconvolution microscope, and image processing techniques for signal recovery postimaging using SoftWorX and Imaris software. We present a method to derive mean square displacement curves revealing some of the biophysical properties of the motion. Finally, we describe a method in R to identify tracts of directed motions (DMs) in mixed trajectories. These approaches enable a deeper understanding of the mechanisms of heterochromatin dynamics and genome stability in the three-dimensional context of the nucleus and have broad applicability in the field of nuclear dynamics.
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Affiliation(s)
| | | | - Harianto Tjong
- University of Southern California, Los Angeles, CA, United States
| | - Hannah Hopp
- University of Southern California, Los Angeles, CA, United States
| | - Devika Das
- University of Southern California, Los Angeles, CA, United States
| | - Frank Alber
- University of Southern California, Los Angeles, CA, United States
| | - Irene Chiolo
- University of Southern California, Los Angeles, CA, United States.
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91
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Cryo-EM structure of human ATR-ATRIP complex. Cell Res 2017; 28:143-156. [PMID: 29271416 DOI: 10.1038/cr.2017.158] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/01/2017] [Accepted: 12/05/2017] [Indexed: 12/18/2022] Open
Abstract
ATR (ataxia telangiectasia-mutated and Rad3-related) protein kinase and ATRIP (ATR-interacting protein) form a complex and play a critical role in response to replication stress and DNA damage. Here, we determined the cryo-electron microscopy (EM) structure of the human ATR-ATRIP complex at 4.7 Å resolution and built an atomic model of the C-terminal catalytic core of ATR (residues 1 521-2 644) at 3.9 Å resolution. The complex adopts a hollow "heart" shape, consisting of two ATR monomers in distinct conformations. The EM map for ATRIP reveals 14 HEAT repeats in an extended "S" shape. The conformational flexibility of ATR allows ATRIP to properly lock the N-termini of the two ATR monomers to favor ATR-ATRIP complex formation and functional diversity. The isolated "head-head" and "tail-tail" each adopts a pseudo 2-fold symmetry. The catalytic pockets face outward and substrate access is not restricted by inhibitory elements. Our studies provide a structural basis for understanding the assembly of the ATR-ATRIP complex and a framework for characterizing ATR-mediated DNA repair pathways.
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92
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Wang X, Ran T, Zhang X, Xin J, Zhang Z, Wu T, Wang W, Cai G. 3.9 Å structure of the yeast Mec1-Ddc2 complex, a homolog of human ATR-ATRIP. Science 2017; 358:1206-1209. [DOI: 10.1126/science.aan8414] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 11/01/2017] [Indexed: 12/12/2022]
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93
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Zafar MK, Eoff RL. Translesion DNA Synthesis in Cancer: Molecular Mechanisms and Therapeutic Opportunities. Chem Res Toxicol 2017; 30:1942-1955. [PMID: 28841374 DOI: 10.1021/acs.chemrestox.7b00157] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The genomic landscape of cancer is one marred by instability, but the mechanisms that underlie these alterations are multifaceted and remain a topic of intense research. Cellular responses to DNA damage and/or replication stress can affect genome stability in tumors and influence the response of patients to therapy. In addition to direct repair, DNA damage tolerance (DDT) is an element of genomic maintenance programs that contributes to the etiology of several types of cancer. DDT mechanisms primarily act to resolve replication stress, and this can influence the effectiveness of genotoxic drugs. Translesion DNA synthesis (TLS) is an important component of DDT that facilitates direct bypass of DNA adducts and other barriers to replication. The central role of TLS in the bypass of drug-induced DNA lesions, the promotion of tumor heterogeneity, and the involvement of these enzymes in the maintenance of the cancer stem cell niche presents an opportunity to leverage inhibition of TLS as a way of improving existing therapies. In the review that follows, we summarize mechanisms of DDT, misregulation of TLS in cancer, and discuss the potential for targeting these pathways as a means of improving cancer therapies.
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Affiliation(s)
- Maroof K Zafar
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
| | - Robert L Eoff
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
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94
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Lin X, Wei F, Whyte P, Tang D. BMI1 reduces ATR activation and signalling caused by hydroxyurea. Oncotarget 2017; 8:89707-89721. [PMID: 29163782 PMCID: PMC5685703 DOI: 10.18632/oncotarget.21111] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 09/03/2017] [Indexed: 01/31/2023] Open
Abstract
BMI1 facilitates DNA damage response (DDR) induced by double strand DNA breaks; however, it remains unknown whether BMI1 functions in single strand DNA (ssDNA) lesions-initiated DDR. We report here that BMI1 reduces hydroxyurea-elicited ATR activation, thereby reducing the S-phase checkpoints. Hydroxyurea induces ssDNA lesions, which activate ATR through binding TOPBP1 as evidenced by phosphorylation of ATR at threonine 1989 (ATRpT1989). ATR subsequently phosphorylates H2AX at serine 139 (γH2AX) and CHK1 at serine 345 (CHK1pS345), leading to phosphorylation of CDK1 at tyrosine 15 (CDK1pY15) and S-phase arrest. BMI1 overexpression reduced γH2AX, CHK1pS345, CDK1pY15, S-phase arrest, and ATR activation in HU-treated MCF7 and DU145 cells, whereas BMI1 knockdown enhanced these events. BMI1 contains a ring finger, helix-turn, proline/serine domain and two nuclear localization signals (NLS). Individual deletion of these domains did not abolish BMI1-derived reductions of CHK1pS345 in MCF7 cells following HU exposure, suggesting that these structural features are not essential for BMI1 to attenuate ATR-mediated CHK1pS345. BMI1 interacts with both TOPBP1 and ATR. Furthermore, all of our BMI1 mutants associate with endogenous TOPBP1. It has previously been established that association of TOPBP1 and ATR is required for ATR activation. Thus, our results suggest that BMI1 decreases ATR activation through a mechanism that involves binding to TOPBP1 and/or ATR.
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Affiliation(s)
- Xiaozeng Lin
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Father Sean O'Sullivan Research Institute, Hamilton, Ontario, Canada.,The Hamilton Center for Kidney Research, St. Joseph's Hospital, Hamilton, Ontario, Canada
| | - Fengxiang Wei
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Father Sean O'Sullivan Research Institute, Hamilton, Ontario, Canada.,The Hamilton Center for Kidney Research, St. Joseph's Hospital, Hamilton, Ontario, Canada.,The Genetics Laboratory, Longgang District Maternity and Child Healthcare Hospital, Longgang District, Shenzhen, Guangdong, P.R. China
| | - Peter Whyte
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Damu Tang
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Father Sean O'Sullivan Research Institute, Hamilton, Ontario, Canada.,The Hamilton Center for Kidney Research, St. Joseph's Hospital, Hamilton, Ontario, Canada
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95
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Moody C. Mechanisms by which HPV Induces a Replication Competent Environment in Differentiating Keratinocytes. Viruses 2017; 9:v9090261. [PMID: 28925973 PMCID: PMC5618027 DOI: 10.3390/v9090261] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 09/14/2017] [Accepted: 09/15/2017] [Indexed: 12/15/2022] Open
Abstract
Human papillomaviruses (HPV) are the causative agents of cervical cancer and are also associated with other genital malignancies, as well as an increasing number of head and neck cancers. HPVs have evolved their life cycle to contend with the different cell states found in the stratified epithelium. Initial infection and viral genome maintenance occurs in the proliferating basal cells of the stratified epithelium, where cellular replication machinery is abundant. However, the productive phase of the viral life cycle, including productive replication, late gene expression and virion production, occurs upon epithelial differentiation, in cells that normally exit the cell cycle. This review outlines how HPV interfaces with specific cellular signaling pathways and factors to provide a replication-competent environment in differentiating cells.
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Affiliation(s)
- Cary Moody
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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96
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Narayan S, Jaiswal AS, Sharma R, Nawab A, Duckworth LV, Law BK, Zajac-Kaye M, George TJ, Sharma J, Sharma AK, Hromas RA. NSC30049 inhibits Chk1 pathway in 5-FU-resistant CRC bulk and stem cell populations. Oncotarget 2017; 8:57246-57264. [PMID: 28915668 PMCID: PMC5593639 DOI: 10.18632/oncotarget.19778] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 07/20/2017] [Indexed: 01/20/2023] Open
Abstract
The 5-fluorouracil (5-FU) treatment induces DNA damage and stalling of DNA replication forks. These stalled replication forks then collapse to form one sided double-strand breaks, leading to apoptosis. However, colorectal cancer (CRC) stem cells rapidly repair the stalled/collapsed replication forks and overcome treatment effects. Recent evidence suggests a critical role of checkpoint kinase 1 (Chk1) in preventing the replicative stress. Therefore, Chk1 kinase has been a target for developing mono or combination therapeutic agents. In the present study, we have identified a novel orphan molecule NSC30049 (NSC49L) that is effective alone, and in combination potentiates 5-FU-mediated growth inhibition of CRC heterogeneous bulk and FOLFOX-resistant cell lines in culture with minimal effect on normal colonic epithelial cells. It also inhibits the sphere forming activity of CRC stem cells, and decreases the expression levels of mRNAs of CRC stem cell marker genes. Results showed that NSC49L induces 5-FU-mediated S-phase cell cycle arrest due to increased load of DNA damage and increased γ-H2AX staining as a mechanism of cytotoxicity. The pharmacokinetic analysis showed a higher bioavailability of this compound, however, with a short plasma half-life. The drug is highly tolerated by animals with no pathological aberrations. Furthermore, NSC49L showed very potent activity in a HDTX model of CRC stem cell tumors either alone or in combination with 5-FU. Thus, NSC49L as a single agent or combined with 5-FU can be developed as a therapeutic agent by targeting the Chk1 pathway in 5-FU-resistant CRC heterogeneous bulk and CRC stem cell populations.
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Affiliation(s)
- Satya Narayan
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, FL 32610, USA
| | - Aruna S. Jaiswal
- Department of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Ritika Sharma
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, FL 32610, USA
| | - Akbar Nawab
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, FL 32610, USA
| | - Lizette Vila Duckworth
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Brian K. Law
- Department of Pharmacology and Experimental Therapeutics, University of Florida, Gainesville, FL 32610, USA
| | - Maria Zajac-Kaye
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, FL 32610, USA
| | - Thomas J. George
- Department of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Jay Sharma
- Celprogen, Inc., Torrance, CA 90503, USA
| | - Arun K. Sharma
- Department of Pharmacology, Penn State Cancer Institute, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Robert A. Hromas
- Department of Medicine, University of Florida, Gainesville, FL 32610, USA
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97
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Saldivar JC, Cortez D, Cimprich KA. The essential kinase ATR: ensuring faithful duplication of a challenging genome. Nat Rev Mol Cell Biol 2017; 18:622-636. [PMID: 28811666 DOI: 10.1038/nrm.2017.67] [Citation(s) in RCA: 538] [Impact Index Per Article: 76.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
One way to preserve a rare book is to lock it away from all potential sources of damage. Of course, an inaccessible book is also of little use, and the paper and ink will continue to degrade with age in any case. Like a book, the information stored in our DNA needs to be read, but it is also subject to continuous assault and therefore needs to be protected. In this Review, we examine how the replication stress response that is controlled by the kinase ataxia telangiectasia and Rad3-related (ATR) senses and resolves threats to DNA integrity so that the DNA remains available to read in all of our cells. We discuss the multiple data that have revealed an elegant yet increasingly complex mechanism of ATR activation. This involves a core set of components that recruit ATR to stressed replication forks, stimulate kinase activity and amplify ATR signalling. We focus on the activities of ATR in the control of cell cycle checkpoints, origin firing and replication fork stability, and on how proper regulation of these processes is crucial to ensure faithful duplication of a challenging genome.
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Affiliation(s)
- Joshua C Saldivar
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, California 94305-5441, USA
| | - David Cortez
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, California 94305-5441, USA
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98
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Bournique E, Dall'Osto M, Hoffmann JS, Bergoglio V. Role of specialized DNA polymerases in the limitation of replicative stress and DNA damage transmission. Mutat Res 2017; 808:62-73. [PMID: 28843435 DOI: 10.1016/j.mrfmmm.2017.08.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 01/31/2023]
Abstract
Replication stress is a strong and early driving force for genomic instability and tumor development. Beside replicative DNA polymerases, an emerging group of specialized DNA polymerases is involved in the technical assistance of the replication machinery in order to prevent replicative stress and its deleterious consequences. During S-phase, altered progression of the replication fork by endogenous or exogenous impediments induces replicative stress, causing cells to reach mitosis with genomic regions not fully duplicated. Recently, specific mechanisms to resolve replication intermediates during mitosis with the aim of limiting DNA damage transmission to daughter cells have been identified. In this review, we detail the two major actions of specialized DNA polymerases that limit DNA damage transmission: the prevention of replicative stress by non-B DNA replication and the recovery of stalled replication forks.
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Affiliation(s)
- Elodie Bournique
- CRCT, Université de Toulouse, Inserm, CNRS, UPS Equipe Labellisée Ligue Contre le Cancer, Laboratoire d'Excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037, Toulouse, France
| | - Marina Dall'Osto
- CRCT, Université de Toulouse, Inserm, CNRS, UPS Equipe Labellisée Ligue Contre le Cancer, Laboratoire d'Excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037, Toulouse, France
| | - Jean-Sébastien Hoffmann
- CRCT, Université de Toulouse, Inserm, CNRS, UPS Equipe Labellisée Ligue Contre le Cancer, Laboratoire d'Excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037, Toulouse, France
| | - Valérie Bergoglio
- CRCT, Université de Toulouse, Inserm, CNRS, UPS Equipe Labellisée Ligue Contre le Cancer, Laboratoire d'Excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037, Toulouse, France.
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99
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Blackford AN, Jackson SP. ATM, ATR, and DNA-PK: The Trinity at the Heart of the DNA Damage Response. Mol Cell 2017; 66:801-817. [PMID: 28622525 DOI: 10.1016/j.molcel.2017.05.015] [Citation(s) in RCA: 1189] [Impact Index Per Article: 169.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 04/28/2017] [Accepted: 05/16/2017] [Indexed: 01/09/2023]
Abstract
In vertebrate cells, the DNA damage response is controlled by three related kinases: ATM, ATR, and DNA-PK. It has been 20 years since the cloning of ATR, the last of the three to be identified. During this time, our understanding of how these kinases regulate DNA repair and associated events has grown profoundly, although major questions remain unanswered. Here, we provide a historical perspective of their discovery and discuss their established functions in sensing and responding to genotoxic stress. We also highlight what is known regarding their structural similarities and common mechanisms of regulation, as well as emerging non-canonical roles and how our knowledge of ATM, ATR, and DNA-PK is being translated to benefit human health.
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Affiliation(s)
- Andrew N Blackford
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK; Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
| | - Stephen P Jackson
- Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
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100
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Baretić D, Pollard HK, Fisher DI, Johnson CM, Santhanam B, Truman CM, Kouba T, Fersht AR, Phillips C, Williams RL. Structures of closed and open conformations of dimeric human ATM. SCIENCE ADVANCES 2017; 3:e1700933. [PMID: 28508083 PMCID: PMC5425235 DOI: 10.1126/sciadv.1700933] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 04/19/2017] [Indexed: 05/31/2023]
Abstract
ATM (ataxia-telangiectasia mutated) is a phosphatidylinositol 3-kinase-related protein kinase (PIKK) best known for its role in DNA damage response. ATM also functions in oxidative stress response, insulin signaling, and neurogenesis. Our electron cryomicroscopy (cryo-EM) suggests that human ATM is in a dynamic equilibrium between closed and open dimers. In the closed state, the PIKK regulatory domain blocks the peptide substrate-binding site, suggesting that this conformation may represent an inactive or basally active enzyme. The active site is held in this closed conformation by interaction with a long helical hairpin in the TRD3 (tetratricopeptide repeats domain 3) domain of the symmetry-related molecule. The open dimer has two protomers with only a limited contact interface, and it lacks the intermolecular interactions that block the peptide-binding site in the closed dimer. This suggests that the open conformation may be more active. The ATM structure shows the detailed topology of the regulator-interacting N-terminal helical solenoid. The ATM conformational dynamics shown by the structures represent an important step in understanding the enzyme regulation.
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Affiliation(s)
- Domagoj Baretić
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Hannah K. Pollard
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Darwin Building, Cambridge CB4 0WG, UK
| | - David I. Fisher
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Darwin Building, Cambridge CB4 0WG, UK
| | | | - Balaji Santhanam
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Caroline M. Truman
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Darwin Building, Cambridge CB4 0WG, UK
| | - Tomas Kouba
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Alan R. Fersht
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Christopher Phillips
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Darwin Building, Cambridge CB4 0WG, UK
| | - Roger L. Williams
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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