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Thote V, Dinesh S, Sharma S. Prediction of deleterious non-synonymous SNPs of human MDC1 gene: an in silico approach. Syst Biol Reprod Med 2024; 70:101-112. [PMID: 38630598 DOI: 10.1080/19396368.2024.2325699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 02/24/2024] [Indexed: 04/19/2024]
Abstract
MDC1 (Mediator of DNA damage Checkpoint protein 1) functions to facilitate the localization of numerous DNA damage response (DDR) components to DNA double-strand break sites. MDC1 is an integral component in preserving genomic stability and appropriate DDR regulation. There haven't been systematic investigations of MDC1 mutations that induce cancer and genomic instability. Variations in nsSNPs have the potential to modify the protein chemistry and their function. Describing functional SNPs in disease-associated genes presents a significant conundrum for investigators, it is possible to assess potential functional SNPs before conducting larger population examinations. Multiple sequences and structure-based bioinformatics strategies were implemented in the current in-silico investigation to discern potential nsSNPs of the MDC1 genes. The nsSNPs were identified with SIFT, SNAP2, Align GVGD, PolyPhen-2, and PANTHER, and their stability was determined with MUpro. The conservation, solvent accessibility, and structural effects of the mutations were identified with ConSurf, NetSurfP-2.0, and SAAFEC-SEQ respectively. Cancer-related analysis of the nsSNPs was conducted using cBioPortal and TCGA web servers. The present study appraised five nsSNPs (P1426T, P69S, P194R, P203L, and H131Y) as probably mutilating due to their existence in highly conserved regions and propensity to deplete protein stability. The nsSNPs P194R, P203L, and H131Y were concluded as deleterious and possibly damaging from the 5 prediction tools. The functional nsSNP P194R mutation is associated with skin cutaneous melanoma while no significant records were found for other nsSNPs. The present study concludes that the highly deleterious P194R mutations can potentially induce genomic instability and contribute to various cancers' pathogenesis. Developing drugs targeting these mutations can undoubtedly be advantageous in large population-based studies, particularly in the development of precision medicine.
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Affiliation(s)
| | - Susha Dinesh
- Department of Bioinformatics, BioNome, Bengaluru, India
| | - Sameer Sharma
- Department of Bioinformatics, BioNome, Bengaluru, India
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Pandya K, Singh N. In silico study reveals unconventional interactions between MDC1 of DDR and Beclin-1 of autophagy. Mol Divers 2023; 27:2789-2802. [PMID: 36482226 DOI: 10.1007/s11030-022-10579-2] [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: 09/02/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022]
Abstract
DNA damage response (DDR) and autophagy are concerned with maintaining cellular homeostasis and dysregulation of these two pathways lead to pathologic conditions including tumorigenesis. Autophagy is activated as a protective mechanism during DDR which is indicative of their functional cooperativity but the molecular mechanism leading to the convergence of these two pathways during genotoxic stress remains elusive. In this study, through in silico analysis, we have shown an interaction between the Mediator of DNA damage checkpoint 1 (MDC1), an important DDR-associated protein, and Beclin-1, an autophagy inducer. MDC1 is an adaptor or scaffold protein known to regulate DDR, apoptosis, and cell cycle progression. While, Beclin-1 is involved in autophagosome nucleation and exhibits affinity for binding to Fork-head-associated domain (FHA) containing proteins. The FHA domain is commonly conserved in DDR-related proteins including MDC1. Through molecular docking, we have predicted the modeled complex between the MDC1 FHA domain and the Beclin-1 Coiled coil domain (CCD). The docking complex was modeled using ClusPro2.0, based on the crystal structure for the dimerized MDC1 FHA domain and Beclin-1 CCD. The complex stability and binding affinities were assessed using a Ramachandran plot, MD simulation, MM/GBSA, and PRODIGY webserver. Finally, the hot-spot residues at the interface were determined using computational alanine scanning by the DrugScorePPI webserver. Our analysis unveils significant interaction between MDC1 and Beclin-1, involving hydrogen bonds, non-bonded contacts, and salt bridges and indicates MDC1 possibly recruits Beclin-1 to the DSBs, as a consequence of which Beclin-1 is able to modulate DDR.
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Affiliation(s)
- Kavya Pandya
- Department of Biotechnology and Bioengineering, Indian Institute of Advanced Research, Gandhinagar, India
| | - Neeru Singh
- Department of Biotechnology and Bioengineering, Indian Institute of Advanced Research, Gandhinagar, India.
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DNA damage response revisited: the p53 family and its regulators provide endless cancer therapy opportunities. Exp Mol Med 2022; 54:1658-1669. [PMID: 36207426 PMCID: PMC9636249 DOI: 10.1038/s12276-022-00863-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 07/22/2022] [Accepted: 08/01/2022] [Indexed: 12/29/2022] Open
Abstract
Antitumor therapeutic strategies that fundamentally rely on the induction of DNA damage to eradicate and inhibit the growth of cancer cells are integral approaches to cancer therapy. Although DNA-damaging therapies advance the battle with cancer, resistance, and recurrence following treatment are common. Thus, searching for vulnerabilities that facilitate the action of DNA-damaging agents by sensitizing cancer cells is an active research area. Therefore, it is crucial to decipher the detailed molecular events involved in DNA damage responses (DDRs) to DNA-damaging agents in cancer. The tumor suppressor p53 is active at the hub of the DDR. Researchers have identified an increasing number of genes regulated by p53 transcriptional functions that have been shown to be critical direct or indirect mediators of cell fate, cell cycle regulation, and DNA repair. Posttranslational modifications (PTMs) primarily orchestrate and direct the activity of p53 in response to DNA damage. Many molecules mediating PTMs on p53 have been identified. The anticancer potential realized by targeting these molecules has been shown through experiments and clinical trials to sensitize cancer cells to DNA-damaging agents. This review briefly acknowledges the complexity of DDR pathways/networks. We specifically focus on p53 regulators, protein kinases, and E3/E4 ubiquitin ligases and their anticancer potential.
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Qin B, Yu J, Zhao F, Huang J, Zhou Q, Lou Z. Dynamic recruitment of UFM1-specific peptidase 2 to the DNA double-strand breaks regulated by WIP1. GENOME INSTABILITY & DISEASE 2022; 3:217-226. [PMID: 36042814 PMCID: PMC9418083 DOI: 10.1007/s42764-022-00076-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/17/2022] [Accepted: 07/24/2022] [Indexed: 10/29/2022]
Abstract
The ufmylation ligase-UFL1 promotes ATM activation by monoufmylating H4 at K31 in a positive-feedback loop after double-strand breaks (DSB) occur, whereas UFM1 Specific Peptidase 2 (UfSP2) suppresses ATM activation, but the mechanism of recruitment of UfSP2 to the DSB finetuning DNA damage response is still not clear. Here, we report that UfSP2 foci formation is delayed compared to UFL1 foci formation following the radiation insult. Mechanistically, UfSP2 binds to the MRN complex in absence of DSB. Irradiation-induced phosphorylation of UfSP2 by ATM leads to the dissociation of UfSP2 from the MRN complex. This phosphorylation can be removed by the phosphatase WIP1, thereby UfSP2 is recruited to the DSBs, deufmylating H4 and suppressing ATM activation. In summary, we identify a mechanism of delicately negative modulation of ATM activation by UfSP2 and rewires ATM activation pathways.
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Affiliation(s)
- Bo Qin
- Department of Oncology, Mayo Clinic, Rochester, MN 55905 USA
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905 USA
| | - Jia Yu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905 USA
| | - Fei Zhao
- Department of Oncology, Mayo Clinic, Rochester, MN 55905 USA
| | - Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, MN 55905 USA
| | - Qin Zhou
- Department of Oncology, Mayo Clinic, Rochester, MN 55905 USA
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN 55905 USA
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Kieffer SR, Lowndes NF. Immediate-Early, Early, and Late Responses to DNA Double Stranded Breaks. Front Genet 2022; 13:793884. [PMID: 35173769 PMCID: PMC8841529 DOI: 10.3389/fgene.2022.793884] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/10/2022] [Indexed: 12/18/2022] Open
Abstract
Loss or rearrangement of genetic information can result from incorrect responses to DNA double strand breaks (DSBs). The cellular responses to DSBs encompass a range of highly coordinated events designed to detect and respond appropriately to the damage, thereby preserving genomic integrity. In analogy with events occurring during viral infection, we appropriate the terms Immediate-Early, Early, and Late to describe the pre-repair responses to DSBs. A distinguishing feature of the Immediate-Early response is that the large protein condensates that form during the Early and Late response and are resolved upon repair, termed foci, are not visible. The Immediate-Early response encompasses initial lesion sensing, involving poly (ADP-ribose) polymerases (PARPs), KU70/80, and MRN, as well as rapid repair by so-called ‘fast-kinetic’ canonical non-homologous end joining (cNHEJ). Initial binding of PARPs and the KU70/80 complex to breaks appears to be mutually exclusive at easily ligatable DSBs that are repaired efficiently by fast-kinetic cNHEJ; a process that is PARP-, ATM-, 53BP1-, Artemis-, and resection-independent. However, at more complex breaks requiring processing, the Immediate-Early response involving PARPs and the ensuing highly dynamic PARylation (polyADP ribosylation) of many substrates may aid recruitment of both KU70/80 and MRN to DSBs. Complex DSBs rely upon the Early response, largely defined by ATM-dependent focal recruitment of many signalling molecules into large condensates, and regulated by complex chromatin dynamics. Finally, the Late response integrates information from cell cycle phase, chromatin context, and type of DSB to determine appropriate pathway choice. Critical to pathway choice is the recruitment of p53 binding protein 1 (53BP1) and breast cancer associated 1 (BRCA1). However, additional factors recruited throughout the DSB response also impact upon pathway choice, although these remain to be fully characterised. The Late response somehow channels DSBs into the appropriate high-fidelity repair pathway, typically either ‘slow-kinetic’ cNHEJ or homologous recombination (HR). Loss of specific components of the DSB repair machinery results in cells utilising remaining factors to effect repair, but often at the cost of increased mutagenesis. Here we discuss the complex regulation of the Immediate-Early, Early, and Late responses to DSBs proceeding repair itself.
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Genetically Engineered Live-Attenuated Middle East Respiratory Syndrome Coronavirus Viruses Confer Full Protection against Lethal Infection. mBio 2021; 12:mBio.00103-21. [PMID: 33653888 PMCID: PMC8092200 DOI: 10.1128/mbio.00103-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
There are no approved vaccines against the life-threatening Middle East respiratory syndrome coronavirus (MERS-CoV). Attenuated vaccines have proven their potential to induce strong and long-lasting immune responses. We have previously described that severe acute respiratory syndrome coronavirus (SARS-CoV) envelope (E) protein is a virulence factor. Based on this knowledge, a collection of mutants carrying partial deletions spanning the C-terminal domain of the E protein (rMERS-CoV-E*) has been generated using a reverse genetics system. One of these mutants, MERS-CoV-E*Δ2in, was attenuated and provided full protection in a challenge with virulent MERS-CoV after a single immunization dose. The MERS-CoV-E*Δ2in mutant was stable as it maintained its attenuation after 16 passages in cell cultures and has been selected as a promising vaccine candidate.IMPORTANCE The emergence of the new highly pathogenic human coronavirus SARS-CoV-2 that has already infected more than 80 million persons, killing nearly two million of them, clearly indicates the need to design efficient and safe vaccines protecting from these coronaviruses. Modern vaccines can be derived from virus-host interaction research directed to the identification of signaling pathways essential for virus replication and for virus-induced pathogenesis, in order to learn how to attenuate these viruses and design vaccines. Using a reverse genetics system developed in our laboratory, an infectious cDNA clone of MERS-CoV was engineered. Using this cDNA, we sequentially deleted several predicted and conserved motifs within the envelope (E) protein of MERS-CoV, previously associated with the presence of virulence factors. The in vitro and in vivo evaluation of these deletion mutants highlighted the relevance of predicted linear motifs in viral pathogenesis. Two of them, an Atg8 protein binding motif (Atg8-BM), and a forkhead-associated binding motif (FHA-BM), when deleted, rendered an attenuated virus that was evaluated as a vaccine candidate, leading to full protection against challenge with a lethal dose of MERS-CoV. This approach can be extended to the engineering of vaccines protecting against the new pandemic SARS-CoV-2.
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Cooperative Blockade of CK2 and ATM Kinases Drives Apoptosis in VHL-Deficient Renal Carcinoma Cells through ROS Overproduction. Cancers (Basel) 2021; 13:cancers13030576. [PMID: 33540838 PMCID: PMC7867364 DOI: 10.3390/cancers13030576] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 01/26/2021] [Accepted: 01/26/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Renal cell carcinoma (RCC) is the eighth leading malignancy in the world, accounting for 4% of all cancers with poor outcome when metastatic. Protein kinases are highly druggable proteins, which are often aberrantly activated in cancers. The aim of our study was to identify candidate targets for metastatic clear cell renal cell carcinoma therapy, using chemo-genomic-based high-throughput screening. We found that the combined inhibition of the CK2 and ATM kinases in renal tumor cells and patient-derived tumor samples induces synthetic lethality. Mechanistic investigations unveil that this drug combination triggers apoptosis through HIF-2α-(Hypoxic inducible factor HIF-2α) dependent reactive oxygen species (ROS) overproduction, giving a new option for patient care in metastatic RCC. Abstract Kinase-targeted agents demonstrate antitumor activity in advanced metastatic clear cell renal cell carcinoma (ccRCC), which remains largely incurable. Integration of genomic approaches through small-molecules and genetically based high-throughput screening holds the promise of improved discovery of candidate targets for cancer therapy. The 786-O cell line represents a model for most ccRCC that have a loss of functional pVHL (von Hippel-Lindau). A multiplexed assay was used to study the cellular fitness of a panel of engineered ccRCC isogenic 786-O VHL− cell lines in response to a collection of targeted cancer therapeutics including kinase inhibitors, allowing the interrogation of over 2880 drug–gene pairs. Among diverse patterns of drug sensitivities, investigation of the mechanistic effect of one selected drug combination on tumor spheroids and ex vivo renal tumor slice cultures showed that VHL-defective ccRCC cells were more vulnerable to the combined inhibition of the CK2 and ATM kinases than wild-type VHL cells. Importantly, we found that HIF-2α acts as a key mediator that potentiates the response to combined CK2/ATM inhibition by triggering ROS-dependent apoptosis. Importantly, our findings reveal a selective killing of VHL-deficient renal carcinoma cells and provide a rationale for a mechanism-based use of combined CK2/ATM inhibitors for improved patient care in metastatic VHL-ccRCC.
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Yu J, Qin B, Lou Z. Ubiquitin and ubiquitin-like molecules in DNA double strand break repair. Cell Biosci 2020; 10:13. [PMID: 32071713 PMCID: PMC7014694 DOI: 10.1186/s13578-020-0380-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 01/30/2020] [Indexed: 12/23/2022] Open
Abstract
Both environmental and endogenous factors induce various forms of DNA damage. DNA double strand break (DSB) is the most deleterious DNA lesion. The swift initiation of a complexed network of interconnected pathways to repair the DNA lesion is essential for cell survival. In the past years, the roles of ubiquitin and ubiquitin-like proteins in DNA damage response and DNA repair has been explored. These findings help us better understand the complicated mechanism of DSB signaling pathways.
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Affiliation(s)
- Jia Yu
- 1Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905 USA
| | - Bo Qin
- 1Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905 USA.,2Department of Oncology, Mayo Clinic, Rochester, MN 55905 USA.,3Gastrointestinal Research Unit, Mayo Clinic, Rochester, MN 55905 USA
| | - Zhenkun Lou
- 2Department of Oncology, Mayo Clinic, Rochester, MN 55905 USA
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Mahapatra K, Roy S. An insight into the mechanism of DNA damage response in plants- role of SUPPRESSOR OF GAMMA RESPONSE 1: An overview. Mutat Res 2020; 819-820:111689. [PMID: 32004947 DOI: 10.1016/j.mrfmmm.2020.111689] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/31/2019] [Accepted: 01/23/2020] [Indexed: 02/03/2023]
Abstract
Because of their sessile lifestyle, plants are inescapably exposed to various kinds of environmental stresses throughout their lifetime. Therefore, to regulate their growth and development, plants constantly monitor the environmental signals and respond appropriately. However, these environmental stress factors, along with some endogenous metabolites, generated in response to environmental stress factors often induce various forms of DNA damage in plants and thus promote genome instability. To maintain the genomic integrity, plants have developed an extensive, sophisticated and coordinated cellular signaling mechanism known as DNA damage response or DDR. DDR evokes a signaling process which initiates with the sensing of DNA damage and followed by the subsequent activation of downstream pathways in many directions to repair and eliminate the harmful effects of DNA damages. SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1), one of the newly identified components of DDR in plant genome, appears to play central role in this signaling network. SOG1 is a member of NAC [NO APICAL MERISTEM (NAM), ARABIDOPSIS TRANSCRIPTION ACTIVATION FACTOR (ATAF), CUP-SHAPED COTYLEDON (CUC)] domain family of transcription factors and involved in a diverse array of function in plants, encompassing transcriptional response to DNA damage, cell cycle checkpoint functions, ATAXIA-TELANGIECTASIA-MUTATED (ATM) or ATAXIA TELANGIECTASIA AND RAD3-RELATED (ATR) mediated activation of DNA damage response and repair, functioning in programmed cell death and regulation of induction of endoreduplication. Although most of the functional studies on SOG1 have been reported in Arabidopsis, some recent reports have indicated diverse functions of SOG1 in various other plant species, including Glycine max, Medicago truncatula, Sorghum bicolour, Oryza sativa and Zea mays, respectively. The remarkable functional diversity shown by SOG1 protein indicates its multitasking capacity. In this review, we integrate information mainly related to functional aspects of SOG1 in the context of DDR in plants. Considering the important role of SOG1 in DDR and its functional diversity, in-depth functional study of this crucial regulatory protein can provide further potential information on genome stability maintenance mechanism in plants in the context of changing environmental condition.
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Affiliation(s)
- Kalyan Mahapatra
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Golapbag Campus, Burdwan, 713 104, West Bengal, India
| | - Sujit Roy
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Golapbag Campus, Burdwan, 713 104, West Bengal, India.
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Salguero I, Belotserkovskaya R, Coates J, Sczaniecka-Clift M, Demir M, Jhujh S, Wilson MD, Jackson SP. MDC1 PST-repeat region promotes histone H2AX-independent chromatin association and DNA damage tolerance. Nat Commun 2019; 10:5191. [PMID: 31729360 PMCID: PMC6858307 DOI: 10.1038/s41467-019-12929-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 10/03/2019] [Indexed: 02/02/2023] Open
Abstract
Histone H2AX and MDC1 are key DNA repair and DNA-damage signalling proteins. When DNA double-strand breaks (DSBs) occur, H2AX is phosphorylated and then recruits MDC1, which in turn serves as a docking platform to promote the localization of other factors, including 53BP1, to DSB sites. Here, by using CRISPR-Cas9 engineered human cell lines, we identify a hitherto unknown, H2AX-independent, function of MDC1 mediated by its PST-repeat region. We show that the PST-repeat region directly interacts with chromatin via the nucleosome acidic patch and mediates DNA damage-independent association of MDC1 with chromatin. We find that this region is largely functionally dispensable when the canonical γH2AX-MDC1 pathway is operative but becomes critical for 53BP1 recruitment to DNA-damage sites and cell survival following DSB induction when H2AX is not available. Consequently, our results suggest a role for MDC1 in activating the DDR in areas of the genome lacking or depleted of H2AX.
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Affiliation(s)
- Israel Salguero
- Wellcome Trust/CRUK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Rimma Belotserkovskaya
- Wellcome Trust/CRUK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Julia Coates
- Wellcome Trust/CRUK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Matylda Sczaniecka-Clift
- Wellcome Trust/CRUK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Mukerrem Demir
- Wellcome Trust/CRUK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Satpal Jhujh
- Wellcome Trust/CRUK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Marcus D Wilson
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh, EH9 3JR, UK
| | - Stephen P Jackson
- Wellcome Trust/CRUK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.
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Luo Y, Wu J, Zou J, Cao Y, He Y, Ling H, Zeng T. BCL10 in cell survival after DNA damage. Clin Chim Acta 2019; 495:301-308. [PMID: 31047877 DOI: 10.1016/j.cca.2019.04.077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/21/2019] [Accepted: 04/23/2019] [Indexed: 01/01/2023]
Abstract
The complex defense mechanism of the DNA damage response (DDR) developed by cells during long-term evolution is an important mechanism for maintaining the stability of the genome. Defects in the DDR pathway can lead to the occurrence of various diseases, including tumor development. Most cancer treatments cause DNA damage and apoptosis. However, cancer cells have the natural ability to repair this damage and inhibit apoptosis, ultimately leading to the development of drug resistance. Therefore, investigating the mechanism of DNA damage may contribute markedly to the future treatment of cancer. The CARMA-BCL10-MALT1 (CBM) complex formed by B cell lymphoma/leukemia 10 (BCL10) regulates apoptosis by activating NF-κB signaling. BCL10 is involved in the formation of complexes that antagonize apoptosis and contribute to cell survival after DNA damage, with cytoplasmic BCL10 entering the nucleus to promote DNA damage repair, including histone ubiquitination and the recruitment of homologous recombination (HR) repair factors. This article reviews the role of BCL10 in cell survival following DNA damage.
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Affiliation(s)
- Yichen Luo
- Key Laboratory of Tumor Cellular & Molecular Pathology, College of Hunan Province, Cancer Research Institute, University of South China,Hengyang, Hunan 421001, China; Hunan Provincial Education Department document (Approval number: 2014-405], Hunan Province Cooperative innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan 421001, China
| | - Jing Wu
- Key Laboratory of Tumor Cellular & Molecular Pathology, College of Hunan Province, Cancer Research Institute, University of South China,Hengyang, Hunan 421001, China; Hunan Provincial Education Department document (Approval number: 2014-405], Hunan Province Cooperative innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan 421001, China
| | - Juan Zou
- Key Laboratory of Tumor Cellular & Molecular Pathology, College of Hunan Province, Cancer Research Institute, University of South China,Hengyang, Hunan 421001, China; Hunan Provincial Education Department document (Approval number: 2014-405], Hunan Province Cooperative innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan 421001, China
| | - Yijing Cao
- Key Laboratory of Tumor Cellular & Molecular Pathology, College of Hunan Province, Cancer Research Institute, University of South China,Hengyang, Hunan 421001, China; Hunan Provincial Education Department document (Approval number: 2014-405], Hunan Province Cooperative innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan 421001, China
| | - Yan He
- Key Laboratory of Tumor Cellular & Molecular Pathology, College of Hunan Province, Cancer Research Institute, University of South China,Hengyang, Hunan 421001, China; Department of Pathology, Longgang Central Hospital, Shenzhen, Guangdong 518000, China
| | - Hui Ling
- Key Laboratory of Tumor Cellular & Molecular Pathology, College of Hunan Province, Cancer Research Institute, University of South China,Hengyang, Hunan 421001, China; Hunan Provincial Education Department document (Approval number: 2014-405], Hunan Province Cooperative innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan 421001, China.
| | - Tiebing Zeng
- Hunan Provincial Education Department document (Approval number: 2014-405], Hunan Province Cooperative innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan 421001, China; Institute of Pathogenic Biology and Key Laboratory of Special Pathogen Prevention and Control of Hunan Province, University of South China, Hengyang, Hunan 421001, China.
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12
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Qin B, Yu J, Nowsheen S, Wang M, Tu X, Liu T, Li H, Wang L, Lou Z. UFL1 promotes histone H4 ufmylation and ATM activation. Nat Commun 2019; 10:1242. [PMID: 30886146 PMCID: PMC6423285 DOI: 10.1038/s41467-019-09175-0] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 02/21/2019] [Indexed: 12/20/2022] Open
Abstract
The ataxia-telangiectasia mutated (ATM) kinase, an upstream kinase of the DNA damage response (DDR), is rapidly activated following DNA damage, and phosphorylates its downstream targets to launch DDR signaling. However, the mechanism of ATM activation is still not completely understood. Here we report that UFM1 specific ligase 1 (UFL1), an ufmylation E3 ligase, is important for ATM activation. UFL1 is recruited to double strand breaks by the MRE11/RAD50/NBS1 complex, and monoufmylates histone H4 following DNA damage. Monoufmylated histone H4 is important for Suv39h1 and Tip60 recruitment. Furthermore, ATM phosphorylates UFL1 at serine 462, enhancing UFL1 E3 ligase activity and promoting ATM activation in a positive feedback loop. These findings reveal that ufmylation of histone H4 by UFL1 is an important step for amplification of ATM activation and maintenance of genomic integrity.
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Affiliation(s)
- Bo Qin
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jia Yu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Somaira Nowsheen
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
- Mayo Medical Scientist Training Program, Mayo Medical School and Mayo Graduate School, Mayo Clinic, Rochester, MN, 55905, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
| | - Xinyi Tu
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Tongzheng Liu
- Institute of Tumor Pharmacology, Jinan University, 510632, Guangzhou, China
| | - Honglin Li
- Department of Biochemistry & Molecular Biology, Cancer Center, Georgia Regents University, Augusta, GA, 30912, USA
| | - Liewei Wang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA.
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13
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Testa E, Nardozi D, Antinozzi C, Faieta M, Di Cecca S, Caggiano C, Fukuda T, Bonanno E, Zhenkun L, Maldonado A, Roig I, Di Giacomo M, Barchi M. H2AFX and MDC1 promote maintenance of genomic integrity in male germ cells. J Cell Sci 2018; 131:jcs.214411. [PMID: 29437857 DOI: 10.1242/jcs.214411] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 01/31/2018] [Indexed: 12/18/2022] Open
Abstract
In somatic cells, H2afx and Mdc1 are close functional partners in DNA repair and damage response. However, it is not known whether they are also involved in the maintenance of genome integrity in meiosis. By analyzing chromosome dynamics in H2afx-/- spermatocytes, we found that the synapsis of autosomes and X-Y chromosomes was impaired in a fraction of cells. Such defects correlated with an abnormal recombination profile. Conversely, Mdc1 was dispensable for the synapsis of the autosomes and played only a minor role in X-Y synapsis, compared with the action of H2afx This suggested that those genes have non-overlapping functions in chromosome synapsis. However, we observed that both genes play a similar role in the assembly of MLH3 onto chromosomes, a key step in crossover formation. Moreover, we show that H2afx and Mdc1 cooperate in promoting the activation of the recombination-dependent checkpoint, a mechanism that restrains the differentiation of cells with unrepaired DSBs. This occurs by a mechanism that involves P53. Overall, our data show that, in male germ cells, H2afx and Mdc1 promote the maintenance of genome integrity.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Erika Testa
- Department of Biomedicine and Prevention, Section of Anatomy, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Daniela Nardozi
- Department of Biomedicine and Prevention, Section of Anatomy, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Cristina Antinozzi
- Department of Biomedicine and Prevention, Section of Anatomy, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Monica Faieta
- Department of Biomedicine and Prevention, Section of Anatomy, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Stefano Di Cecca
- Department of Biomedicine and Prevention, Section of Anatomy, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Cinzia Caggiano
- Department of Biomedicine and Prevention, Section of Anatomy, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Tomoyuki Fukuda
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, 951-8510 Niigata, Japan.,Graduate School of Biological Sciences, Nara Institute of Science and Technology, 630-0192 Nara, Japan
| | - Elena Bonanno
- Department of Experimental Medicine and Surgery, Section of Pathological Anatomy, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Lou Zhenkun
- Division of Oncology Research, Department of Oncology, Mayo Clinic, Rochester, MN 55905 USA
| | - Andros Maldonado
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Ignasi Roig
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | | | - Marco Barchi
- Department of Biomedicine and Prevention, Section of Anatomy, University of Rome Tor Vergata, 00133 Rome, Italy
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14
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LRH1 enhances cell resistance to chemotherapy by transcriptionally activating MDC1 expression and attenuating DNA damage in human breast cancer. Oncogene 2018; 37:3243-3259. [DOI: 10.1038/s41388-018-0193-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 01/30/2018] [Accepted: 02/02/2018] [Indexed: 11/08/2022]
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15
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Lee NS, Chang HR, Kim S, Ji JH, Lee J, Lee HJ, Seo Y, Kang M, Han JS, Myung K, Kim Y, Kim H. Ring finger protein 126 (RNF126) suppresses ionizing radiation-induced p53-binding protein 1 (53BP1) focus formation. J Biol Chem 2017; 293:588-598. [PMID: 29167269 PMCID: PMC5767864 DOI: 10.1074/jbc.m116.765602] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 11/19/2017] [Indexed: 11/06/2022] Open
Abstract
Cells have evolved sophisticated mechanisms to maintain genomic integrity in response to DNA damage. Ionizing radiation (IR)-induced DNA damage results in the formation of IR-induced foci (iRIF) in the nucleus. The iRIF formation is part of the DNA damage response (DDR), which is an essential signaling cascade that must be strictly regulated because either the loss of or an augmented DDR leads to loss of genome integrity. Accordingly, negative regulation of the DDR is as critical as its activation. In this study, we have identified ring finger protein 126 (RNF126) as a negative regulator of the DDR from a screen of iRIF containing 53BP1. RNF126 overexpression abolishes not only the formation of 53BP1 iRIF but also of RNF168, FK2, RAP80, and BRCA1. However, the iRIF formation of γH2AX, MDC1, and RNF8 is maintained, indicating that RNF126 acts between RNF8 and RNF168 during the DDR. In addition, RNF126 overexpression consistently results in the loss of RNF168-mediated H2A monoubiquitination at lysine 13/15 and inhibition of the non-homologous end joining capability. Taken together, our findings reveal that RNF126 is a novel factor involved in the negative regulation of DDR, which is important for sustaining genomic integrity.
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Affiliation(s)
- Nam Soo Lee
- From the Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Hae Ryung Chang
- the Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Soomi Kim
- From the Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jae-Hoon Ji
- the Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Joorak Lee
- From the Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Hyun Ji Lee
- the Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Yoojeong Seo
- the Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Misun Kang
- the Center for Genomic Integrity, Institute for Basic Science, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea, and
| | - Joo Seok Han
- the Center for Genomic Integrity, Institute for Basic Science, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea, and
| | - Kyungjae Myung
- the Center for Genomic Integrity, Institute for Basic Science, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea, and
| | - Yonghwan Kim
- the Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea,
| | - Hongtae Kim
- From the Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea, .,the Center for Neuroscience Imaging Research, Institute for Basic Science, Sungkyunkwan University, Suwon 16419, Republic of Korea
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16
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Almawi AW, Matthews LA, Guarné A. FHA domains: Phosphopeptide binding and beyond. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 127:105-110. [DOI: 10.1016/j.pbiomolbio.2016.12.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 12/06/2016] [Indexed: 01/18/2023]
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17
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Pennisi R, Antoccia A, Leone S, Ascenzi P, di Masi A. Hsp90α regulates ATM and NBN functions in sensing and repair of DNA double-strand breaks. FEBS J 2017. [PMID: 28631426 DOI: 10.1111/febs.14145] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The molecular chaperone heat shock protein 90 (Hsp90α) regulates cell proteostasis and mitigates the harmful effects of endogenous and exogenous stressors on the proteome. Indeed, the inhibition of Hsp90α ATPase activity affects the cellular response to ionizing radiation (IR). Although the interplay between Hsp90α and several DNA damage response (DDR) proteins has been reported, its role in the DDR is still unclear. Here, we show that ataxia-telangiectasia-mutated kinase (ATM) and nibrin (NBN), but not 53BP1, RAD50, and MRE11, are Hsp90α clients as the Hsp90α inhibitor 17-(allylamino)-17-demethoxygeldanamycin (17-AAG) induces ATM and NBN polyubiquitination and proteosomal degradation in normal fibroblasts and lymphoblastoid cell lines. Hsp90α-ATM and Hsp90α-NBN complexes are present in unstressed and irradiated cells, allowing the maintenance of ATM and NBN stability that is required for the MRE11/RAD50/NBN complex-dependent ATM activation and the ATM-dependent phosphorylation of both NBN and Hsp90α in response to IR-induced DNA double-strand breaks (DSBs). Hsp90α forms a complex also with ph-Ser1981-ATM following IR. Upon phosphorylation, NBN dissociates from Hsp90α and translocates at the DSBs, while phThr5/7-Hsp90α is not recruited at the damaged sites. The inhibition of Hsp90α affects nuclear localization of MRE11 and RAD50, impairs DDR signaling (e.g., BRCA1 and CHK2 phosphorylation), and slows down DSBs repair. Hsp90α inhibition does not affect DNA-dependent protein kinase (DNA-PK) activity, which possibly phosphorylates Hsp90α and H2AX after IR. Notably, Hsp90α inhibition causes H2AX phosphorylation in proliferating cells, this possibly indicating replication stress events. Overall, present data shed light on the regulatory role of Hsp90α on the DDR, controlling ATM and NBN stability and influencing the DSBs signaling and repair.
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Affiliation(s)
- Rosa Pennisi
- Department of Sciences, Roma Tre University, Roma, Italy
| | - Antonio Antoccia
- Department of Sciences, Roma Tre University, Roma, Italy.,Istituto Nazionale Biostrutture e Biosistemi, Roma, Italy
| | - Stefano Leone
- Department of Sciences, Roma Tre University, Roma, Italy
| | - Paolo Ascenzi
- Department of Sciences, Roma Tre University, Roma, Italy
| | - Alessandra di Masi
- Department of Sciences, Roma Tre University, Roma, Italy.,Istituto Nazionale Biostrutture e Biosistemi, Roma, Italy
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18
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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: 1167] [Impact Index Per Article: 166.7] [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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19
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Li Z, Shao C, Kong Y, Carlock C, Ahmad N, Liu X. DNA Damage Response-Independent Role for MDC1 in Maintaining Genomic Stability. Mol Cell Biol 2017; 37:e00595-16. [PMID: 28193847 PMCID: PMC5394279 DOI: 10.1128/mcb.00595-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 12/08/2016] [Accepted: 02/06/2017] [Indexed: 02/04/2023] Open
Abstract
MDC1 is a central player in checkpoint activation and subsequent DNA repair following DNA damage. Although MDC1 has been studied extensively, many of its known functions, to date, pertain to the DNA damage response (DDR) pathway. Herein we report a novel function of phosphorylated MDC1 that is independent of ATM and DNA damage and is required for proper mitotic progression and maintenance of genomic stability. We demonstrate that MDC1 is an in vivo target of Plk1 and that phosphorylated MDC1 is dynamically localized to nuclear envelopes, centrosomes, kinetochores, and midbodies. Knockdown of MDC1 or abrogation of Plk1 phosphorylation of MDC1 causes a delay of the prometaphase-metaphase transition. It is significant that mice with reduced levels of MDC1 showed an elevated level of spontaneous tumors in aged animals. Our results demonstrate that MDC1 also plays a fundamentally significant role in maintenance of genomic stability through a DDR-independent pathway.
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Affiliation(s)
- Zhiguo Li
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Chen Shao
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Yifan Kong
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Colin Carlock
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Nihal Ahmad
- Department of Dermatology, University of Wisconsin, Madison, Wisconsin, USA
| | - Xiaoqi Liu
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
- Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
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20
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Jakob B, Taucher-Scholz G. Live Cell Imaging to Study Real-Time ATM-Mediated Recruitment of DNA Repair Complexes to Sites of Ionizing Radiation-Induced DNA Damage. Methods Mol Biol 2017; 1599:287-302. [PMID: 28477127 DOI: 10.1007/978-1-4939-6955-5_21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Measurements of protein recruitment and the formation of repair complexes at DNA double-strand breaks in real time provide valuable insight into the regulation of the early DNA damage response. Here, we describe the use of live cell microscopy in combination with ionizing radiation as a tool to evaluate the influence of ATM and its site-specific phosphorylation of target proteins on these processes. Recommendations are made for the preparation of the cells and the design of specialized cell chambers for the localized (and/or targeted) irradiation with charged particles at accelerator beamlines as well as the microscopic equipment and protocol to obtain high-resolution, sensitive fluorescence measurements.
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Affiliation(s)
- Burkhard Jakob
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, Biophysik, Planckstraße 1, 64291, Darmstadt, Germany.
| | - Gisela Taucher-Scholz
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, Biophysik, Planckstraße 1, 64291, Darmstadt, Germany
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21
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Roos WP, Krumm A. The multifaceted influence of histone deacetylases on DNA damage signalling and DNA repair. Nucleic Acids Res 2016; 44:10017-10030. [PMID: 27738139 PMCID: PMC5137451 DOI: 10.1093/nar/gkw922] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 10/02/2016] [Accepted: 10/05/2016] [Indexed: 12/16/2022] Open
Abstract
Histone/protein deacetylases play multiple roles in regulating gene expression and protein activation and stability. Their deregulation during cancer initiation and progression cause resistance to therapy. Here, we review the role of histone deacetylases (HDACs) and the NAD+ dependent sirtuins (SIRTs) in the DNA damage response (DDR). These lysine deacetylases contribute to DNA repair by base excision repair (BER), nucleotide excision repair (NER), mismatch repair (MMR), non-homologous end joining (NHEJ), homologous recombination (HR) and interstrand crosslink (ICL) repair. Furthermore, we discuss possible mechanisms whereby these histone/protein deacetylases facilitate the switch between DNA double-strand break (DSB) repair pathways, how SIRTs play a central role in the crosstalk between DNA repair and cell death pathways due to their dependence on NAD+, and the influence of small molecule HDAC inhibitors (HDACi) on cancer cell resistance to genotoxin based therapies. Throughout the review, we endeavor to identify the specific HDAC targeted by HDACi leading to therapy sensitization.
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Affiliation(s)
- Wynand Paul Roos
- Institute of Toxicology, Medical Center of the University Mainz, Obere Zahlbacher Str. 67, D-55131 Mainz, Germany
| | - Andrea Krumm
- Institute of Toxicology, Medical Center of the University Mainz, Obere Zahlbacher Str. 67, D-55131 Mainz, Germany
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22
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Francia S, Cabrini M, Matti V, Oldani A, d'Adda di Fagagna F. DICER, DROSHA and DNA damage response RNAs are necessary for the secondary recruitment of DNA damage response factors. J Cell Sci 2016; 129:1468-76. [PMID: 26906421 PMCID: PMC4852722 DOI: 10.1242/jcs.182188] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 02/09/2016] [Indexed: 12/18/2022] Open
Abstract
The DNA damage response (DDR) plays a central role in preserving genome integrity. Recently, we reported that the endoribonucleases DICER and DROSHA contribute to DDR activation by generating small non-coding RNAs, termed DNA damage response RNA (DDRNA), carrying the sequence of the damaged locus. It is presently unclear whether DDRNAs act by promoting the primary recognition of DNA lesions or the secondary recruitment of DDR factors into cytologically detectable foci and consequent signal amplification. Here, we demonstrate that DICER and DROSHA are dispensable for primary recruitment of the DDR sensor NBS1 to DNA damage sites. Instead, the accumulation of the DDR mediators MDC1 and 53BP1 (also known as TP53BP1), markers of secondary recruitment, is reduced in DICER- or DROSHA-inactivated cells. In addition, NBS1 (also known as NBN) primary recruitment is resistant to RNA degradation, consistent with the notion that RNA is dispensable for primary recognition of DNA lesions. We propose that DICER, DROSHA and DDRNAs act in the response to DNA damage after primary recognition of DNA lesions and, together with γH2AX, are essential for enabling the secondary recruitment of DDR factors and fuel the amplification of DDR signaling. Summary: We show that DICER, DROSHA and DNA damage response RNAs are necessary for the secondary recruitment of DNA damage response factors but not essential for primary recognition of DNA lesions.
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Affiliation(s)
- Sofia Francia
- IFOM Foundation - The FIRC Institute of Molecular Oncology Foundation, Via Adamello 16, Milan 20139, Italy Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, Pavia 27100, Italy
| | - Matteo Cabrini
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, Pavia 27100, Italy
| | - Valentina Matti
- IFOM Foundation - The FIRC Institute of Molecular Oncology Foundation, Via Adamello 16, Milan 20139, Italy
| | - Amanda Oldani
- IFOM Foundation - The FIRC Institute of Molecular Oncology Foundation, Via Adamello 16, Milan 20139, Italy
| | - Fabrizio d'Adda di Fagagna
- IFOM Foundation - The FIRC Institute of Molecular Oncology Foundation, Via Adamello 16, Milan 20139, Italy Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, Pavia 27100, Italy
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23
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Cherry AL, Nott TJ, Kelly G, Rulten SL, Caldecott KW, Smerdon SJ. Versatility in phospho-dependent molecular recognition of the XRCC1 and XRCC4 DNA-damage scaffolds by aprataxin-family FHA domains. DNA Repair (Amst) 2015; 35:116-25. [PMID: 26519825 PMCID: PMC4655838 DOI: 10.1016/j.dnarep.2015.10.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/05/2015] [Accepted: 10/05/2015] [Indexed: 11/11/2022]
Abstract
Aprataxin, aprataxin and PNKP-like factor (APLF) and polynucleotide kinase phosphatase (PNKP) are key DNA-repair proteins with diverse functions but which all contain a homologous forkhead-associated (FHA) domain. Their primary binding targets are casein kinase 2-phosphorylated forms of the XRCC1 and XRCC4 scaffold molecules which respectively coordinate single-stranded and double-stranded DNA break repair pathways. Here, we present the high-resolution X-ray structure of a complex of phosphorylated XRCC4 with APLF, the most divergent of the three FHA domain family members. This, combined with NMR and biochemical analysis of aprataxin and APLF binding to singly and multiply-phosphorylated forms of XRCC1 and XRCC4, and comparison with PNKP reveals a pattern of distinct but overlapping binding specificities that are differentially modulated by multi-site phosphorylation. Together, our data illuminate important differences between activities of the three phospho-binding domains, in spite of a close evolutionary relationship between them.
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Affiliation(s)
- Amy L Cherry
- Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Timothy J Nott
- Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Geoffrey Kelly
- MRC Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
| | - Stuart L Rulten
- MRC Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
| | - Keith W Caldecott
- MRC Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
| | - Stephen J Smerdon
- Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK.
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24
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Weng JH, Hsieh YC, Huang CCF, Wei TYW, Lim LH, Chen YH, Ho MR, Wang I, Huang KF, Chen CJ, Tsai MD. Uncovering the Mechanism of Forkhead-Associated Domain-Mediated TIFA Oligomerization That Plays a Central Role in Immune Responses. Biochemistry 2015; 54:6219-29. [PMID: 26389808 DOI: 10.1021/acs.biochem.5b00500] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Forkhead-associated (FHA) domain is the only signaling domain that recognizes phosphothreonine (pThr) specifically. TRAF-interacting protein with an FHA domain (TIFA) was shown to be involved in immune responses by binding with TRAF2 and TRAF6. We recently reported that TIFA is a dimer in solution and that, upon stimulation by TNF-α, TIFA is phosphorylated at Thr9, which triggers TIFA oligomerization via pThr9-FHA domain binding and activates nuclear factor κB (NF-κB). However, the structural mechanism for the functionally important TIFA oligomerization remains to be established. While FHA domain-pThr binding is known to mediate protein dimerization, its role in oligomerization has not been demonstrated at the structural level. Here we report the crystal structures of TIFA (residues 1-150, with the unstructured C-terminal tail truncated) and its complex with the N-terminal pThr9 peptide (residues 1-15), which show unique features in the FHA structure (intrinsic dimer and extra β-strand) and in its interaction with the pThr peptide (with residues preceding rather than following pThr). These structural features support previous and additional functional analyses. Furthermore, the structure of the complex suggests that the pThr9-FHA domain interaction can occur only between different sets of dimers rather than between the two protomers within a dimer, providing the structural mechanism for TIFA oligomerization. Our results uncover the mechanism of FHA domain-mediated oligomerization in a key step of immune responses and expand the paradigm of FHA domain structure and function.
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Affiliation(s)
- Jui-Hung Weng
- Institute of Biological Chemistry, Academia Sinica , Taipei, Taiwan.,Taiwan International Graduate Program, Academia Sinica , Taipei, Taiwan.,Institute of Biochemical Sciences, Department of Chemistry, National Tsing Hua University , Hsinchu, Taiwan
| | - Yin-Cheng Hsieh
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center , Hsinchu, Taiwan
| | - Chia-Chi Flora Huang
- Institute of Biological Chemistry, Academia Sinica , Taipei, Taiwan.,Taiwan International Graduate Program, Academia Sinica , Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University , Taipei, Taiwan
| | - Tong-You Wade Wei
- Institute of Biological Chemistry, Academia Sinica , Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University , Taipei, Taiwan
| | - Liang-Hin Lim
- Institute of Biological Chemistry, Academia Sinica , Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University , Taipei, Taiwan
| | - Yu-Hou Chen
- Institute of Biological Chemistry, Academia Sinica , Taipei, Taiwan
| | - Meng-Ru Ho
- Institute of Biological Chemistry, Academia Sinica , Taipei, Taiwan
| | - Iren Wang
- Institute of Biological Chemistry, Academia Sinica , Taipei, Taiwan
| | - Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica , Taipei, Taiwan
| | - Chun-Jung Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center , Hsinchu, Taiwan
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica , Taipei, Taiwan.,Taiwan International Graduate Program, Academia Sinica , Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University , Taipei, Taiwan
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25
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Luo S, Xin X, Du LL, Ye K, Wei Y. Dimerization Mediated by a Divergent Forkhead-associated Domain Is Essential for the DNA Damage and Spindle Functions of Fission Yeast Mdb1. J Biol Chem 2015; 290:21054-21066. [PMID: 26160178 DOI: 10.1074/jbc.m115.642538] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Indexed: 01/13/2023] Open
Abstract
MDC1 is a key factor of DNA damage response in mammalian cells. It possesses two phospho-binding domains. In its C terminus, a tandem BRCA1 C-terminal domain binds phosphorylated histone H2AX, and in its N terminus, a forkhead-associated (FHA) domain mediates a phosphorylation-enhanced homodimerization. The FHA domain of the Drosophila homolog of MDC1, MU2, also forms a homodimer but utilizes a different dimer interface. The functional importance of the dimerization of MDC1 family proteins is uncertain. In the fission yeast Schizosaccharomyces pombe, a protein sharing homology with MDC1 in the tandem BRCA1 C-terminal domain, Mdb1, regulates DNA damage response and mitotic spindle functions. Here, we report the crystal structure of the N-terminal 91 amino acids of Mdb1. Despite a lack of obvious sequence conservation to the FHA domain of MDC1, this region of Mdb1 adopts an FHA-like fold and is therefore termed Mdb1-FHA. Unlike canonical FHA domains, Mdb1-FHA lacks all the conserved phospho-binding residues. It forms a stable homodimer through an interface distinct from those of MDC1 and MU2. Mdb1-FHA is important for the localization of Mdb1 to DNA damage sites and the spindle midzone, contributes to the roles of Mdb1 in cellular responses to genotoxins and an antimicrotubule drug, and promotes in vitro binding of Mdb1 to a phospho-H2A peptide. The defects caused by the loss of Mdb1-FHA can be rescued by fusion with either of two heterologous dimerization domains, suggesting that the main function of Mdb1-FHA is mediating dimerization. Our data support that FHA-mediated dimerization is conserved for MDC1 family proteins.
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Affiliation(s)
- Shukun Luo
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xiaoran Xin
- National Institute of Biological Sciences, Beijing 102206, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing 102206, China.
| | - Keqiong Ye
- National Institute of Biological Sciences, Beijing 102206, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yi Wei
- National Institute of Biological Sciences, Beijing 102206, China
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Wu SH, Wu TY, Hsiao YT, Lin JH, Hsu SC, Hsia TC, Yang ST, Hsu WH, Chung JG. Bufalin induces cell death in human lung cancer cells through disruption of DNA damage response pathways. THE AMERICAN JOURNAL OF CHINESE MEDICINE 2014; 42:729-42. [PMID: 24871662 DOI: 10.1142/s0192415x14500475] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Bufalin is a key component of a Chinese medicine (Chan Su) and has been proved effective in killing various cancer cells. Its role in inducing DNA damage and the inhibition of the DNA damage response (DDR) has been reported, but none have studied such action in lung cancer in detail. In this study, we demonstrated bufalin-induced DNA damage and condensation in NCI-H460 cells through a comet assay and DAPI staining, respectively. Western blotting indicated that bufalin suppressed the protein levels associated with DNA damage and repair, such as a DNA dependent serine/threonine protein kinase (DNA-PK), DNA repair proteins breast cancer 1, early onset (BRCA1), 14-3-3 σ (an important checkpoint keeper of DDR), mediator of DNA damage checkpoint 1 (MDC1), O6-methylguanine-DNA methyltransferase (MGMT) and p53 (tumor suppressor protein). Bufalin could activate phosphorylated p53 in NCI-H460 cells. DNA damage in NCI-H460 cells after treatment with bufalin up-regulated its ATM and ATR genes, which encode proteins functioning as sensors in DDR, and also up-regulated the gene expression (mRNA) of BRCA1 and DNA-PK. But bufalin suppressed the gene expression (mRNA) of p53 and 14-3-3 σ, however, bufalin did not significantly affect the mRNA of MGMT. In conclusion, bufalin induced DNA damage in NCI-H460 cells and also inhibited its DNA repair and checkpoint function.
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Affiliation(s)
- Shin-Hwar Wu
- Institute of Clinical Medical Science, China Medical University, Taichung, Taiwan, ROC , Division of Critical Care Medicine, Department of Medicine, Changhua Christian Hospital, Taiwan
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27
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Hirota K, Tsuda M, Murai J, Takagi T, Keka IS, Narita T, Fujita M, Sasanuma H, Kobayashi J, Takeda S. SUMO-targeted ubiquitin ligase RNF4 plays a critical role in preventing chromosome loss. Genes Cells 2014; 19:743-54. [PMID: 25205350 DOI: 10.1111/gtc.12173] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 07/26/2014] [Indexed: 01/08/2023]
Abstract
RING finger protein 4 (RNF4) represents a subclass of ubiquitin ligases that target proteins modified by the small ubiquitin-like modifier (SUMO) for ubiquitin-mediated degradation. We disrupted the RNF4 gene in chicken DT40 cells and found that the resulting RNF4(-/-) cells gradually lost proliferation capability. Strikingly, this compromised proliferation was associated with an unprecedented cellular effect: the gradual decrease in the number of intact chromosomes. In the 6 weeks after gene targeting, there was a 25% reduction in the DNA content of the RNF4(-/-) cells. Regarding trisomic chromosome 2, 60% of the RNF4(-/-) cells lost one homologue, suggesting that DNA loss was mediated by whole chromosome loss. To determine the cause of this chromosome loss, we examined cell-cycle checkpoint pathways. RNF4(-/-) cells showed a partial defect in the spindle assembly checkpoint, premature dissociation of sister chromatids, and a marked increase in the number of lagging chromosomes at anaphase. Thus, combined defects in SAC and sister chromatid cohesion may result in increased lagging chromosomes, leading to chromosome loss without accompanying chromosome gain in RNF4(-/-) cells. We therefore propose that RNF4 plays a novel role in preventing the loss of intact chromosomes and ensures the maintenance of chromosome integrity.
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Affiliation(s)
- Kouji Hirota
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto, 606-8501, Japan; Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo, 192-0397, Japan
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28
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Zhao H, Zhu M, Dou G, Zhao H, Zhu B, Li J, Liao J, Xu X. BCL10 regulates RNF8/RNF168-mediated ubiquitination in the DNA damage response. Cell Cycle 2014; 13:1777-87. [PMID: 24732096 PMCID: PMC4111724 DOI: 10.4161/cc.28707] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Timely and proper cellular response to DNA damage is essential for maintenance of genome stability and integrity. B-cell lymphoma/leukemia 10 (BCL10) facilitates ubiquitination of NEMO in the cytosol, activating NFκB signaling. Translocation and/or point mutations of BCL10 associate with mucosa-associated lymphoid tissue lymphomas and other malignancies. However, the mechanisms by which the resulting aberrant expression of BCL10 leads to cellular oncogenesis are poorly understood. In this report, we found that BCL10 in the nucleus is enriched at the DNA damage sites in an ATM- and RNF8-dependent manner. ATM-dependent phosphorylation of BCL10 promotes its interaction with and presentation of UBC13 to RNF8, and RNF8-mediated ubiquitination of BCL10 enhances binding of BCL10 and UBC13 to RNF168. This allows mono-ubiquitination on H2AX by RNF168 and further poly-ubiquitination by the RNF8/RNF168-containing complex. Depletion of BCL10 compromised homology recombination-mediated DNA double-strand break (DSB) repair because of insufficient recruitment of BRCA1, RAD51, and the ubiquitinated DNA damage response factors. Taken together, our results demonstrate a novel function of BCL10 in delivering UBC13 to RNF8/RNF168 to regulate ubiquitination-mediated DSB signaling and repair.
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Affiliation(s)
- Hongchang Zhao
- Beijing Key Laboratory of DNA Damage Response and College of Life Science; Capital Normal University; Beijing, China
| | - Min Zhu
- Beijing Key Laboratory of DNA Damage Response and College of Life Science; Capital Normal University; Beijing, China
| | - Gelin Dou
- Beijing Key Laboratory of DNA Damage Response and College of Life Science; Capital Normal University; Beijing, China
| | - Hongli Zhao
- Beijing Key Laboratory of DNA Damage Response and College of Life Science; Capital Normal University; Beijing, China
| | - Bingtao Zhu
- Beijing Key Laboratory of DNA Damage Response and College of Life Science; Capital Normal University; Beijing, China
| | - Jing Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Science; Capital Normal University; Beijing, China
| | - Ji Liao
- Beijing Key Laboratory of DNA Damage Response and College of Life Science; Capital Normal University; Beijing, China
| | - Xingzhi Xu
- Beijing Key Laboratory of DNA Damage Response and College of Life Science; Capital Normal University; Beijing, China
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Abstract
In eukaryotic cells, maintenance of genomic stability relies on the coordinated action of a network of cellular processes, including DNA replication, DNA repair, cell-cycle progression, and others. The DNA damage response (DDR) signaling pathway orchestrated by the ATM and ATR kinases is the central regulator of this network in response to DNA damage. Both ATM and ATR are activated by DNA damage and DNA replication stress, but their DNA-damage specificities are distinct and their functions are not redundant. Furthermore, ATM and ATR often work together to signal DNA damage and regulate downstream processes. Here, we will discuss the recent findings and current models of how ATM and ATR sense DNA damage, how they are activated by DNA damage, and how they function in concert to regulate the DDR.
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Affiliation(s)
- Alexandre Maréchal
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
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Scully R, Xie A. Double strand break repair functions of histone H2AX. Mutat Res 2013; 750:5-14. [PMID: 23916969 DOI: 10.1016/j.mrfmmm.2013.07.007] [Citation(s) in RCA: 169] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 07/15/2013] [Accepted: 07/19/2013] [Indexed: 12/12/2022]
Abstract
Chromosomal double strand breaks provoke an extensive reaction in neighboring chromatin, characterized by phosphorylation of histone H2AX on serine 139 of its C-terminal tail (to form "γH2AX"). The γH2AX response contributes to the repair of double strand breaks encountered in a variety of different contexts, including those induced by ionizing radiation, physiologically programmed breaks that characterize normal immune cell development and the pathological exposure of DNA ends triggered by telomere dysfunction. γH2AX also participates in the evolutionarily conserved process of sister chromatid recombination, a homologous recombination pathway involved in the suppression of genomic instability during DNA replication and directly implicated in tumor suppression. At a biochemical level, the γH2AX response provides a compelling example of how the "histone code" is adapted to the regulation of double strand break repair. Here, we review progress in research aimed at understanding how γH2AX contributes to double strand break repair in mammalian cells.
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Affiliation(s)
- Ralph Scully
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, United States.
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31
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Mermershtain I, Glover JNM. Structural mechanisms underlying signaling in the cellular response to DNA double strand breaks. Mutat Res 2013; 750:15-22. [PMID: 23896398 DOI: 10.1016/j.mrfmmm.2013.07.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 07/12/2013] [Accepted: 07/16/2013] [Indexed: 01/04/2023]
Abstract
DNA double strand breaks (DSBs) constitute one of the most dangerous forms of DNA damage. In actively replicating cells, these breaks are first recognized by specialized proteins that initiate a signal transduction cascade that modulates the cell cycle and results in the repair of the breaks by homologous recombination (HR). Protein signaling in response to double strand breaks involves phosphorylation and ubiquitination of chromatin and a variety of associated proteins. Here we review the emerging structural principles that underlie how post-translational protein modifications control protein signaling that emanates from these DNA lesions.
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Affiliation(s)
- Inbal Mermershtain
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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32
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Shiloh Y, Ziv Y. The ATM protein kinase: regulating the cellular response to genotoxic stress, and more. Nat Rev Mol Cell Biol 2013; 14:197-210. [DOI: 10.1038/nrm3546] [Citation(s) in RCA: 1170] [Impact Index Per Article: 106.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Gan H, Cai T, Lin X, Wu Y, Wang X, Yang F, Han C. Integrative proteomic and transcriptomic analyses reveal multiple post-transcriptional regulatory mechanisms of mouse spermatogenesis. Mol Cell Proteomics 2013; 12:1144-57. [PMID: 23325766 DOI: 10.1074/mcp.m112.020123] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mammalian spermatogenesis consists of many cell types and biological processes and serves as an excellent model for studying gene regulation at transcriptional and post-transcriptional levels. Many key proteins, miRNAs, and perhaps piRNAs have been shown to be involved in post-transcriptional regulation of spermatogenesis. However, a systematic method for assessing the relationship between protein and mRNA expression has not been available for studying mechanisms of post-transcriptional regulation. In the present study, we used the iTRAQ-based quantitative proteomic approach to identify 2008 proteins in mouse type A spermatogonia, pachytene spermatocytes, round spermatids, and elongative spermatids with high confidence. Of these proteins, 1194 made up four dynamically changing clusters, which reflect the mitotic amplification, meiosis, and post-meiotic development of germ cells. We identified five major regulatory mechanisms termed "transcript only," "transcript degradation," "translation repression," "translation de-repression," and "protein degradation" based on changes in protein level relative to changes in mRNA level at the mitosis/meiosis transition and the meiosis/post-meiotic development transition. We found that post-transcriptional regulatory mechanisms are related to the generation of piRNAs and antisense transcripts. Our results provide a valuable inventory of proteins produced during mouse spermatogenesis and contribute to elucidating the mechanisms of the post-transcriptional regulation of gene expression in mammalian spermatogenesis.
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Affiliation(s)
- Haiyun Gan
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, PR China
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Dual recognition of phosphoserine and phosphotyrosine in histone variant H2A.X by DNA damage response protein MCPH1. Proc Natl Acad Sci U S A 2012; 109:14381-6. [PMID: 22908299 DOI: 10.1073/pnas.1212366109] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Tyr142, the C-terminal amino acid of histone variant H2A.X is phosphorylated by WSTF (Williams-Beuren syndrome transcription factor), a component of the WICH complex (WSTF-ISWI chromatin-remodeling complex), under basal conditions in the cell. In response to DNA double-strand breaks (DSBs), H2A.X is instantaneously phosphorylated at Ser139 by the kinases ATM and ATR and is progressively dephosphorylated at Tyr142 by the Eya1 and Eya3 tyrosine phosphatases, resulting in a temporal switch from a postulated diphosphorylated (pSer139, pTyr142) to monophosphorylated (pSer139) H2A.X state. How mediator proteins interpret these two signals remains a question of fundamental interest. We provide structural, biochemical, and cellular evidence that Microcephalin (MCPH1), an early DNA damage response protein, can read both modifications via its tandem BRCA1 C-terminal (BRCT) domains, thereby emerging as a versatile sensor of H2A.X phosphorylation marks. We show that MCPH1 recruitment to sites of DNA damage is linked to both states of H2A.X.
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35
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Intermolecular binding between TIFA-FHA and TIFA-pT mediates tumor necrosis factor alpha stimulation and NF-κB activation. Mol Cell Biol 2012; 32:2664-73. [PMID: 22566686 DOI: 10.1128/mcb.00438-12] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The forkhead-associated (FHA) domain recognizes phosphothreonine (pT) with high specificity and functional diversity. TIFA (TRAF-interacting protein with an FHA domain) is the smallest FHA-containing human protein. Its overexpression was previously suggested to provoke NF-κB activation, yet its exact roles in this signaling pathway and the underlying molecular mechanism remain unclear. Here we identify a novel threonine phosphorylation site on TIFA and show that this phosphorylated threonine (pT) binds with the FHA domain of TIFA, leading to TIFA oligomerization and TIFA-mediated NF-κB activation. Detailed analysis indicated that unphosphorylated TIFA exists as an intrinsic dimer and that the FHA-pT9 binding occurs between different dimers of TIFA. In addition, silencing of endogenous TIFA resulted in attenuation of tumor necrosis factor alpha (TNF-α)-mediated downstream signaling. We therefore propose that the TIFA FHA-pT9 binding provides a previously unidentified link between TNF-α stimulation and NF-κB activation. The intermolecular FHA-pT9 binding between dimers also represents a new mechanism for the FHA domain.
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36
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Luo S, Ye K. Dimerization, but not phosphothreonine binding, is conserved between the forkhead-associated domains of Drosophila MU2 and human MDC1. FEBS Lett 2012; 586:344-9. [PMID: 22273583 DOI: 10.1016/j.febslet.2012.01.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Accepted: 01/15/2012] [Indexed: 10/14/2022]
Abstract
Mutator 2 (MU2) in Drosophila melanogaster has been proposed to be the ortholog of human MDC1, a key mediator in DNA damage response. The forkhead-associated (FHA) domain of MDC1 is a dimerization module regulated by trans binding to phosphothreonine 4 from another molecule. Here we present the crystal structure of the MU2 FHA domain at 1.9Å resolution, revealing its evolutionarily conserved role in dimerization. As compared to the MDC1 FHA domain, the MU2 FHA domain dimerizes using a different and more stable interface and contains a degenerate phosphothreonine-binding pocket. Our results suggest that the MU2 dimerization is constitutive and lacks phosphorylation-mediated regulation.
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Affiliation(s)
- Shukun Luo
- College of Biological Sciences, China Agricultural University, Beijing, China
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