1
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Huang P, Wang Y, Zhang P, Li Q. Ubiquitin-specific peptidase 1: assessing its role in cancer therapy. Clin Exp Med 2023; 23:2953-2966. [PMID: 37093451 DOI: 10.1007/s10238-023-01075-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/11/2023] [Indexed: 04/25/2023]
Abstract
Reversible protein ubiquitination represents an essential determinator of cellular homeostasis, and the ubiquitin-specific enzymes, particularly deubiquitinases (DUBs), are emerging as promising targets for drug development. DUBs are composed of seven different subfamilies, out of which ubiquitin-specific proteases (USPs) are the largest family with 56 members. One of the well-characterized USPs is USP1, which contributes to several cellular biological processes including DNA damage response, immune regulation, cell proliferation, apoptosis, and migration. USP1 levels and activity are regulated by multiple mechanisms, including transcription regulation, phosphorylation, autocleavage, and proteasomal degradation, ensuring that the cellular function of USP1 is performed in a suitably modulated spatio-temporal manner. Moreover, USP1 with deregulated expression and activity are found in several human cancers, indicating that targeting USP1 is a feasible therapeutic approach in anti-cancer treatment. In this review, we highlight the essential role of USP1 in cancer development and the regulatory landscape of USP1 activity, which might provide novel insights into cancer treatment.
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Affiliation(s)
- Peng Huang
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
- West China Biomedical Big Data Center, Sichuan University, Chengdu, 610041, Sichuan, China
| | - YuHan Wang
- Department of Anorectal, Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- School of Integrated Traditional Chinese and Western Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - PengFei Zhang
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
- West China Biomedical Big Data Center, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Qiu Li
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
- West China Biomedical Big Data Center, Sichuan University, Chengdu, 610041, Sichuan, China.
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2
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Saldanha J, Rageul J, Patel JA, Kim H. The Adaptive Mechanisms and Checkpoint Responses to a Stressed DNA Replication Fork. Int J Mol Sci 2023; 24:10488. [PMID: 37445667 PMCID: PMC10341514 DOI: 10.3390/ijms241310488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
DNA replication is a tightly controlled process that ensures the faithful duplication of the genome. However, DNA damage arising from both endogenous and exogenous assaults gives rise to DNA replication stress associated with replication fork slowing or stalling. Therefore, protecting the stressed fork while prompting its recovery to complete DNA replication is critical for safeguarding genomic integrity and cell survival. Specifically, the plasticity of the replication fork in engaging distinct DNA damage tolerance mechanisms, including fork reversal, repriming, and translesion DNA synthesis, enables cells to overcome a variety of replication obstacles. Furthermore, stretches of single-stranded DNA generated upon fork stalling trigger the activation of the ATR kinase, which coordinates the cellular responses to replication stress by stabilizing the replication fork, promoting DNA repair, and controlling cell cycle and replication origin firing. Deregulation of the ATR checkpoint and aberrant levels of chronic replication stress is a common characteristic of cancer and a point of vulnerability being exploited in cancer therapy. Here, we discuss the various adaptive responses of a replication fork to replication stress and the roles of ATR signaling that bring fork stabilization mechanisms together. We also review how this knowledge is being harnessed for the development of checkpoint inhibitors to trigger the replication catastrophe of cancer cells.
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Affiliation(s)
- Joanne Saldanha
- The Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Julie Rageul
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jinal A Patel
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Hyungjin Kim
- The Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
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3
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Meng Y, Zhou M, Wang T, Zhang G, Tu Y, Gong S, Zhang Y, Christiani DC, Au W, Liu Y, Xia ZL. Occupational lead exposure on genome-wide DNA methylation and DNA damage. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 304:119252. [PMID: 35385786 DOI: 10.1016/j.envpol.2022.119252] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/17/2022] [Accepted: 03/30/2022] [Indexed: 02/05/2023]
Abstract
Lead (Pb) exposure can induce DNA damage and alter DNA methylation but their inter-relationships have not been adequately determined. Our overall aims were to explore such relationships and to evaluate underlying epigenetic mechanisms of Pb-induced genotoxicity in Chinese workers. Blood Pb levels (BLLs) were determined and used as individual's Pb-exposure dose and the Comet assay (i.e., % tail DNA) was conducted to evaluate DNA damage. In the screening assay, 850 K BeadChip sequencing was performed on peripheral blood from 10 controls (BLLs ≤100 μg/L) and 20 exposed workers (i.e., 10 DNA-damaged and 10 DNA-undamaged workers). Using the technique, differentially methylated positions (DMPs) between the controls and the exposed workers were identified. In addition, DMPs were identified between the DNA-undamaged and DNA-damaged workers (% tail DNA >2.14%). In our validation assay, methylation levels of four candidate genes were measured by pyrosequencing in an independent sample set (n = 305), including RRAGC (Ras related GTP binding C), USP1 (Ubiquitin specific protease 1), COPS7B (COP9 signalosome subunit 7 B) and CHEK1 (Checkpoint kinase 1). The result of comparisons between the controls and the Pb-exposed workers show that DMPs were significantly enriched in genes related to nerve conduction and cell cycle. Between DNA-damaged group and DNA-undamaged group, differentially methylated genes were enriched in the pathways related to cell cycle and DNA integrity checkpoints. Additionally, methylation levels of RRAGC and USP1 were negatively associated with BLLs (P < 0.05), and the former mediated 19.40% of the effect of Pb on the % tail DNA. These findings collectively indicated that Pb-induced DNA damage was closely related to methylation of genes in cell cycle regulation, and methylation levels of RRAGC were involved in Pb-induced genotoxicity.
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Affiliation(s)
- Yu Meng
- Department of Occupational Health & Toxicology, School of Public Health, Fudan University, Shanghai, China
| | - Mengyu Zhou
- The MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Tuanwei Wang
- Department of Occupational Health & Toxicology, School of Public Health, Fudan University, Shanghai, China
| | - Guanghui Zhang
- Department of Environmental Health, College of Preventive Medicine, Army Medical University, Chongqing, China; Department of Occupational & Environmental Health, School of Public Health, Xinxiang Medical University, Xinxiang, Henan Province, China
| | - Yuting Tu
- Department of Occupational Health & Toxicology, School of Public Health, Fudan University, Shanghai, China
| | - Shiyang Gong
- Department of Occupational Health & Toxicology, School of Public Health, Fudan University, Shanghai, China
| | - Yunxia Zhang
- Department of Occupational Health & Toxicology, School of Public Health, Fudan University, Shanghai, China
| | - David C Christiani
- Environmental Medicine and Epidemiology Program, Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - William Au
- University of Medicine, Pharmacy, Science and Technology, Targu Mures, Romania, and Shantou University Medical College, Shantou, China
| | - Yun Liu
- The MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Zhao-Lin Xia
- Department of Occupational Health & Toxicology, School of Public Health, Fudan University, Shanghai, China; School of Public Health, Xinjiang Medical University, Urumqi, China.
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4
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USP1-trapping lesions as a source of DNA replication stress and genomic instability. Nat Commun 2022; 13:1740. [PMID: 35365626 PMCID: PMC8975806 DOI: 10.1038/s41467-022-29369-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 03/08/2022] [Indexed: 12/16/2022] Open
Abstract
The deubiquitinase USP1 is a critical regulator of genome integrity through the deubiquitylation of Fanconi Anemia proteins and the DNA replication processivity factor, proliferating cell nuclear antigen (PCNA). Uniquely, following UV irradiation, USP1 self-inactivates through autocleavage, which enables its own degradation and in turn, upregulates PCNA monoubiquitylation. However, the functional role for this autocleavage event during physiological conditions remains elusive. Herein, we discover that cells harboring an autocleavage-defective USP1 mutant, while still able to robustly deubiquitylate PCNA, experience more replication fork-stalling and premature fork termination events. Using super-resolution microscopy and live-cell single-molecule tracking, we show that these defects are related to the inability of this USP1 mutant to be properly recycled from sites of active DNA synthesis, resulting in replication-associated lesions. Furthermore, we find that the removal of USP1 molecules from DNA is facilitated by the DNA-dependent metalloprotease Spartan to counteract the cytotoxicity caused by “USP1-trapping”. We propose a utility of USP1 inhibitors in cancer therapy based on their ability to induce USP1-trapping lesions and consequent replication stress and genomic instability in cancer cells, similar to how non-covalent DNA-protein crosslinks cause cytotoxicity by imposing steric hindrances upon proteins involved in DNA transactions. Here the authors provide mechanistic insights into how auto-cleavage of the USP1 deubiquitinase regulates DNA replication and genome stability. Implications for the targeting of USP1 activity via protein-DNA trapping in cancer therapy are discussed.
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5
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Lancey C, Tehseen M, Bakshi S, Percival M, Takahashi M, Sobhy MA, Raducanu VS, Blair K, Muskett FW, Ragan TJ, Crehuet R, Hamdan SM, De Biasio A. Cryo-EM structure of human Pol κ bound to DNA and mono-ubiquitylated PCNA. Nat Commun 2021; 12:6095. [PMID: 34667155 PMCID: PMC8526622 DOI: 10.1038/s41467-021-26251-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/22/2021] [Indexed: 11/26/2022] Open
Abstract
Y-family DNA polymerase κ (Pol κ) can replicate damaged DNA templates to rescue stalled replication forks. Access of Pol κ to DNA damage sites is facilitated by its interaction with the processivity clamp PCNA and is regulated by PCNA mono-ubiquitylation. Here, we present cryo-EM reconstructions of human Pol κ bound to DNA, an incoming nucleotide, and wild type or mono-ubiquitylated PCNA (Ub-PCNA). In both reconstructions, the internal PIP-box adjacent to the Pol κ Polymerase-Associated Domain (PAD) docks the catalytic core to one PCNA protomer in an angled orientation, bending the DNA exiting the Pol κ active site through PCNA, while Pol κ C-terminal domain containing two Ubiquitin Binding Zinc Fingers (UBZs) is invisible, in agreement with disorder predictions. The ubiquitin moieties are partly flexible and extend radially away from PCNA, with the ubiquitin at the Pol κ-bound protomer appearing more rigid. Activity assays suggest that, when the internal PIP-box interaction is lost, Pol κ is retained on DNA by a secondary interaction between the UBZs and the ubiquitins flexibly conjugated to PCNA. Our data provide a structural basis for the recruitment of a Y-family TLS polymerase to sites of DNA damage. Translesion Synthesis is a process that enables cells to overcome the deleterious effects of replication stalling caused by DNA lesions. Here the authors present a Cryo-EM structure of human Y-family DNA polymerase k (Pol k) bound to PCNA, P/T DNA and an incoming nucleotide; and propose a model for polymerase switching in which “carrier state” Pol k is recruited to PCNA.
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Affiliation(s)
- Claudia Lancey
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester, LE1 7HB, UK
| | - Muhammad Tehseen
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Souvika Bakshi
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester, LE1 7HB, UK
| | - Matthew Percival
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester, LE1 7HB, UK
| | - Masateru Takahashi
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Mohamed A Sobhy
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Vlad S Raducanu
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Kerry Blair
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester, LE1 7HB, UK
| | - Frederick W Muskett
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester, LE1 7HB, UK
| | - Timothy J Ragan
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester, LE1 7HB, UK
| | - Ramon Crehuet
- CSIC-Institute for Advanced Chemistry of Catalonia (IQAC) C/ Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Samir M Hamdan
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
| | - Alfredo De Biasio
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester, LE1 7HB, UK. .,Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
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6
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Jang SW, Kim JM. Mutation of aspartic acid 199 in USP1 disrupts its deubiquitinating activity and impairs DNA repair. FEBS Lett 2021; 595:1997-2006. [PMID: 34128540 DOI: 10.1002/1873-3468.14152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/08/2021] [Accepted: 06/10/2021] [Indexed: 11/06/2022]
Abstract
The deubiquitinating enzyme USP1 contains highly conserved motifs forming its catalytic center. Recently, the COSMIC mutation database identified a mutation in USP1 at Asp-199 in endometrial cancer. Here, we investigated the role of Asp-199 for USP1 function. The mutation of aspartic acid to alanine (D199A) resulted in failure of USP1 to undergo autocleavage and form a complex with ubiquitin, indicating D199A Usp1 is catalytically inactive. The D199A mutation did not affect the interaction with Uaf1. Moreover, D199A Usp1 had defects in deubiquitination of FANCD2 and PCNA and displayed reduced FANCD2 foci formation and DNA repair efficiency. Furthermore, mutation of Asp-199 to glutamic acid resulted in phenotypes similar to the D199A mutation. Collectively, our findings demonstrate the importance of Asp-199 for USP1 activity and suggest the implications of USP1 downregulation in cancer.
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Affiliation(s)
- Seok Won Jang
- Department of Pharmacology, Chonnam National University Medical School, Jellanamdo, Korea
| | - Jung Min Kim
- Department of Pharmacology, Chonnam National University Medical School, Jellanamdo, Korea
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7
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HMCES Maintains Replication Fork Progression and Prevents Double-Strand Breaks in Response to APOBEC Deamination and Abasic Site Formation. Cell Rep 2021; 31:107705. [PMID: 32492421 PMCID: PMC7313144 DOI: 10.1016/j.celrep.2020.107705] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/28/2020] [Accepted: 05/06/2020] [Indexed: 01/12/2023] Open
Abstract
5-Hydroxymethylcytosine (5hmC) binding, ES-cell-specific (HMCES) crosslinks to apurinic or apyrimidinic (AP, abasic) sites in single-strand DNA (ssDNA). To determine whether HMCES responds to the ssDNA abasic site in cells, we exploited the activity of apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3A (APOBEC3A). APOBEC3A preferentially deaminates cytosines to uracils in ssDNA, which are then converted to abasic sites by uracil DNA glycosylase. We find that HMCES-deficient cells are hypersensitive to nuclear APOBEC3A localization. HMCES relocalizes to chromatin in response to nuclear APOBEC3A and protects abasic sites from processing into double-strand breaks (DSBs). Abasic sites induced by APOBEC3A slow both leading and lagging strand synthesis, and HMCES prevents further slowing of the replication fork by translesion synthesis (TLS) polymerases zeta (Polζ) and kappa (Polκ). Thus, our study provides direct evidence that HMCES responds to ssDNA abasic sites in cells to prevent DNA cleavage and balance the engagement of TLS polymerases. Mehta et al. use APOBEC3A to demonstrate that HMCES responds to ssDNA abasic sites in cells and prevents replication fork collapse. APOBEC3A-induced abasic sites slow both leading and lagging strand polymerization, and HMCES engagement prevents further fork slowing because of the action of TLS polymerases zeta (Polζ) and kappa (Polκ).
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8
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Quinet A, Tirman S, Cybulla E, Meroni A, Vindigni A. To skip or not to skip: choosing repriming to tolerate DNA damage. Mol Cell 2021; 81:649-658. [PMID: 33515486 PMCID: PMC7935405 DOI: 10.1016/j.molcel.2021.01.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/21/2020] [Accepted: 01/06/2021] [Indexed: 12/14/2022]
Abstract
Accurate DNA replication is constantly threatened by DNA lesions arising from endogenous and exogenous sources. Specialized DNA replication stress response pathways ensure replication fork progression in the presence of DNA lesions with minimal delay in fork elongation. These pathways broadly include translesion DNA synthesis, template switching, and replication fork repriming. Here, we discuss recent advances toward our understanding of the mechanisms that regulate the fine-tuned balance between these different replication stress response pathways. We also discuss the molecular pathways required to fill single-stranded DNA gaps that accumulate throughout the genome after repriming and the biological consequences of using repriming instead of other DNA damage tolerance pathways on genome integrity and cell fitness.
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Affiliation(s)
- Annabel Quinet
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Stephanie Tirman
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Emily Cybulla
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Alice Meroni
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
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9
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Cipolla L, Bertoletti F, Maffia A, Liang CC, Lehmann AR, Cohn MA, Sabbioneda S. UBR5 interacts with the replication fork and protects DNA replication from DNA polymerase η toxicity. Nucleic Acids Res 2020; 47:11268-11283. [PMID: 31586398 PMCID: PMC6868395 DOI: 10.1093/nar/gkz824] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 09/06/2019] [Accepted: 09/25/2019] [Indexed: 11/26/2022] Open
Abstract
Accurate DNA replication is critical for the maintenance of genome integrity and cellular survival. Cancer-associated alterations often involve key players of DNA replication and of the DNA damage-signalling cascade. Post-translational modifications play a fundamental role in coordinating replication and repair and central among them is ubiquitylation. We show that the E3 ligase UBR5 interacts with components of the replication fork, including the translesion synthesis (TLS) polymerase polη. Depletion of UBR5 leads to replication problems, such as slower S-phase progression, resulting in the accumulation of single stranded DNA. The effect of UBR5 knockdown is related to a mis-regulation in the pathway that controls the ubiquitylation of histone H2A (UbiH2A) and blocking this modification is sufficient to rescue the cells from replication problems. We show that the presence of polη is the main cause of replication defects and cell death when UBR5 is silenced. Finally, we unveil a novel interaction between polη and H2A suggesting that UbiH2A could be involved in polη recruitment to the chromatin and the regulation of TLS.
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Affiliation(s)
- Lina Cipolla
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, Italy
| | - Federica Bertoletti
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, Italy
| | - Antonio Maffia
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, Italy
| | - Chih-Chao Liang
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Alan R Lehmann
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Martin A Cohn
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Simone Sabbioneda
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, Italy
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10
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Mansilla SF, De La Vega MB, Calzetta NL, Siri SO, Gottifredi V. CDK-Independent and PCNA-Dependent Functions of p21 in DNA Replication. Genes (Basel) 2020; 11:genes11060593. [PMID: 32481484 PMCID: PMC7349641 DOI: 10.3390/genes11060593] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/13/2020] [Accepted: 05/15/2020] [Indexed: 12/12/2022] Open
Abstract
p21Waf/CIP1 is a small unstructured protein that binds and inactivates cyclin-dependent kinases (CDKs). To this end, p21 levels increase following the activation of the p53 tumor suppressor. CDK inhibition by p21 triggers cell-cycle arrest in the G1 and G2 phases of the cell cycle. In the absence of exogenous insults causing replication stress, only residual p21 levels are prevalent that are insufficient to inhibit CDKs. However, research from different laboratories has demonstrated that these residual p21 levels in the S phase control DNA replication speed and origin firing to preserve genomic stability. Such an S-phase function of p21 depends fully on its ability to displace partners from chromatin-bound proliferating cell nuclear antigen (PCNA). Vice versa, PCNA also regulates p21 by preventing its upregulation in the S phase, even in the context of robust p21 induction by irradiation. Such a tight regulation of p21 in the S phase unveils the potential that CDK-independent functions of p21 may have for the improvement of cancer treatments.
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11
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Guo F, Kong WN, Feng YC, Lv J, Zhao G, Wu HL, Ai L, Zhou X, Cai XL, Sun W, Ma XM. Comprehensive Analysis of the Expression and Prognosis for MCMs in Human Gastric Cancer. Technol Cancer Res Treat 2020; 19:1533033820970688. [PMID: 33167799 PMCID: PMC7658509 DOI: 10.1177/1533033820970688] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 09/12/2020] [Accepted: 10/05/2020] [Indexed: 12/24/2022] Open
Abstract
PURPOSES Minichromosome maintenance (MCM) proteins play an important role in replication and cell cycle progression. Even so, their expression and prognostic roles in cancer remain controversial. METHODS To address this issue, the study investigated the roles of MCMs in the prognosis of GC by using ONCOMINE, GEPIA2, UALCAN, Cancer Cell Line Encyclopedia (CCLE), the Human Protein Atlas, Kaplan-Meier Plotter, cBioPortal, GeneMANIA, and DAVID databases. RESULTS Over expressions of mRNA and cell lines were found in all members of the MCM family, and MCMs were found to be significantly associated with pathological tumor grades in GC patients. Besides, higher mRNA expressions of MCM1/5/7 were found to be significantly associated with shorter overall survival (OS) and progression-free survival (FP) in GC patients, while higher mRNA expression of MCM4/6/9 were connected with favorable OS and FP. Moreover, a high mutation rate of MCMs (68%) was also observed in GC patients. CONCLUSIONS The results indicated that MCM1/5/7 were potential targets of precision therapy for patients with GC. And MCM4/6/9 were new biomarkers for the prognosis of GC. The results of the study will contribute to supplement the existing knowledge, and help to explore therapeutic targets and enhance the accuracy of prognosis for patients with GC.
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Affiliation(s)
- Fan Guo
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Laboratory Center, Tumor Hospital Affiliated to Xinjiang Medical University, Urumqi, Xinjiang, China
- First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Wei-Na Kong
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Laboratory Center, Tumor Hospital Affiliated to Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Yang-Chun Feng
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Laboratory Center, Tumor Hospital Affiliated to Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Jie Lv
- First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Gang Zhao
- Department of Blood transfusion, Affiliated Traditional Chinese Medicine Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Hui-Li Wu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Laboratory Center, Tumor Hospital Affiliated to Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Le Ai
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Laboratory Center, Tumor Hospital Affiliated to Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Xuan Zhou
- First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Xuan-Lin Cai
- College of Basic Medicine of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Wei Sun
- Department of Thoracic Surgery, Tumor Hospital Affiliated to Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Xiu-Min Ma
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Laboratory Center, Tumor Hospital Affiliated to Xinjiang Medical University, Urumqi, Xinjiang, China
- First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
- College of Basic Medicine of Xinjiang Medical University, Urumqi, Xinjiang, China
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12
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Mammalian DNA Polymerase Kappa Activity and Specificity. Molecules 2019; 24:molecules24152805. [PMID: 31374881 PMCID: PMC6695781 DOI: 10.3390/molecules24152805] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/27/2019] [Accepted: 07/30/2019] [Indexed: 12/31/2022] Open
Abstract
DNA polymerase (pol) kappa is a Y-family translesion DNA polymerase conserved throughout all domains of life. Pol kappa is special6 ized for the ability to copy DNA containing minor groove DNA adducts, especially N2-dG adducts, as well as to extend primer termini containing DNA damage or mismatched base pairs. Pol kappa generally cannot copy DNA containing major groove modifications or UV-induced photoproducts. Pol kappa can also copy structured or non-B-form DNA, such as microsatellite DNA, common fragile sites, and DNA containing G quadruplexes. Thus, pol kappa has roles both in maintaining and compromising genomic integrity. The expression of pol kappa is altered in several different cancer types, which can lead to genome instability. In addition, many cancer-associated single-nucleotide polymorphisms have been reported in the POLK gene, some of which are associated with poor survival and altered chemotherapy response. Because of this, identifying inhibitors of pol kappa is an active area of research. This review will address these activities of pol kappa, with a focus on lesion bypass and cellular mutagenesis.
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Rageul J, Weinheimer AS, Park JJ, Kim H. Proteolytic control of genome integrity at the replication fork. DNA Repair (Amst) 2019; 81:102657. [PMID: 31324531 DOI: 10.1016/j.dnarep.2019.102657] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Faithful duplication of the genome is critical for the survival of an organism and prevention of malignant transformation. Accurate replication of a large amount of genetic information in a timely manner is one of the most challenging cellular processes and is often perturbed by intrinsic and extrinsic barriers to DNA replication fork progression, a phenomenon referred to as DNA replication stress. Elevated DNA replication stress is a primary source of genomic instability and one of the key hallmarks of cancer. Therefore, targeting DNA replication stress is an emerging concept for cancer therapy. The replication machinery associated with PCNA and other regulatory factors coordinates the synthesis and repair of DNA strands at the replication fork. The dynamic interaction of replication protein complexes with DNA is essential for sensing and responding to various signaling events relevant to DNA replication and damage. Thus, the disruption of the spatiotemporal regulation of protein homeostasis at the replication fork impairs genome integrity, which often involves the deregulation of ubiquitin-mediated proteolytic signaling. Notably, emerging evidence has highlighted the role of the AAA+ATPase VCP/p97 in extracting ubiquitinated protein substrates from the chromatin and facilitating the turnover of genome surveillance factors during DNA replication and repair. Here, we review recent advances in our understanding of chromatin-associated degradation pathways at the replication fork and the implication of these findings for cancer therapy.
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Affiliation(s)
- Julie Rageul
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, New York, 11794, USA
| | - Alexandra S Weinheimer
- Biochemistry and Structural Biology graduate program, Stony Brook University, New York 11794, USA
| | - Jennifer J Park
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, New York, 11794, USA
| | - Hyungjin Kim
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, New York, 11794, USA; Stony Brook Cancer Center, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York, 11794, USA.
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Ketkar A, Maddukuri L, Penthala NR, Reed MR, Zafar MK, Crooks PA, Eoff RL. Inhibition of Human DNA Polymerases Eta and Kappa by Indole-Derived Molecules Occurs through Distinct Mechanisms. ACS Chem Biol 2019; 14:1337-1351. [PMID: 31082191 DOI: 10.1021/acschembio.9b00304] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Overexpression of human DNA polymerase kappa (hpol κ) in glioblastoma is associated with shorter survival time and resistance to the alkylating agent temozolomide (TMZ), making it an attractive target for the development of small-molecule inhibitors. We previously reported on the development and characterization of indole barbituric acid-derived (IBA) inhibitors of translesion DNA synthesis polymerases (TLS pols). We have now identified a potent and selective inhibitor of hpol κ based on the indole-aminoguanidine (IAG) chemical scaffold. The most promising IAG analogue, IAG-10, exhibited greater inhibitory action against hpol κ than any other human Y-family member, as well as pols from the A-, B-, and X-families. Inhibition of hpol κ by IAG analogues appears to proceed through a mechanism that is distinct from inhibition of hpol η based on changes in DNA binding affinity and nucleotide insertion kinetics. By way of comparison, both IAG and IBA analogues inhibited binary complex formation by hpol κ and ternary complex formation by hpol η. Decreasing the concentration of enzyme and DNA in the reaction mixture lowered the IC50 value of IAG-10 to submicromolar values, consistent with inhibition of binary complex formation for hpol κ. Chemical footprinting experiments revealed that IAG-10 binds to a cleft between the finger, little finger, and N-clasp domains on hpol κ and that this likely disrupts the interaction between the N-clasp and the TLS pol core. In cell culture, IAG-10 potentiated the antiproliferative activity and DNA damaging effects of TMZ in hpol κ-proficient cells but not in hpol κ-deficient cells, indicative of a target-dependent effect. Mutagenic replication across alkylation damage increased in hpol κ-proficient cells treated with IAG-10, while no change in mutation frequency was observed for hpol κ-deficient cells. In summary, we developed a potent and selective small-molecule inhibitor of hpol κ that takes advantage of structural features unique to this TLS enzyme to potentiate TMZ, a standard-of-care drug used in the treatment of malignant brain tumors. Furthermore, the IAG scaffold represents a new chemical space for the exploration of TLS pol inhibitors, which could prove useful as a strategy for improving patient response to genotoxic drugs.
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Affiliation(s)
- Amit Ketkar
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205-7199, United States
| | - Leena Maddukuri
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205-7199, United States
| | - Narsimha R. Penthala
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205-7199, United States
| | - Megan R. Reed
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205-7199, United States
| | - Maroof K. Zafar
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205-7199, United States
| | - Peter A. Crooks
- Department of Pharmaceutical Sciences, 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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15
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Gallo D, Brown GW. Post-replication repair: Rad5/HLTF regulation, activity on undamaged templates, and relationship to cancer. Crit Rev Biochem Mol Biol 2019; 54:301-332. [PMID: 31429594 DOI: 10.1080/10409238.2019.1651817] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/12/2019] [Accepted: 07/31/2019] [Indexed: 12/18/2022]
Abstract
The eukaryotic post-replication repair (PRR) pathway allows completion of DNA replication when replication forks encounter lesions on the DNA template and are mediated by post-translational ubiquitination of the DNA sliding clamp proliferating cell nuclear antigen (PCNA). Monoubiquitinated PCNA recruits translesion synthesis (TLS) polymerases to replicate past DNA lesions in an error-prone manner while addition of K63-linked polyubiquitin chains signals for error-free template switching to the sister chromatid. Central to both branches is the E3 ubiquitin ligase and DNA helicase Rad5/helicase-like transcription factor (HLTF). Mutations in PRR pathway components lead to genomic rearrangements, cancer predisposition, and cancer progression. Recent studies have challenged the notion that the PRR pathway is involved only in DNA lesion tolerance and have shed new light on its roles in cancer progression. Molecular details of Rad5/HLTF recruitment and function at replication forks have emerged. Mounting evidence indicates that PRR is required during lesion-less replication stress, leading to TLS polymerase activity on undamaged templates. Analysis of PRR mutation status in human cancers and PRR function in cancer models indicates that down regulation of PRR activity is a viable strategy to inhibit cancer cell growth and reduce chemoresistance. Here, we review these findings, discuss how they change our views of current PRR models, and look forward to targeting the PRR pathway in the clinic.
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Affiliation(s)
- David Gallo
- Department of Biochemistry and Donnelly Centre, University of Toronto , Toronto , Canada
| | - Grant W Brown
- Department of Biochemistry and Donnelly Centre, University of Toronto , Toronto , Canada
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Tonzi P, Huang TT. Role of Y-family translesion DNA polymerases in replication stress: Implications for new cancer therapeutic targets. DNA Repair (Amst) 2019; 78:20-26. [PMID: 30954011 DOI: 10.1016/j.dnarep.2019.03.016] [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: 03/08/2019] [Revised: 03/26/2019] [Accepted: 03/28/2019] [Indexed: 12/18/2022]
Abstract
DNA replication stress, defined as the slowing or stalling of replication forks, is considered an emerging hallmark of cancer and a major contributor to genomic instability associated with tumorigenesis (Macheret and Halazonetis, 2015). Recent advances have been made in attempting to target DNA repair factors involved in alleviating replication stress to potentiate genotoxic treatments. Various inhibitors of ATR and Chk1, the two major kinases involved in the intra-S-phase checkpoint, are currently in Phase I and II clinical trials [2]. In addition, currently approved inhibitors of Poly-ADP Ribose Polymerase (PARP) show synthetic lethality in cells that lack double-strand break repair such as in BRCA1/2 deficient tumors [3]. These drugs have also been shown to exacerbate replication stress by creating a DNA-protein crosslink, termed PARP 'trapping', and this is now thought to contribute to the therapeutic efficacy. Translesion synthesis (TLS) is a mechanism whereby special repair DNA polymerases accommodate and tolerate various DNA lesions to allow for damage bypass and continuation of DNA replication (Yang and Gao, 2018). This class of proteins is best characterized by the Y-family, encompassing DNA polymerases (Pols) Kappa, Eta, Iota, and Rev1. While best studied for their ability to bypass physical lesions on the DNA, there is accumulating evidence for these proteins in coping with various natural replication fork barriers and alleviating replication stress. In this mini-review, we will highlight some of these recent advances, and discuss why targeting the TLS pathway may be a mechanism of enhancing cancer-associated replication stress. Exacerbation of replication stress can lead to increased genome instability, which can be toxic to cancer cells and represent a therapeutic vulnerability.
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Affiliation(s)
- Peter Tonzi
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Tony T Huang
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA.
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17
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Suan Lim K, Li H, Roberts EA, Gaudiano EF, Clairmont C, Sambel L, Ponnienselvan K, Liu JC, Yang C, Kozono D, Parmar K, Yusufzai T, Zheng N, D’Andrea AD. USP1 Is Required for Replication Fork Protection in BRCA1-Deficient Tumors. Mol Cell 2018; 72:925-941.e4. [PMID: 30576655 PMCID: PMC6390489 DOI: 10.1016/j.molcel.2018.10.045] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 08/23/2018] [Accepted: 10/29/2018] [Indexed: 12/15/2022]
Abstract
BRCA1-deficient tumor cells have defects in homologous-recombination repair and replication fork stability, resulting in PARP inhibitor sensitivity. Here, we demonstrate that a deubiquitinase, USP1, is upregulated in tumors with mutations in BRCA1. Knockdown or inhibition of USP1 resulted in replication fork destabilization and decreased viability of BRCA1-deficient cells, revealing a synthetic lethal relationship. USP1 binds to and is stimulated by fork DNA. A truncated form of USP1, lacking its DNA-binding region, was not stimulated by DNA and failed to localize and protect replication forks. Persistence of monoubiquitinated PCNA at the replication fork was the mechanism of cell death in the absence of USP1. Taken together, USP1 exhibits DNA-mediated activation at the replication fork, protects the fork, and promotes survival in BRCA1-deficient cells. Inhibition of USP1 may be a useful treatment for a subset of PARP-inhibitor-resistant BRCA1-deficient tumors with acquired replication fork stabilization.
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Affiliation(s)
- Kah Suan Lim
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Heng Li
- Department of Pharmacology, University of Washington, Seattle, WA, 98195, USA
| | - Emma A. Roberts
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Emily F. Gaudiano
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Connor Clairmont
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Larissa Sambel
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA,Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | | | - Jessica C. Liu
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Chunyu Yang
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA,Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - David Kozono
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Kalindi Parmar
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA,Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Timur Yusufzai
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Ning Zheng
- Department of Pharmacology, University of Washington, Seattle, WA, 98195, USA,Howard Hughes Medical Institute, Box 357280, Seattle, WA
| | - Alan D. D’Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA,Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
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18
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Tonzi P, Yin Y, Lee CWT, Rothenberg E, Huang TT. Translesion polymerase kappa-dependent DNA synthesis underlies replication fork recovery. eLife 2018; 7:41426. [PMID: 30422114 PMCID: PMC6251625 DOI: 10.7554/elife.41426] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 11/12/2018] [Indexed: 12/31/2022] Open
Abstract
DNA replication stress is often defined by the slowing or stalling of replication fork progression leading to local or global DNA synthesis inhibition. Failure to resolve replication stress in a timely manner contribute toward cell cycle defects, genome instability and human disease; however, the mechanism for fork recovery remains poorly defined. Here, we show that the translesion DNA polymerase (Pol) kappa, a DinB orthologue, has a unique role in both protecting and restarting stalled replication forks under conditions of nucleotide deprivation. Importantly, Pol kappa-mediated DNA synthesis during hydroxyurea (HU)-dependent fork restart is regulated by both the Fanconi Anemia (FA) pathway and PCNA polyubiquitination. Loss of Pol kappa prevents timely rescue of stalled replication forks, leading to replication-associated genomic instability, and a p53-dependent cell cycle defect. Taken together, our results identify a previously unanticipated role for Pol kappa in promoting DNA synthesis and replication stress recovery at sites of stalled forks.
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Affiliation(s)
- Peter Tonzi
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, United States
| | - Yandong Yin
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, United States
| | - Chelsea Wei Ting Lee
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, United States
| | - Eli Rothenberg
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, United States
| | - Tony T Huang
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, United States
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19
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Stankovic-Valentin N, Melchior F. Control of SUMO and Ubiquitin by ROS: Signaling and disease implications. Mol Aspects Med 2018; 63:3-17. [PMID: 30059710 DOI: 10.1016/j.mam.2018.07.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 05/23/2018] [Accepted: 07/27/2018] [Indexed: 01/06/2023]
Abstract
Reversible post-translational modifications (PTMs) ensure rapid signal transmission from sensors to effectors. Reversible modification of proteins by the small proteins Ubiquitin and SUMO are involved in virtually all cellular processes and can modify thousands of proteins. Ubiquitination or SUMOylation is the reversible attachment of these modifiers to lysine residues of a target via isopeptide bond formation. These modifications require ATP and an enzymatic cascade composed of three classes of proteins: E1 activating enzymes, E2 conjugating enzymes and E3 ligases. The reversibility of the modification is ensured by specific isopeptidases. E1 and E2 enzymes, some E3 ligases and most isopeptidases have catalytic cysteine residues, which make them potentially susceptible for oxidation. Indeed, an increasing number of examples reveal regulation of ubiquitination and SUMOylation by reactive oxygen species, both in the context of redox signaling and in severe oxidative stress. Importantly, ubiquitination and SUMOylation play essential roles in the regulation of ROS homeostasis, participating in the control of ROS production and clearance. In this review, we will discuss the interplay between ROS homeostasis, Ubiquitin and SUMO pathways and the implications for the oxidative stress response and cell signaling.
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Affiliation(s)
- Nicolas Stankovic-Valentin
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ - ZMBH Alliance, Heidelberg, Germany.
| | - Frauke Melchior
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ - ZMBH Alliance, Heidelberg, Germany.
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20
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Fernandez-Vidal A, Vignard J, Mirey G. Around and beyond 53BP1 Nuclear Bodies. Int J Mol Sci 2017; 18:ijms18122611. [PMID: 29206178 PMCID: PMC5751214 DOI: 10.3390/ijms18122611] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 11/27/2017] [Accepted: 12/01/2017] [Indexed: 12/17/2022] Open
Abstract
Within the nucleus, sub-nuclear domains define territories where specific functions occur. Nuclear bodies (NBs) are dynamic structures that concentrate nuclear factors and that can be observed microscopically. Recently, NBs containing the p53 binding protein 1 (53BP1), a key component of the DNA damage response, were defined. Interestingly, 53BP1 NBs are visualized during G1 phase, in daughter cells, while DNA damage was generated in mother cells and not properly processed. Unlike most NBs involved in transcriptional processes, replication has proven to be key for 53BP1 NBs, with replication stress leading to the formation of these large chromatin domains in daughter cells. In this review, we expose the composition and organization of 53BP1 NBs and focus on recent findings regarding their regulation and dynamics. We then concentrate on the importance of the replication stress, examine the relation of 53BP1 NBs with DNA damage and discuss their dysfunction.
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Affiliation(s)
- Anne Fernandez-Vidal
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, 31027 Toulouse, France.
| | - Julien Vignard
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, 31027 Toulouse, France.
| | - Gladys Mirey
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, 31027 Toulouse, France.
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21
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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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22
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Jo U, Cai W, Wang J, Kwon Y, D’Andrea AD, Kim H. PCNA-Dependent Cleavage and Degradation of SDE2 Regulates Response to Replication Stress. PLoS Genet 2016; 12:e1006465. [PMID: 27906959 PMCID: PMC5131917 DOI: 10.1371/journal.pgen.1006465] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 11/04/2016] [Indexed: 12/15/2022] Open
Abstract
Maintaining genomic integrity during DNA replication is essential for cellular survival and for preventing tumorigenesis. Proliferating cell nuclear antigen (PCNA) functions as a processivity factor for DNA replication, and posttranslational modification of PCNA plays a key role in coordinating DNA repair against replication-blocking lesions by providing a platform to recruit factors required for DNA repair and cell cycle control. Here, we identify human SDE2 as a new genome surveillance factor regulated by PCNA interaction. SDE2 contains an N-terminal ubiquitin-like (UBL) fold, which is cleaved at a diglycine motif via a PCNA-interacting peptide (PIP) box and deubiquitinating enzyme activity. The cleaved SDE2 is required for negatively regulating ultraviolet damage-inducible PCNA monoubiquitination and counteracting replication stress. The cleaved SDE2 products need to be degraded by the CRL4CDT2 ubiquitin E3 ligase in a cell cycle- and DNA damage-dependent manner, and failure to degrade SDE2 impairs S phase progression and cellular survival. Collectively, this study uncovers a new role for CRL4CDT2 in protecting genomic integrity against replication stress via regulated proteolysis of PCNA-associated SDE2 and provides insights into how an integrated UBL domain within linear polypeptide sequence controls protein stability and function. Preserving genomic integrity during DNA replication is essential for preventing tumorigenesis. The CRL4CDT2 ubiquitin E3 ligase plays a unique role in this pathway by coupling proteolysis to interaction with the DNA replication processivity factor PCNA, in order to ensure selective elimination of key factors in cell cycle regulation. However, the mechanisms by which CRL4CDT2 directly regulates replication-associated DNA repair remain elusive. In this work, we identify a new human protein called SDE2 that helps cells relieve replication stress and ensure completing DNA replication process, whose activity is regulated by PCNA interaction and CRL4CDT2. We show that SDE2 is cleaved by PCNA interaction and ubiquitin signaling to generate a functional C-terminal product. The cleaved SDE2 negatively regulates PCNA monoubiquitination required for relieving replication stress. Conversely, the cleaved SDE2 fragments need to be degraded, and failure to degrade SDE2 impairs S phase progression and cellular survival. Our findings uncover the role of CRL4CDT2-proteolytic signaling coupled to PCNA in protecting genomic integrity against replication stress. Knowledge on such mechanism will be useful to identify novel cancer therapeutic interventions exploiting deregulated ubiquitin signaling and SDE2 activities in cancer.
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Affiliation(s)
- Ukhyun Jo
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, United States of America
| | - Winson Cai
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, United States of America
| | - Jingming Wang
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, United States of America
| | - Yoojin Kwon
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, United States of America
| | - Alan D. D’Andrea
- Department of Radiation Oncology and Center for DNA damage and Repair, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Hyungjin Kim
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, United States of America
- * E-mail:
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23
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Mansilla SF, Bertolin AP, Bergoglio V, Pillaire MJ, González Besteiro MA, Luzzani C, Miriuka SG, Cazaux C, Hoffmann JS, Gottifredi V. Cyclin Kinase-independent role of p21 CDKN1A in the promotion of nascent DNA elongation in unstressed cells. eLife 2016; 5. [PMID: 27740454 PMCID: PMC5120883 DOI: 10.7554/elife.18020] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 10/07/2016] [Indexed: 01/01/2023] Open
Abstract
The levels of the cyclin-dependent kinase (CDK) inhibitor p21 are low in S phase and insufficient to inhibit CDKs. We show here that endogenous p21, instead of being residual, it is functional and necessary to preserve the genomic stability of unstressed cells. p21depletion slows down nascent DNA elongation, triggers permanent replication defects and promotes the instability of hard-to-replicate genomic regions, namely common fragile sites (CFS). The p21’s PCNA interacting region (PIR), and not its CDK binding domain, is needed to prevent the replication defects and the genomic instability caused by p21 depletion. The alternative polymerase kappa is accountable for such defects as they were not observed after simultaneous depletion of both p21 and polymerase kappa. Hence, in CDK-independent manner, endogenous p21 prevents a type of genomic instability which is not triggered by endogenous DNA lesions but by a dysregulation in the DNA polymerase choice during genomic DNA synthesis. DOI:http://dx.doi.org/10.7554/eLife.18020.001 Cancer develops when cells in the body mutate in ways that allow them to rapidly grow and divide. To protect cells from becoming cancerous, various molecules act like guardians to prevent cells from dividing when their DNA is damaged, or if they are short of energy. Other guardian molecules monitor the DNA copying process to ensure that the newly-made DNA is as identical as possible to the original DNA template. A protein called p21 belongs to the first group of guardian molecules: DNA damage triggers the production of p21, which prevents the cell from copying its DNA. This role relies on a section of the protein called the CDK binding domain. Cells that have already started to copy their genetic material also have low levels of p21. Mansilla et al. used human cells to investigate whether p21 is also involved in the process of copying DNA. The experiments show that the low levels of p21 act to increase the speed at which the DNA is copied. This activity helps to ensure that all of the cell’s DNA is copied within the time available, including sections of DNA that are harder to copy because they are more fragile and prone to damage. This newly identified role does not involve the CDK binding domain, but instead requires a different section of the p21 protein known as the PCNA interacting region. Mansilla et al. propose that p21 plays a dual role in protecting us from developing cancer. The PCNA interacting region is also found in other proteins that are involved in copying DNA. Therefore, a future challenge is to find out how these proteins interact with each other to ensure that cells accurately copy their DNA in a timely fashion. DOI:http://dx.doi.org/10.7554/eLife.18020.002
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Affiliation(s)
- Sabrina F Mansilla
- Fundación Instituto Leloir-Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Agustina P Bertolin
- Fundación Instituto Leloir-Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Valérie Bergoglio
- Centre de Recherches en Cancérologie de Toulouse, Toulouse, France.,INSERM, Universite Paul Sabatier-CNRS, Université de Toulouse, Toulouse, France.,Laboratoire d'Excellence TOUCAN, Toulouse, France.,Equipe labellisée La Ligue contre le Cancer, Toulouse, France
| | - Marie-Jeanne Pillaire
- Centre de Recherches en Cancérologie de Toulouse, Toulouse, France.,INSERM, Universite Paul Sabatier-CNRS, Université de Toulouse, Toulouse, France.,Laboratoire d'Excellence TOUCAN, Toulouse, France.,Equipe labellisée La Ligue contre le Cancer, Toulouse, France
| | - Marina A González Besteiro
- Fundación Instituto Leloir-Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Carlos Luzzani
- Laboratorio de Investigaciones Aplicadas en Neurociencias, Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia, Belén de Escobar, Argentina
| | - Santiago G Miriuka
- Laboratorio de Investigaciones Aplicadas en Neurociencias, Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia, Belén de Escobar, Argentina
| | - Christophe Cazaux
- Centre de Recherches en Cancérologie de Toulouse, Toulouse, France.,INSERM, Universite Paul Sabatier-CNRS, Université de Toulouse, Toulouse, France.,Laboratoire d'Excellence TOUCAN, Toulouse, France.,Equipe labellisée La Ligue contre le Cancer, Toulouse, France
| | - Jean-Sébastien Hoffmann
- Centre de Recherches en Cancérologie de Toulouse, Toulouse, France.,INSERM, Universite Paul Sabatier-CNRS, Université de Toulouse, Toulouse, France.,Laboratoire d'Excellence TOUCAN, Toulouse, France.,Equipe labellisée La Ligue contre le Cancer, Toulouse, France
| | - Vanesa Gottifredi
- Fundación Instituto Leloir-Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
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24
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Kim JK, Yeom M, Hong JK, Song I, Lee YS, Guengerich FP, Choi JY. Six Germline Genetic Variations Impair the Translesion Synthesis Activity of Human DNA Polymerase κ. Chem Res Toxicol 2016; 29:1741-1754. [PMID: 27603496 DOI: 10.1021/acs.chemrestox.6b00244] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
DNA polymerase (pol) κ efficiently catalyzes error-free translesion DNA synthesis (TLS) opposite bulky N2-guanyl lesions induced by carcinogens such as polycyclic aromatic hydrocarbons. We investigated the biochemical effects of nine human nonsynonymous germline POLK variations on the TLS properties of pol κ, utilizing recombinant pol κ (residues 1-526) enzymes and DNA templates containing an N2-CH2(9-anthracenyl)G (N2-AnthG), 8-oxo-7,8-dihydroguanine (8-oxoG), O6-methyl(Me)G, or an abasic site. In steady-state kinetic analyses, the R246X, R298H, T473A, and R512W variants displayed 7- to 18-fold decreases in kcat/Km for dCTP insertion opposite G and N2-AnthG, with 2- to 3-fold decreases in DNA binding affinity, compared to that of the wild-type, and further showed 5- to 190-fold decreases in kcat/Km for next-base extension from C paired with N2-AnthG. The A471V variant showed 2- to 4-fold decreases in kcat/Km for correct nucleotide insertion opposite and beyond G (or N2-AnthG) compared to that of the wild-type. These five hypoactive variants also showed similar patterns of attenuation of TLS activity opposite 8-oxoG, O6-MeG, and abasic lesions. By contrast, the T44M variant exhibited 7- to 11-fold decreases in kcat/Km for dCTP insertion opposite N2-AnthG and O6-MeG (as well as for dATP insertion opposite an abasic site) but not opposite both G and 8-oxoG, nor beyond N2-AnthG, compared to that of the wild-type. These results suggest that the R246X, R298H, T473A, R512W, and A471V variants cause a general catalytic impairment of pol κ opposite G and all four lesions, whereas the T44M variant induces opposite lesion-dependent catalytic impairment, i.e., only opposite O6-MeG, abasic, and bulky N2-G lesions but not opposite G and 8-oxoG, in pol κ, which might indicate that these hypoactive pol κ variants are genetic factors in modifying individual susceptibility to genotoxic carcinogens in certain subsets of populations.
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Affiliation(s)
- Jae-Kwon Kim
- Division of Pharmacology, Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine , Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Mina Yeom
- Division of Pharmacology, Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine , Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Jin-Kyung Hong
- Division of Pharmacology, Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine , Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Insil Song
- Division of Pharmacology, Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine , Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Young-Sam Lee
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology , Daegu 42988, Republic of Korea
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine , Nashville, Tennessee 37232-0146, United States
| | - Jeong-Yun Choi
- Division of Pharmacology, Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine , Suwon, Gyeonggi-do 16419, Republic of Korea
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25
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Bostian ACL, Eoff RL. Aberrant Kynurenine Signaling Modulates DNA Replication Stress Factors and Promotes Genomic Instability in Gliomas. Chem Res Toxicol 2016; 29:1369-80. [PMID: 27482758 DOI: 10.1021/acs.chemrestox.6b00255] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Metabolism of the essential amino acid L-tryptophan (TRP) is implicated in a number of neurological conditions including depression, neurodegenerative diseases, and cancer. The TRP catabolite kynurenine (KYN) has recently emerged as an important neuroactive factor in brain tumor pathogenesis, with additional studies implicating KYN in other types of cancer. Often highlighted as a modulator of the immune response and a contributor to immune escape for malignant tumors, it is well-known that KYN has effects on the production of the coenzyme nicotinamide adenine dinucleotide (NAD(+)), which can have a direct impact on DNA repair, replication, cell division, redox signaling, and mitochondrial function. Additional effects of KYN signaling are imparted through its role as an endogenous agonist for the aryl hydrocarbon receptor (AhR), and it is largely through activation of the AhR that KYN appears to mediate malignant progression in gliomas. We have recently reported on the ability of KYN signaling to modulate expression of human DNA polymerase kappa (hpol κ), a translesion enzyme involved in bypass of bulky DNA lesions and activation of the replication stress response. Given the impact of KYN on NAD(+) production, AhR signaling, and translesion DNA synthesis, it follows that dysregulation of KYN signaling in cancer may promote malignancy through alterations in the level of endogenous DNA damage and replication stress. In this perspective, we discuss the connections between KYN signaling, DNA damage tolerance, and genomic instability, as they relate to cancer.
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Affiliation(s)
- April C L Bostian
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , 4301 W. Markham Street, Little Rock, Arkansas 72205-7199, United States
| | - Robert L Eoff
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , 4301 W. Markham Street, Little Rock, Arkansas 72205-7199, United States
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26
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Cukras S, Lee E, Palumbo E, Benavidez P, Moldovan GL, Kee Y. The USP1-UAF1 complex interacts with RAD51AP1 to promote homologous recombination repair. Cell Cycle 2016; 15:2636-2646. [PMID: 27463890 DOI: 10.1080/15384101.2016.1209613] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
USP1 deubiquitinating enzyme and its stoichiometric binding partner UAF1 play an essential role in promoting DNA homologous recombination (HR) repair in response to various types of DNA damaging agents. Deubiquitination of FANCD2 may be attributed to the key role of USP1-UAF1 complex in regulating HR repair, however whether USP1-UAF1 promotes HR repair independently of FANCD2 deubiquitination is not known. Here we show evidence that the USP1-UAF1 complex has a FANCD2-independent function in promoting HR repair. Proteomic search of UAF1-interacting proteins revealed that UAF1 associates with RAD51AP1, a RAD51-interacting protein implicated in HR repair. We show that UAF1 mediates the interaction between USP1 and RAD51AP1, and that depletion of USP1 or UAF1 led to a decreased stability of RAD51AP1. Protein interaction mapping analysis identified some key residues within RAD51AP1 required for interacting with the USP1-UAF1 complex. Cells expressing the UAF1 interaction-deficient mutant of RAD51AP1 show increased chromosomal aberrations in response to Mitomycin C treatment. Moreover, similar to the RAD51AP1 depleted cells, the cells expressing UAF1-interaction deficient RAD51AP1 display persistent RAD51 foci following DNA damage exposure, indicating that these factors regulate a later step during the HR repair. These data altogether suggest that the USP1-UAF1 complex promotes HR repair via multiple mechanisms: through FANCD2 deubiquitination, as well as by interacting with RAD51AP1.
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Affiliation(s)
- Scott Cukras
- a Department of Cell Biology , Microbiology, and Molecular Biology, College of Arts and Sciences, University of South Florida , Tampa , FL , USA
| | - Euiho Lee
- a Department of Cell Biology , Microbiology, and Molecular Biology, College of Arts and Sciences, University of South Florida , Tampa , FL , USA
| | - Emily Palumbo
- a Department of Cell Biology , Microbiology, and Molecular Biology, College of Arts and Sciences, University of South Florida , Tampa , FL , USA
| | - Pamela Benavidez
- a Department of Cell Biology , Microbiology, and Molecular Biology, College of Arts and Sciences, University of South Florida , Tampa , FL , USA
| | - George-Lucian Moldovan
- b Department of Biochemistry and Molecular Biology , Pennsylvania State University College of Medicine , Hershey , PA , USA
| | - Younghoon Kee
- a Department of Cell Biology , Microbiology, and Molecular Biology, College of Arts and Sciences, University of South Florida , Tampa , FL , USA
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27
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Cipolla L, Maffia A, Bertoletti F, Sabbioneda S. The Regulation of DNA Damage Tolerance by Ubiquitin and Ubiquitin-Like Modifiers. Front Genet 2016; 7:105. [PMID: 27379156 PMCID: PMC4904029 DOI: 10.3389/fgene.2016.00105] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 05/25/2016] [Indexed: 11/13/2022] Open
Abstract
DNA replication is an extremely complex process that needs to be executed in a highly accurate manner in order to propagate the genome. This task requires the coordination of a number of enzymatic activities and it is fragile and prone to arrest after DNA damage. DNA damage tolerance provides a last line of defense that allows completion of DNA replication in the presence of an unrepaired template. One of such mechanisms is called post-replication repair (PRR) and it is used by the cells to bypass highly distorted templates caused by damaged bases. PRR is extremely important for the cellular life and performs the bypass of the damage both in an error-free and in an error-prone manner. In light of these two possible outcomes, PRR needs to be tightly controlled in order to prevent the accumulation of mutations leading ultimately to genome instability. Post-translational modifications of PRR proteins provide the framework for this regulation with ubiquitylation and SUMOylation playing a pivotal role in choosing which pathway to activate, thus controlling the different outcomes of damage bypass. The proliferating cell nuclear antigen (PCNA), the DNA clamp for replicative polymerases, plays a central role in the regulation of damage tolerance and its modification by ubiquitin, and SUMO controls both the error-free and error-prone branches of PRR. Furthermore, a significant number of polymerases are involved in the bypass of DNA damage possess domains that can bind post-translational modifications and they are themselves target for ubiquitylation. In this review, we will focus on how ubiquitin and ubiquitin-like modifications can regulate the DNA damage tolerance systems and how they control the recruitment of different proteins to the replication fork.
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Affiliation(s)
- Lina Cipolla
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia Italia
| | - Antonio Maffia
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia Italia
| | - Federica Bertoletti
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia Italia
| | - Simone Sabbioneda
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia Italia
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28
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Olazabal-Herrero A, García-Santisteban I, Rodríguez JA. Mutations in the ‘Fingers’ subdomain of the deubiquitinase USP1 modulate its function and activity. FEBS J 2016; 283:929-46. [DOI: 10.1111/febs.13648] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/16/2015] [Accepted: 01/08/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Anne Olazabal-Herrero
- Department of Genetics, Physical Anthropology and Animal Physiology; University of the Basque Country (UPV/EHU); Leioa Spain
| | - Iraia García-Santisteban
- Department of Genetics, Physical Anthropology and Animal Physiology; University of the Basque Country (UPV/EHU); Leioa Spain
| | - Jose Antonio Rodríguez
- Department of Genetics, Physical Anthropology and Animal Physiology; University of the Basque Country (UPV/EHU); Leioa Spain
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29
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Federico MB, Vallerga MB, Radl A, Paviolo NS, Bocco JL, Di Giorgio M, Soria G, Gottifredi V. Chromosomal Integrity after UV Irradiation Requires FANCD2-Mediated Repair of Double Strand Breaks. PLoS Genet 2016; 12:e1005792. [PMID: 26765540 PMCID: PMC4712966 DOI: 10.1371/journal.pgen.1005792] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 12/17/2015] [Indexed: 12/29/2022] Open
Abstract
Fanconi Anemia (FA) is a rare autosomal recessive disorder characterized by hypersensitivity to inter-strand crosslinks (ICLs). FANCD2, a central factor of the FA pathway, is essential for the repair of double strand breaks (DSBs) generated during fork collapse at ICLs. While lesions different from ICLs can also trigger fork collapse, the contribution of FANCD2 to the resolution of replication-coupled DSBs generated independently from ICLs is unknown. Intriguingly, FANCD2 is readily activated after UV irradiation, a DNA-damaging agent that generates predominantly intra-strand crosslinks but not ICLs. Hence, UV irradiation is an ideal tool to explore the contribution of FANCD2 to the DNA damage response triggered by DNA lesions other than ICL repair. Here we show that, in contrast to ICL-causing agents, UV radiation compromises cell survival independently from FANCD2. In agreement, FANCD2 depletion does not increase the amount of DSBs generated during the replication of UV-damaged DNA and is dispensable for UV-induced checkpoint activation. Remarkably however, FANCD2 protects UV-dependent, replication-coupled DSBs from aberrant processing by non-homologous end joining, preventing the accumulation of micronuclei and chromatid aberrations including non-homologous chromatid exchanges. Hence, while dispensable for cell survival, FANCD2 selectively safeguards chromosomal stability after UV-triggered replication stress.
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Affiliation(s)
- María Belén Federico
- Cell Cycle and Genomic Stability Laboratory, Fundación Instituto Leloir, IIBBA/ CONICET, Buenos Aires, Argentina
| | - María Belén Vallerga
- Cell Cycle and Genomic Stability Laboratory, Fundación Instituto Leloir, IIBBA/ CONICET, Buenos Aires, Argentina
| | - Analía Radl
- Laboratorio de Dosimetría Biológica, Autoridad Regulatoria Nuclear, Buenos Aires, Argentina
| | - Natalia Soledad Paviolo
- Cell Cycle and Genomic Stability Laboratory, Fundación Instituto Leloir, IIBBA/ CONICET, Buenos Aires, Argentina
| | - José Luis Bocco
- Centro de Investigaciones en Bioquímica Clínica e Inmunología/ CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Marina Di Giorgio
- Laboratorio de Dosimetría Biológica, Autoridad Regulatoria Nuclear, Buenos Aires, Argentina
| | - Gastón Soria
- Centro de Investigaciones en Bioquímica Clínica e Inmunología/ CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Vanesa Gottifredi
- Cell Cycle and Genomic Stability Laboratory, Fundación Instituto Leloir, IIBBA/ CONICET, Buenos Aires, Argentina
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30
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Bostian ACL, Maddukuri L, Reed MR, Savenka T, Hartman JH, Davis L, Pouncey DL, Miller GP, Eoff RL. Kynurenine Signaling Increases DNA Polymerase Kappa Expression and Promotes Genomic Instability in Glioblastoma Cells. Chem Res Toxicol 2015; 29:101-8. [PMID: 26651356 DOI: 10.1021/acs.chemrestox.5b00452] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Overexpression of the translesion synthesis polymerase hpol κ in glioblastomas has been linked to poor patient prognosis; however, the mechanism promoting higher expression in these tumors remains unknown. We determined that activation of the aryl hydrocarbon receptor (AhR) pathway in glioblastoma cells leads to increased hpol κ mRNA and protein levels. We blocked nuclear translocation and DNA binding by AhR in glioblastoma cells using a small-molecule and observed decreased hpol κ expression. Pharmacological inhibition of tryptophan-2,3-dioxygenase (TDO), the enzyme largely responsible for activating AhR in glioblastoma, led to a decrease in the endogenous AhR agonist kynurenine and a corresponding decrease in hpol κ protein levels. Importantly, we discovered that inhibiting TDO activity, AhR signaling, or suppressing hpol κ expression with RNA interference led to decreased chromosomal damage in glioblastoma cells. Epistasis assays further supported the idea that TDO activity, activation of AhR signaling, and the resulting overexpression of hpol κ function primarily in the same pathway to increase endogenous DNA damage. These findings indicate that upregulation of hpol κ through glioblastoma-specific TDO activity and activation of AhR signaling likely contributes to the high levels of replication stress and genomic instability observed in these tumors.
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Affiliation(s)
- April C L Bostian
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
| | - Leena Maddukuri
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
| | - Megan R Reed
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
| | - Tatsiana Savenka
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
| | - Jessica H Hartman
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
| | - Lauren Davis
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
| | - Dakota L Pouncey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
| | - Grover P Miller
- 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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31
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Kashiwaba SI, Kanao R, Masuda Y, Kusumoto-Matsuo R, Hanaoka F, Masutani C. USP7 Is a Suppressor of PCNA Ubiquitination and Oxidative-Stress-Induced Mutagenesis in Human Cells. Cell Rep 2015; 13:2072-80. [PMID: 26673319 DOI: 10.1016/j.celrep.2015.11.014] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 09/27/2015] [Accepted: 11/02/2015] [Indexed: 11/16/2022] Open
Abstract
Mono-ubiquitinated PCNA activates error-prone DNA polymerases; therefore, strict regulation of PCNA mono-ubiquitination is crucial in avoiding undesired mutagenesis. In this study, we used an in vitro assay system to identify USP7 as a deubiquitinating enzyme of mono-ubiquitinated PCNA. Suppression of USP1, a previously identified PCNA deubiquitinase, or USP7 increased UV- and H2O2-induced PCNA mono-ubiquitination in a distinct and additive manner, suggesting that USP1 and USP7 make different contributions to PCNA deubiquitination in human cells. Cell-cycle-synchronization analyses revealed that USP7 suppression increased H2O2-induced PCNA ubiquitination throughout interphase, whereas USP1 suppression specifically increased ubiquitination in S-phase cells. UV-induced mutagenesis was elevated in USP1-suppressed cells, whereas H2O2-induced mutagenesis was elevated in USP7-suppressed cells. These results suggest that USP1 suppresses UV-induced mutations produced in a manner involving DNA replication, whereas USP7 suppresses H2O2-induced mutagenesis involving cell-cycle-independent processes such as DNA repair.
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Affiliation(s)
- Shu-ichiro Kashiwaba
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Nagoya 464-8601, Japan
| | - Rie Kanao
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Nagoya 464-8601, Japan
| | - Yuji Masuda
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Nagoya 464-8601, Japan; Department of Toxicogenomics, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Rika Kusumoto-Matsuo
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Nagoya 464-8601, Japan
| | - Fumio Hanaoka
- Faculty of Science, Gakushuin University, Tokyo 171-8588, Japan
| | - Chikahide Masutani
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Nagoya 464-8601, Japan.
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32
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Abstract
Both proteolytic and nonproteolytic functions of ubiquitination are essential regulatory mechanisms for promoting DNA repair and the DNA damage response in mammalian cells. Deubiquitinating enzymes (DUBs) have emerged as key players in the maintenance of genome stability. In this minireview, we discuss the recent findings on human DUBs that participate in genome maintenance, with a focus on the role of DUBs in the modulation of DNA repair and DNA damage signaling.
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33
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Rad51 recombinase prevents Mre11 nuclease-dependent degradation and excessive PrimPol-mediated elongation of nascent DNA after UV irradiation. Proc Natl Acad Sci U S A 2015; 112:E6624-33. [PMID: 26627254 DOI: 10.1073/pnas.1508543112] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
After UV irradiation, DNA polymerases specialized in translesion DNA synthesis (TLS) aid DNA replication. However, it is unclear whether other mechanisms also facilitate the elongation of UV-damaged DNA. We wondered if Rad51 recombinase (Rad51), a factor that escorts replication forks, aids replication across UV lesions. We found that depletion of Rad51 impairs S-phase progression and increases cell death after UV irradiation. Interestingly, Rad51 and the TLS polymerase polη modulate the elongation of nascent DNA in different ways, suggesting that DNA elongation after UV irradiation does not exclusively rely on TLS events. In particular, Rad51 protects the DNA synthesized immediately before UV irradiation from degradation and avoids excessive elongation of nascent DNA after UV irradiation. In Rad51-depleted samples, the degradation of DNA was limited to the first minutes after UV irradiation and required the exonuclease activity of the double strand break repair nuclease (Mre11). The persistent dysregulation of nascent DNA elongation after Rad51 knockdown required Mre11, but not its exonuclease activity, and PrimPol, a DNA polymerase with primase activity. By showing a crucial contribution of Rad51 to the synthesis of nascent DNA, our results reveal an unanticipated complexity in the regulation of DNA elongation across UV-damaged templates.
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34
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Kanemaru Y, Suzuki T, Niimi N, Grúz P, Matsumoto K, Adachi N, Honma M, Nohmi T. Catalytic and non-catalytic roles of DNA polymerase κ in the protection of human cells against genotoxic stresses. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2015; 56:650-62. [PMID: 26031400 DOI: 10.1002/em.21961] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 05/13/2015] [Accepted: 05/26/2015] [Indexed: 05/07/2023]
Abstract
DNA polymerase κ (Pol κ) is a specialized DNA polymerase involved in translesion DNA synthesis. Although its bypass activities across lesions are well characterized in biochemistry, its cellular protective roles against genotoxic insults are still elusive. To better understand the in vivo protective roles, we have established a human cell line deficient in the expression of Pol κ (KO) and another expressing catalytically dead Pol κ (CD), to examine the cytotoxic sensitivity to 11 genotoxins including ultraviolet C light (UV). These cell lines were established in a genetic background of Nalm-6-MSH+, a human lymphoblastic cell line that has high efficiency for gene targeting, and functional p53 and mismatch repair activities. We classified the genotoxins into four groups. Group 1 includes benzo[a]pyrene diolepoxide, mitomycin C, and bleomycin, where the sensitivity was equally higher in KO and CD than in the cell line expressing wild-type Pol κ (WT). Group 2 includes hydrogen peroxide and menadione, where hypersensitivity was observed only in KO. Group 3 includes methyl methanesulfonate and ethyl methanesulfonate, where hypersensitivity was observed only in CD. Group 4 includes UV and three chemicals, where the chemicals exhibited similar cytotoxicity to all three cell lines. The results suggest that Pol κ not only protects cells from genotoxic DNA lesions via DNA polymerase activities, but also contributes to genome integrity by acting as a non-catalytic protein against oxidative damage caused by hydrogen peroxide and menadione. The non-catalytic roles of Pol κ in protection against oxidative damage by hydrogen peroxide are discussed.
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Affiliation(s)
- Yuki Kanemaru
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Setagaya-Ku, Tokyo, 158-8501, Japan
- Division of Toxicology, Department of Pharmacology Toxicology and Therapeutics, Showa University School of Pharmacy, Shinagawa-Ku, Tokyo, 142-0064, Japan
| | - Tetsuya Suzuki
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Setagaya-Ku, Tokyo, 158-8501, Japan
| | - Naoko Niimi
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Setagaya-Ku, Tokyo, 158-8501, Japan
| | - Petr Grúz
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Setagaya-Ku, Tokyo, 158-8501, Japan
| | - Kyomu Matsumoto
- Toxicology Division, The Institute of Environmental Toxicology, Joso-Shi, Ibaraki, 303-0043, Japan
| | - Noritaka Adachi
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa, 236-0027, Japan
| | - Masamitsu Honma
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Setagaya-Ku, Tokyo, 158-8501, Japan
| | - Takehiko Nohmi
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Setagaya-Ku, Tokyo, 158-8501, Japan
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35
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Masuda Y, Kanao R, Kaji K, Ohmori H, Hanaoka F, Masutani C. Different types of interaction between PCNA and PIP boxes contribute to distinct cellular functions of Y-family DNA polymerases. Nucleic Acids Res 2015; 43:7898-910. [PMID: 26170230 PMCID: PMC4652755 DOI: 10.1093/nar/gkv712] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 07/01/2015] [Indexed: 11/29/2022] Open
Abstract
Translesion DNA synthesis (TLS) by the Y-family DNA polymerases Polη, Polι and Polκ, mediated via interaction with proliferating cell nuclear antigen (PCNA), is a crucial pathway that protects human cells against DNA damage. We report that Polη has three PCNA-interacting protein (PIP) boxes (PIP1, 2, 3) that contribute differentially to two distinct functions, stimulation of DNA synthesis and promotion of PCNA ubiquitination. The latter function is strongly associated with formation of nuclear Polη foci, which co-localize with PCNA. We also show that Polκ has two functionally distinct PIP boxes, like Polη, whereas Polι has a single PIP box involved in stimulation of DNA synthesis. All three polymerases were additionally stimulated by mono-ubiquitinated PCNA in vitro. The three PIP boxes and a ubiquitin-binding zinc-finger of Polη exert redundant and additive effects in vivo via distinct molecular mechanisms. These findings provide an integrated picture of the orchestration of TLS polymerases.
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Affiliation(s)
- Yuji Masuda
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan Department of Toxicogenomics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Rie Kanao
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Kentaro Kaji
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Haruo Ohmori
- Department of Gene Information, Institute for Virus Research, Kyoto University, Sakyo-ku, Kyoto 606-8517, Japan Department of Life Science, Graduate School of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
| | - Fumio Hanaoka
- Department of Life Science, Graduate School of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
| | - Chikahide Masutani
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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Bertolin AP, Mansilla SF, Gottifredi V. The identification of translesion DNA synthesis regulators: Inhibitors in the spotlight. DNA Repair (Amst) 2015; 32:158-164. [PMID: 26002196 DOI: 10.1016/j.dnarep.2015.04.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Over the past half-century, we have become increasingly aware of the ubiquity of DNA damage. Under the constant exposure to exogenous and endogenous genomic stress, cells must attempt to replicate damaged DNA. The encounter of replication forks with DNA lesions triggers several cellular responses, including the activation of translesion DNA synthesis (TLS), which largely depends upon specialized DNA polymerases with flexible active sites capable of accommodating bulky DNA lesions. A detrimental aspect of TLS is its intrinsic mutagenic nature, and thus the activity of the TLS polymerases must ideally be restricted to synthesis on damaged DNA templates. Despite their potential clinical importance in chemotherapy, TLS inhibitors have been difficult to identify since a direct assay designed to quantify genomic TLS events is still unavailable. Herein we discuss the methods that have been used to validate TLS inhibitors such as USP1, p21 and Spartan, highlighting research that has revealed their contribution to the control of DNA synthesis on damaged and undamaged templates.
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Affiliation(s)
- A P Bertolin
- Cell Cycle Genomic Instability Laboratory, Fundación Instituto Leloir, IIBBA-CONICET, Buenos, Aires, Argentina
| | - S F Mansilla
- Cell Cycle Genomic Instability Laboratory, Fundación Instituto Leloir, IIBBA-CONICET, Buenos, Aires, Argentina
| | - V Gottifredi
- Cell Cycle Genomic Instability Laboratory, Fundación Instituto Leloir, IIBBA-CONICET, Buenos, Aires, Argentina.
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Wahi D, Jamal S, Goyal S, Singh A, Jain R, Rana P, Grover A. Cheminformatics models based on machine learning approaches for design of USP1/UAF1 abrogators as anticancer agents. SYSTEMS AND SYNTHETIC BIOLOGY 2015; 9:33-43. [PMID: 25972987 DOI: 10.1007/s11693-015-9162-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 01/14/2015] [Accepted: 01/23/2015] [Indexed: 12/17/2022]
Abstract
Cancer cells have upregulated DNA repair mechanisms, enabling them survive DNA damage induced during repeated rapid cell divisions and targeted chemotherapeutic treatments. Cancer cell proliferation and survival targeting via inhibition of DNA repair pathways is currently a very promiscuous anti-tumor approach. The deubiquitinating enzyme, USP1 is known to promote DNA repair via complexing with UAF1. The USP1/UAF1 complex is responsible for regulating DNA break repair pathways such as trans-lesion synthesis pathway, Fanconi anemia pathway and homologous recombination. Thus, USP1/UAF1 inhibition poses as an efficient anti-cancer strategy. The recently made available high throughput screen data for anti USP1/UAF1 activity prompted us to compute bioactivity predictive models that could help in screening for potential USP1/UAF1 inhibitors having anti-cancer properties. The current study utilizes publicly available high throughput screen data set of chemical compounds evaluated for their potential USP1/UAF1 inhibitory effect. A machine learning approach was devised for generation of computational models that could predict for potential anti USP1/UAF1 biological activity of novel anticancer compounds. Additional efficacy of active compounds was screened by applying SMARTS filter to eliminate molecules with non-drug like features. The structural fragment analysis was further performed to explore structural properties of the molecules. We demonstrated that modern machine learning approaches could be efficiently employed in building predictive computational models and their predictive performance is statistically accurate. The structure fragment analysis revealed the structures that could play an important role in identification of USP1/UAF1 inhibitors.
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Affiliation(s)
- Divya Wahi
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Salma Jamal
- Department of Bioscience and Biotechnology, Banasthali University, Tonk, 304022 Rajasthan India
| | - Sukriti Goyal
- Department of Bioscience and Biotechnology, Banasthali University, Tonk, 304022 Rajasthan India
| | - Aditi Singh
- Department of Biotechnology, TERI University, Plot No. 10, Institutional Area, Vasant Kunj, New Delhi, 110 070 India
| | - Ritu Jain
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Preeti Rana
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
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38
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Tan KW, Pham TM, Furukohri A, Maki H, Akiyama MT. Recombinase and translesion DNA polymerase decrease the speed of replication fork progression during the DNA damage response in Escherichia coli cells. Nucleic Acids Res 2015; 43:1714-25. [PMID: 25628359 PMCID: PMC4330395 DOI: 10.1093/nar/gkv044] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The SOS response is a DNA damage response pathway that serves as a general safeguard of genome integrity in bacteria. Extensive studies of the SOS response in Escherichia coli have contributed to establishing the key concepts of cellular responses to DNA damage. However, how the SOS response impacts on the dynamics of DNA replication fork movement remains unknown. We found that inducing the SOS response decreases the mean speed of individual replication forks by 30–50% in E. coli cells, leading to a 20–30% reduction in overall DNA synthesis. dinB and recA belong to a group of genes that are upregulated during the SOS response, and encode the highly conserved proteins DinB (also known as DNA polymerase IV) and RecA, which, respectively, specializes in translesion DNA synthesis and functions as the central recombination protein. Both genes were independently responsible for the SOS-dependent slowdown of replication fork progression. Furthermore, fork speed was reduced when each gene was ectopically expressed in SOS-uninduced cells to the levels at which they are expressed in SOS-induced cells. These results clearly indicate that the increased expression of dinB and recA performs a novel role in restraining the progression of an unperturbed replication fork during the SOS response.
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Affiliation(s)
- Kang Wei Tan
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Tuan Minh Pham
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Asako Furukohri
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hisaji Maki
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Masahiro Tatsumi Akiyama
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
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Pillaire MJ, Bétous R, Hoffmann JS. Role of DNA polymerase κ in the maintenance of genomic stability. Mol Cell Oncol 2014; 1:e29902. [PMID: 27308312 PMCID: PMC4905163 DOI: 10.4161/mco.29902] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 06/20/2014] [Accepted: 06/23/2014] [Indexed: 12/28/2022]
Abstract
To ensure high cell viability and genomic stability, cells have evolved two major mechanisms to deal with the constant challenge of DNA replication fork arrest during S phase of the cell cycle: (1) induction of the ataxia telangiectasia and Rad3-related (ATR) replication checkpoint mechanism, and (2) activation of a pathway that bypasses DNA damage and DNA with abnormal structure and is mediated by translesion synthesis (TLS) Y-family DNA polymerases. This review focuses on how DNA polymerase kappa (Pol κ), one of the most highly conserved TLS DNA polymerases, is involved in each of these pathways and thereby coordinates them to choreograph the response to a stalled replication fork. We also describe how loss of Pol κ regulation, which occurs frequently in human cancers, affects genomic stability and contributes to cancer development.
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Affiliation(s)
- Marie-Jeanne Pillaire
- Labellisée Ligue contre le Cancer 2013; INSERM Unit 1037; CNRS ERL 5294; Cancer Research Center of Toulouse; CHU Purpan; Toulouse, France; Université Paul Sabatier; University of Toulouse III; Toulouse, France
| | - Rémy Bétous
- Labellisée Ligue contre le Cancer 2013; INSERM Unit 1037; CNRS ERL 5294; Cancer Research Center of Toulouse; CHU Purpan; Toulouse, France; Université Paul Sabatier; University of Toulouse III; Toulouse, France
| | - Jean-Sébastien Hoffmann
- Labellisée Ligue contre le Cancer 2013; INSERM Unit 1037; CNRS ERL 5294; Cancer Research Center of Toulouse; CHU Purpan; Toulouse, France; Université Paul Sabatier; University of Toulouse III; Toulouse, France
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40
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Jacq X, Kemp M, Martin NMB, Jackson SP. Deubiquitylating enzymes and DNA damage response pathways. Cell Biochem Biophys 2014; 67:25-43. [PMID: 23712866 PMCID: PMC3756857 DOI: 10.1007/s12013-013-9635-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Covalent post-translational modification of proteins by ubiquitin and ubiquitin-like factors has emerged as a general mechanism to regulate myriad intra-cellular processes. The addition and removal of ubiquitin or ubiquitin-like proteins from factors has recently been demonstrated as a key mechanism to modulate DNA damage response (DDR) pathways. It is thus, timely to evaluate the potential for ubiquitin pathway enzymes as DDR drug targets for therapeutic intervention. The synthetic lethal approach provides exciting opportunities for the development of targeted therapies to treat cancer: most tumours have lost critical DDR pathways, and thus rely more heavily on the remaining pathways, while normal tissues are still equipped with all DDR pathways. Here, we review key deubiquitylating enzymes (DUBs) involved in DDR pathways, and describe how targeting DUBs may lead to selective therapies to treat cancer patients.
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Affiliation(s)
- Xavier Jacq
- MISSION Therapeutics Ltd, Babraham Research Campus, Cambridge, CB22 3AT, UK.
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41
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Villamil MA, Liang Q, Zhuang Z. The WD40-repeat protein-containing deubiquitinase complex: catalysis, regulation, and potential for therapeutic intervention. Cell Biochem Biophys 2014; 67:111-26. [PMID: 23797609 DOI: 10.1007/s12013-013-9637-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Ubiquitination has emerged as an essential signaling mechanism in eukaryotes. Deubiquitinases (DUBs) counteract the activities of the ubiquitination machinery and provide another level of control in cellular ubiquitination. Not surprisingly, DUBs are subjected to stringent regulations. Besides regulation by the noncatalytic domains present in the DUB sequences, DUB-interacting proteins are increasingly realized as essential regulators for DUB activity and function. This review focuses on DUBs that are associated with WD40-repeat proteins. Many human ubiquitin-specific proteases (USPs) were found to interact with WD40-repeat proteins, but little is known as to how this interaction regulates the activity and function of USPs. In recent years, significant progress has been made in understanding a prototypical WD40-repeat protein-containing DUB complex that comprises USP1 and USP1-associated factor 1 (UAF1). It has been shown that UAF1 activates USP1 through a potential active-site modulation, and the complex formation between USP1 and UAF1 is regulated by serine phosphorylation. Recently, human USPs have been recognized as a promising target class for inhibitor discovery. Small molecule inhibitors targeting several human USPs have been reported. USP1 is involved in two major DNA damage response pathways, DNA translesion synthesis and the Fanconi anemia pathway. Inhibiting the USP1/UAF1 deubiquitinase complex represents a new strategy to potentiate cancer cells to DNA-crosslinking agents and to overcome resistance that has plagued clinical cancer chemotherapy. The progress in inhibitor discovery against USPs and the WD40-repeat protein-containing USP complex will be discussed.
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Affiliation(s)
- Mark A Villamil
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, DE 19716, USA
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42
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Békés M, Okamoto K, Crist SB, Jones MJ, Chapman JR, Brasher BB, Melandri FD, Ueberheide BM, Denchi EL, Huang TT. DUB-resistant ubiquitin to survey ubiquitination switches in mammalian cells. Cell Rep 2013; 5:826-38. [PMID: 24210823 DOI: 10.1016/j.celrep.2013.10.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 09/05/2013] [Accepted: 10/03/2013] [Indexed: 11/29/2022] Open
Abstract
The ubiquitin-modification status of proteins in cells is highly dynamic and maintained by specific ligation machineries (E3 ligases) that tag proteins with ubiquitin or by deubiquitinating enzymes (DUBs) that remove the ubiquitin tag. The development of tools that offset this balance is critical in characterizing signaling pathways that utilize such ubiquitination switches. Herein, we generated a DUB-resistant ubiquitin mutant that is recalcitrant to cleavage by various families of DUBs both in vitro and in mammalian cells. As a proof-of-principle experiment, ectopic expression of the uncleavable ubiquitin stabilized monoubiquitinated PCNA in the absence of DNA damage and also revealed a defect in the clearance of the DNA damage response at unprotected telomeres. Importantly, a proteomic survey using the uncleavable ubiquitin identified ubiquitinated substrates, validating the DUB-resistant ubiquitin expression system as a valuable tool for interrogating cell signaling pathways.
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Affiliation(s)
- Miklós Békés
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
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43
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Lv L, Wang F, Ma X, Yang Y, Wang Z, Liu H, Li X, Liu Z, Zhang T, Huang M, Friedberg EC, Tang TS, Guo C. Mismatch repair protein MSH2 regulates translesion DNA synthesis following exposure of cells to UV radiation. Nucleic Acids Res 2013; 41:10312-22. [PMID: 24038355 PMCID: PMC3905884 DOI: 10.1093/nar/gkt793] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Translesion DNA synthesis (TLS) can use specialized DNA polymerases to insert and/or extend nucleotides across lesions, thereby limiting stalled replication fork collapse and the potential for cell death. Recent studies have shown that monoubiquitinated proliferating cell nuclear antigen (PCNA) plays an important role in recruitment of Y-family TLS polymerases to stalled replication forks after DNA damage treatment. To explore the possible roles of other factors that regulate the ultraviolet (UV)-induced assembly of specialized DNA polymerases at arrested replication forks, we performed immunoprecipitation experiments combined with mass spectrometry and established that DNA polymerase kappa (Polκ) can partner with MSH2, an important mismatch repair protein associated with hereditary non-polyposis colorectal cancer. We found that depletion of MSH2 impairs PCNA monoubiquitination and the formation of foci containing Polκ and other TLS polymerases after UV irradiation of cells. Interestingly, expression of MSH2 in Rad18-deficient cells increased UV-induced Polκ and REV1 focus formation without detectable changes in PCNA monoubiquitination, indicating that MSH2 can regulate post-UV focus formation by specialized DNA polymerases in both PCNA monoubiquitination-dependent and -independent fashions. Moreover, we observed that MSH2 can facilitate TLS across cyclobutane pyrimidine dimers photoproducts in living cells, presenting a novel role of MSH2 in post-UV cellular responses.
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Affiliation(s)
- Lingna Lv
- Laboratory of Cancer Genomics and Individualized Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China and Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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Coggins GE, Maddukuri L, Penthala NR, Hartman JH, Eddy S, Ketkar A, Crooks PA, Eoff RL. N-Aroyl indole thiobarbituric acids as inhibitors of DNA repair and replication stress response polymerases. ACS Chem Biol 2013; 8:1722-9. [PMID: 23679919 DOI: 10.1021/cb400305r] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Using a robust and quantitative assay, we have identified a novel class of DNA polymerase inhibitors that exhibits some specificity against an enzyme involved in resistance to anti-cancer drugs, namely, human DNA polymerase eta (hpol η). In our initial screen, we identified the indole thiobarbituric acid (ITBA) derivative 5-((1-(2-bromobenzoyl)-5-chloro-1H-indol-3-yl)methylene)-2-thioxodihydropyrimidine-4,6(1H,5H)-dione (ITBA-12) as an inhibitor of the Y-family DNA member hpol η, an enzyme that has been associated with increased resistance to cisplatin and doxorubicin treatments. An additional seven DNA polymerases from different subfamilies were tested for inhibition by ITBA-12. Hpol η was the most potently inhibited enzyme (30 ± 3 μM), with hpol β, hpol γ, and hpol κ exhibiting comparable but higher IC50 values of 41 ± 24, 49 ± 6, and 59 ± 11 μM, respectively. The other polymerases tested had IC50 values closer to 80 μM. Steady-state kinetic analysis was used to investigate the mechanism of polymerase inhibition by ITBA-12. Based on changes in the Michaelis constant, it was determined that ITBA-12 acts as an allosteric (or partial) competitive inhibitor of dNTP binding. The parent ITBA scaffold was modified to produce 20 derivatives and establish structure-activity relationships by testing for inhibition of hpol η. Two compounds with N-naphthoyl Ar-substituents, ITBA-16 and ITBA-19, were both found to have improved potency against hpol η with IC50 values of 16 ± 3 μM and 17 ± 3 μM, respectively. Moreover, the specificity of ITBA-16 was improved relative to that of ITBA-12. The presence of a chloro substituent at position 5 on the indole ring appears to be crucial for effective inhibition of hpol η, with the indole N-1-naphthoyl and N-2-naphthoyl analogues being the most potent inhibitors of hpol η. These results provide a framework from which second-generation ITBA derivatives may be developed against specialized polymerases that are involved in mechanisms of radio- and chemo-resistance.
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Affiliation(s)
- Grace E. Coggins
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37232-0146,
United States
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45
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García-Santisteban I, Peters GJ, Giovannetti E, Rodríguez JA. USP1 deubiquitinase: cellular functions, regulatory mechanisms and emerging potential as target in cancer therapy. Mol Cancer 2013; 12:91. [PMID: 23937906 PMCID: PMC3750636 DOI: 10.1186/1476-4598-12-91] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 07/30/2013] [Indexed: 01/12/2023] Open
Abstract
Reversible protein ubiquitination is emerging as a key process for maintaining cell homeostasis, and the enzymes that participate in this process, in particular E3 ubiquitin ligases and deubiquitinases (DUBs), are increasingly being regarded as candidates for drug discovery. Human DUBs are a group of approximately 100 proteins, whose cellular functions and regulatory mechanisms remain, with some exceptions, poorly characterized. One of the best-characterized human DUBs is ubiquitin-specific protease 1 (USP1), which plays an important role in the cellular response to DNA damage. USP1 levels, localization and activity are modulated through several mechanisms, including protein-protein interactions, autocleavage/degradation and phosphorylation, ensuring that USP1 function is carried out in a properly regulated spatio-temporal manner. Importantly, USP1 expression is deregulated in certain types of human cancer, suggesting that USP1 could represent a valid target in cancer therapy. This view has gained recent support with the finding that USP1 inhibition may contribute to revert cisplatin resistance in an in vitro model of non-small cell lung cancer (NSCLC). Here, we describe the current knowledge on the cellular functions and regulatory mechanisms of USP1. We also summarize USP1 alterations found in cancer, combining data from the literature and public databases with our own data. Finally, we discuss the emerging potential of USP1 as a target, integrating published data with our novel findings on the effects of the USP1 inhibitor pimozide in combination with cisplatin in NSCLC cells.
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Affiliation(s)
- Iraia García-Santisteban
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Leioa, Spain
| | - Godefridus J Peters
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Elisa Giovannetti
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Jose Antonio Rodríguez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Leioa, Spain
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46
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Abstract
Genomes are transmitted faithfully from dividing cells to their offspring. Changes that occur during DNA repair, chromosome duplication, and transmission or via recombination provide a natural source of genetic variation. They occur at low frequency because of the intrinsic variable nature of genomes, which we refer to as genome instability. However, genome instability can be enhanced by exposure to external genotoxic agents or as the result of cellular pathologies. We review the causes of genome instability as well as how it results in hyper-recombination, genome rearrangements, and chromosome fragmentation and loss, which are mainly mediated by double-strand breaks or single-strand gaps. Such events are primarily associated with defects in DNA replication and the DNA damage response, and show high incidence at repetitive DNA, non-B DNA structures, DNA-protein barriers, and highly transcribed regions. Identifying the causes of genome instability is crucial to understanding genome dynamics during cell proliferation and its role in cancer, aging, and a number of rare genetic diseases.
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Affiliation(s)
- Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla, 41092 Seville, Spain;
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47
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Mansilla SF, Soria G, Vallerga MB, Habif M, Martínez-López W, Prives C, Gottifredi V. UV-triggered p21 degradation facilitates damaged-DNA replication and preserves genomic stability. Nucleic Acids Res 2013; 41:6942-51. [PMID: 23723248 PMCID: PMC3737556 DOI: 10.1093/nar/gkt475] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Although many genotoxic treatments upregulate the cyclin kinase inhibitor p21, agents such as UV irradiation trigger p21 degradation. This suggests that p21 blocks a process relevant for the cellular response to UV. Here, we show that forced p21 stabilization after UV strongly impairs damaged-DNA replication, which is associated with permanent deficiencies in the recruitment of DNA polymerases from the Y family involved in translesion DNA synthesis), with the accumulation of DNA damage markers and increased genomic instability. Remarkably, such noxious effects disappear when disrupting the proliferating cell nuclear antigen (PCNA) interacting motif of stable p21, thus suggesting that the release of PCNA from p21 interaction is sufficient to allow the recruitment to PCNA of partners (such as Y polymerases) relevant for the UV response. Expression of degradable p21 only transiently delays early replication events and Y polymerase recruitment after UV irradiation. These temporary defects disappear in a manner that correlates with p21 degradation with no detectable consequences on later replication events or genomic stability. Together, our findings suggest that the biological role of UV-triggered p21 degradation is to prevent replication defects by facilitating the tolerance of UV-induced DNA lesions.
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Affiliation(s)
- Sabrina F Mansilla
- Cell Cycle and Genomic Stability Laboratory, Fundación Instituto Leloir-CONICET, Buenos Aires C1405BWE, Argentina
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48
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Deubiquitinases as a signaling target of oxidative stress. Cell Rep 2012; 2:1475-84. [PMID: 23219552 DOI: 10.1016/j.celrep.2012.11.011] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 10/28/2012] [Accepted: 11/14/2012] [Indexed: 02/07/2023] Open
Abstract
Deubiquitinating enzymes (DUBs) constitute a large family of cysteine proteases that have a broad impact on numerous biological and pathological processes, including the regulation of genomic stability. DUBs are often assembled onto multiprotein complexes to assist in their localization and substrate selection, yet it remains unclear how the enzymatic activity of DUBs is modulated by intracellular signals. Herein, we show that bursts of reactive oxygen species (ROS) reversibly inactivate DUBs through the oxidation of the catalytic cysteine residue. Importantly, USP1, a key regulator of genomic stability, is reversibly inactivated upon oxidative stress. This, in part, explains the rapid nature of PCNA monoubiquitination-dependent DNA damage tolerance in response to oxidative DNA damage in replicating cells. We propose that DUBs of the cysteine protease family act as ROS sensors in human cells and that ROS-mediated DUB inactivation is a critical mechanism for fine-tuning stress-activated signaling pathways.
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49
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Sharma S, Helchowski CM, Canman CE. The roles of DNA polymerase ζ and the Y family DNA polymerases in promoting or preventing genome instability. Mutat Res 2012. [PMID: 23195997 DOI: 10.1016/j.mrfmmm.2012.11.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cancer cells display numerous abnormal characteristics which are initiated and maintained by elevated mutation rates and genome instability. Chromosomal DNA is continuously surveyed for the presence of damage or blocked replication forks by the DNA Damage Response (DDR) network. The DDR is complex and includes activation of cell cycle checkpoints, DNA repair, gene transcription, and induction of apoptosis. Duplicating a damaged genome is associated with elevated risks to fork collapse and genome instability. Therefore, the DNA damage tolerance (DDT) pathway is also employed to enhance survival and involves the recruitment of translesion DNA synthesis (TLS) polymerases to sites of replication fork blockade or single stranded DNA gaps left after the completion of replication in order to restore DNA to its double stranded form before mitosis. TLS polymerases are specialized for inserting nucleotides opposite DNA adducts, abasic sites, or DNA crosslinks. By definition, the DDT pathway is not involved in the actual repair of damaged DNA, but provides a mechanism to tolerate DNA lesions during replication thereby increasing survival and lessening the chance for genome instability. However this may be associated with increased mutagenesis. In this review, we will describe the specialized functions of Y family polymerases (Rev1, Polη, Polι and Polκ) and DNA polymerase ζ in lesion bypass, mutagenesis, and prevention of genome instability, the latter due to newly appreciated roles in DNA repair. The recently described role of the Fanconi anemia pathway in regulating Rev1 and Polζ-dependent TLS is also discussed in terms of their involvement in TLS, interstrand crosslink repair, and homologous recombination.
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Affiliation(s)
- Shilpy Sharma
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Corey M Helchowski
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Christine E Canman
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, United States.
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Zhang L, Lubin A, Chen H, Sun Z, Gong F. The deubiquitinating protein USP24 interacts with DDB2 and regulates DDB2 stability. Cell Cycle 2012; 11:4378-84. [PMID: 23159851 PMCID: PMC3552920 DOI: 10.4161/cc.22688] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Damage-specific DNA-binding protein 2 (DDB2) was first isolated as a subunit of the UV-DDB heterodimeric complex that is involved in DNA damage recognition in the nucleotide excision repair pathway (NER). DDB2 is required for efficient repair of CPDs in chromatin and is a component of the CRL4DDB2 E3 ligase that targets XPC, histones and DDB2 itself for ubiquitination. In this study, a yeast two-hybrid screening of a human cDNA library was performed to identify potential DDB2 cellular partners. We identified a deubiquitinating enzyme, USP24, as a likely DDB2-interacting partner. Interaction between DDB2 and USP24 was confirmed by co-precipitation. Importantly, knockdown of USP24 in two human cell lines decreased the steady-state levels of DDB2, indicating that USP24-mediated DDB2 deubiquitination prevents DDB2 degradation. In addition, we demonstrated that USP24 can cleave an ubiquitinated form of DDB2 in vitro. Taken together, our results suggest that the ubiquitin-specific protease USP24 is a novel regulator of DDB2 stability.
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Affiliation(s)
- Ling Zhang
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL USA
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