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Zhang X, Yin M, Hu J. Nucleotide excision repair: a versatile and smart toolkit. Acta Biochim Biophys Sin (Shanghai) 2022; 54:807-819. [PMID: 35975604 PMCID: PMC9828404 DOI: 10.3724/abbs.2022054] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Nucleotide excision repair (NER) is a major pathway to deal with bulky adducts induced by various environmental toxins in all cellular organisms. The two sub-pathways of NER, global genome repair (GGR) and transcription-coupled repair (TCR), differ in the damage recognition modes. In this review, we describe the molecular mechanism of NER in mammalian cells, especially the details of damage recognition steps in both sub-pathways. We also introduce new sequencing methods for genome-wide mapping of NER, as well as recent advances about NER in chromatin by these methods. Finally, the roles of NER factors in repairing oxidative damages and resolving R-loops are discussed.
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Affiliation(s)
| | | | - Jinchuan Hu
- Correspondence address. Tel: +86-21-54237702; E-mail:
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2
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Feltes BC. Revisiting the structural features of the xeroderma pigmentosum proteins: Focus on mutations and knowledge gaps. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 789:108416. [PMID: 35690419 DOI: 10.1016/j.mrrev.2022.108416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 06/15/2023]
Abstract
The nucleotide excision repair pathway is a broadly studied DNA repair mechanism because impairments of its key players, the xeroderma pigmentosum proteins (XPA to XPG), are associated with multiple hereditary diseases. Due to the massive number of novel mutations reported for these proteins and new structural data published every year, proper categorization and discussion of relevant observations is needed to organize this extensive inflow of knowledge. This review aims to revisit the structural data of all XP proteins while updating it with the information developed in of the past six years. Discussions and interpretations of mutation outcomes, mechanisms of action, and knowledge gaps regarding their structures are provided, as well as new perspectives based on recent research.
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Affiliation(s)
- Bruno César Feltes
- Department of Theoretical Informatics, Institute of Informatics, Department of Theoretical Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Department of Genetics, Institute of Bioscience, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Department of Biophysics, Institute of Bioscience, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil.
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3
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Karagün E, Eroz R, Gamsızkan M, Baysak S, Eyup Y, Ozcan Y. Novel mutation identified in the DDB2 gene in patients with xeroderma pigmentosum group-E. Int J Dermatol 2020; 59:989-996. [PMID: 32530099 DOI: 10.1111/ijd.14957] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 03/19/2020] [Accepted: 04/24/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Xeroderma pigmentosum (XP) is a rare photosensitive syndrome, which is divided into eight complementation groups (XP-A to XP-G and XPV) and characterized by skin cancers diagnosed at early age. A family of seven members (age range between 5 and 47 years) with carriers of the novel nonsense mutation that causes XP-E type were included in the current study. METHODS DNA was isolated from peripheral blood samples of the proband, and cancer predisposition genes were sequenced with next-generation sequencing. The demographic features and the laboratory, clinical, and histopathological findings of patients were evaluated. RESULTS In the proband, squamous cell carcinoma was first diagnosed in the right-eye cornea at the age of 13 years and then in the left-eye cornea at the age of 15 years. Later, the patient was diagnosed with basosquamous cell carcinoma on the dorsum of the nose at the age of 18 years. After genetic analysis, a novel nonsense c.1063C>T(p.Arg355Ter) pathogenic variation that causes XP-E type was detected as homozygous in the DDB2 gene of the proband and her siblings, 11 and 5 years of age, and as heterozygous in her parents and a 22-year-old brother. CONCLUSION Because of the occurrence of early termination codon, truncated nonfunctional proteins or proteins with deleterious loss or gain-of-function activities are synthesized in nonsense mutation. Thus, to avoid the development of pathological lesions, it is important that such patients with nonsense mutation stay away from agents that might cause DNA damage and develop an appropriate lifestyle according to this condition.
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Affiliation(s)
| | - Recep Eroz
- Duzce University Medical School, Duzce, Turkey
| | | | | | - Yavuz Eyup
- Duzce University Medical School, Duzce, Turkey
| | - Yunus Ozcan
- Duzce University Medical School, Duzce, Turkey
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4
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Beecher M, Kumar N, Jang S, Rapić-Otrin V, Van Houten B. Expanding molecular roles of UV-DDB: Shining light on genome stability and cancer. DNA Repair (Amst) 2020; 94:102860. [PMID: 32739133 DOI: 10.1016/j.dnarep.2020.102860] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 01/13/2023]
Abstract
UV-damaged DNA binding protein (UV-DDB) is a heterodimeric complex, composed of DDB1 and DDB2, and is involved in global genome nucleotide excision repair. Mutations in DDB2 are associated with xeroderma pigmentosum complementation group E. UV-DDB forms a ubiquitin E3 ligase complex with cullin-4A and RBX that helps to relax chromatin around UV-induced photoproducts through the ubiquitination of histone H2A. After providing a brief historical perspective on UV-DDB, we review our current knowledge of the structure and function of this intriguing repair protein. Finally, this article discusses emerging data suggesting that UV-DDB may have other non-canonical roles in base excision repair and the etiology of cancer.
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Affiliation(s)
- Maria Beecher
- Molecular Pharmacology Graduate Program, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Namrata Kumar
- Molecular Genetics and Developmental Biology Graduate Program, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Sunbok Jang
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Vesna Rapić-Otrin
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Bennett Van Houten
- Molecular Pharmacology Graduate Program, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Molecular Genetics and Developmental Biology Graduate Program, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA.
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5
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Jang S, Kumar N, Beckwitt EC, Kong M, Fouquerel E, Rapić-Otrin V, Prasad R, Watkins SC, Khuu C, Majumdar C, David SS, Wilson SH, Bruchez MP, Opresko PL, Van Houten B. Damage sensor role of UV-DDB during base excision repair. Nat Struct Mol Biol 2019; 26:695-703. [PMID: 31332353 PMCID: PMC6684372 DOI: 10.1038/s41594-019-0261-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 05/28/2019] [Indexed: 12/22/2022]
Abstract
UV-DDB, a key protein in human global nucleotide excision repair (NER), binds avidly to abasic sites and 8-oxo-guanine (8-oxoG), suggesting a noncanonical role in base excision repair (BER). We investigated whether UV-DDB can stimulate BER for these two common forms of DNA damage, 8-oxoG and abasic sites, which are repaired by 8-oxoguanine glycosylase (OGG1) and apurinic/apyrimidinic endonuclease (APE1), respectively. UV-DDB increased both OGG1 and APE1 strand cleavage and stimulated subsequent DNA polymerase β-gap filling activity by 30-fold. Single-molecule real-time imaging revealed that UV-DDB forms transient complexes with OGG1 or APE1, facilitating their dissociation from DNA. Furthermore, UV-DDB moves to sites of 8-oxoG repair in cells, and UV-DDB depletion sensitizes cells to oxidative DNA damage. We propose that UV-DDB is a general sensor of DNA damage in both NER and BER pathways, facilitating damage recognition in the context of chromatin.
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Affiliation(s)
- Sunbok Jang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Namrata Kumar
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Molecular Genetics and Developmental Biology Graduate Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Emily C Beckwitt
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Muwen Kong
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Elise Fouquerel
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Molecular Biophysics and Structural Biology Graduate Program, Carnegie Mellon University and University of Pittsburgh, Pittsburgh, PA, USA
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University and Sydney Kimmel Medical College, Philadelphia, PA, USA
| | - Vesna Rapić-Otrin
- Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
| | - Rajendra Prasad
- Genomic Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Simon C Watkins
- Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, PA, USA
| | - Cindy Khuu
- Department of Chemistry, University of California, Davis, Davis, CA, USA
- Biochemistry, Molecular, Cellular and Developmental Graduate Group, University of California, Davis, Davis, CA, USA
| | - Chandrima Majumdar
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Sheila S David
- Department of Chemistry, University of California, Davis, Davis, CA, USA
- Biochemistry, Molecular, Cellular and Developmental Graduate Group, University of California, Davis, Davis, CA, USA
| | - Samuel H Wilson
- Genomic Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Marcel P Bruchez
- Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Patricia L Opresko
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Molecular Biophysics and Structural Biology Graduate Program, Carnegie Mellon University and University of Pittsburgh, Pittsburgh, PA, USA
| | - Bennett Van Houten
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.
- Molecular Genetics and Developmental Biology Graduate Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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6
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Schoch S, Sen V, Gajewski S, Golubev V, Strauch B, Hartwig A, Köberle B. Activity profile of the cisplatin analogue PN149 in different tumor cell lines. Biochem Pharmacol 2018; 156:109-119. [PMID: 30138622 DOI: 10.1016/j.bcp.2018.08.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 08/17/2018] [Indexed: 12/26/2022]
Abstract
The efficacy of the anticancer drug cisplatin is restricted by tumor cell resistance and occurrence of severe side effects. One strategy to overcome these limitations is the development of new, improved platinum drugs. Previous investigations showed that platinum(IV)-nitroxyl complexes are able to circumvent cisplatin resistance in bladder cancer cells. In the present study the mode of action of the platinum(IV)-nitroxyl complex PN149 was investigated in the bladder cancer cell line RT112 and the renal cell carcinoma cell line A498 on the molecular and cellular level. Gene expression analysis showed that PN149 induced genes related to DNA damage response (RRM2B, GADD45A), cell cycle regulation (CDKN1A, PLK3, PPM1D) as well as those coding for the pro-apoptotic factors PUMA and Noxa. These findings on the transcriptional level were confirmed on the functional level revealing that PN149 treatment increased levels of p53 and resulted in cell cycle arrest and drug-induced cytotoxicity via induction of apoptosis. Regarding the expression of oxidative-stress sensitive genes, PN149 induced FTH1, GCLC, HMOX1 and TXNRD1 but relevant effects were restricted to RT112 cells treated with 50 µM. The pro-inflammatory IL-8 was induced by PN149 in RT112 but not A498 cells indicating a cell-type specific activation. Taken together, PN149 possessed promising activity in different tumor cell lines rendering it an interesting alternative to cisplatin in chemotherapy.
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Affiliation(s)
- Sarah Schoch
- Karlsruhe Institute of Technology, Food Chemistry and Toxicology, Adenauerring 20, 76131 Karlsruhe, Germany
| | - Vasily Sen
- Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka, Moskow Region 142432, Russian Federation
| | - Sabine Gajewski
- Karlsruhe Institute of Technology, Food Chemistry and Toxicology, Adenauerring 20, 76131 Karlsruhe, Germany
| | - Valery Golubev
- Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka, Moskow Region 142432, Russian Federation
| | - Bettina Strauch
- Karlsruhe Institute of Technology, Food Chemistry and Toxicology, Adenauerring 20, 76131 Karlsruhe, Germany
| | - Andrea Hartwig
- Karlsruhe Institute of Technology, Food Chemistry and Toxicology, Adenauerring 20, 76131 Karlsruhe, Germany
| | - Beate Köberle
- Karlsruhe Institute of Technology, Food Chemistry and Toxicology, Adenauerring 20, 76131 Karlsruhe, Germany.
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7
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Han C, Zhao R, Kroger J, He J, Wani G, Wang QE, Wani AA. UV radiation-induced SUMOylation of DDB2 regulates nucleotide excision repair. Carcinogenesis 2017; 38:976-985. [PMID: 28981631 DOI: 10.1093/carcin/bgx076] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/19/2017] [Indexed: 12/22/2022] Open
Abstract
Subunit 2 of DNA damage-binding protein complex (DDB2) is an early sensor of nucleotide excision repair (NER) pathway for eliminating DNA damage induced by UV radiation (UVR) and cisplatin treatments of mammalian cells. DDB2 is modified by ubiquitin and poly(ADP-ribose) (PAR) in response to UVR, and these modifications play a crucial role in regulating NER. Here, using immuno-analysis of irradiated cell extracts, we have identified multiple post-irradiation modifications of DDB2 protein. Interestingly, although the DNA lesions induced by both UVR and cisplatin are corrected by NER, only the UV irradiation, but not the cisplatin treatment, induces any discernable DDB2 modifications. We, for the first time, show that the appearance of UVR-induced DDB2 modifications depend on the binding of DDB2 to the damaged chromatin and the participation of functionally active 26S proteasome. The in vitro and in vivo analysis revealed that SUMO-1 conjugations comprise a significant portion of these UVR-induced DDB2 modifications. Mapping of SUMO-modified sites demonstrated that UVR-induced SUMOylation occurs on Lys-309 residue of DDB2 protein. Mutation of Lys-309 to Arg-309 diminished the DDB2 SUMOylation observable both in vitro and in vivo. Moreover, K309R mutated DDB2 lost its function of recruiting XPC to the DNA damage sites, as well as the ability to repair cyclobutane pyrimidine dimers following cellular UV irradiation. Taken together, our results indicate that DDB2 is modified by SUMOylation upon UV irradiation, and this post-translational modification plays an important role in the initial recognition and processing of UVR-induced DNA damage occurring within the context of chromatin.
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Affiliation(s)
| | | | | | | | | | - Qi-En Wang
- Department of Radiology.,James Cancer Hospital and Solove Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Altaf A Wani
- Department of Radiology.,James Cancer Hospital and Solove Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
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8
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Autophagic UVRAG Promotes UV-Induced Photolesion Repair by Activation of the CRL4(DDB2) E3 Ligase. Mol Cell 2017; 62:507-19. [PMID: 27203177 DOI: 10.1016/j.molcel.2016.04.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/29/2016] [Accepted: 04/11/2016] [Indexed: 01/14/2023]
Abstract
UV-induced DNA damage, a major risk factor for skin cancers, is primarily repaired by nucleotide excision repair (NER). UV radiation resistance-associated gene (UVRAG) is a tumor suppressor involved in autophagy. It was initially isolated as a cDNA partially complementing UV sensitivity in xeroderma pigmentosum (XP), but this was not explored further. Here we show that UVRAG plays an integral role in UV-induced DNA damage repair. It localizes to photolesions and associates with DDB1 to promote the assembly and activity of the DDB2-DDB1-Cul4A-Roc1 (CRL4(DDB2)) ubiquitin ligase complex, leading to efficient XPC recruitment and global genomic NER. UVRAG depletion decreased substrate handover to XPC and conferred UV-damage hypersensitivity. We confirmed the importance of UVRAG for UV-damage tolerance using a Drosophila model. Furthermore, increased UV-signature mutations in melanoma correlate with reduced expression of UVRAG. Our results identify UVRAG as a regulator of CRL4(DDB2)-mediated NER and suggest that its expression levels may influence melanoma predisposition.
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9
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Toga T, Kuraoka I, Watanabe S, Nakano E, Takeuchi S, Nishigori C, Sugasawa K, Iwai S. Fluorescence detection of cellular nucleotide excision repair of damaged DNA. Sci Rep 2014; 4:5578. [PMID: 24993089 PMCID: PMC4081890 DOI: 10.1038/srep05578] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 06/18/2014] [Indexed: 12/31/2022] Open
Abstract
To maintain genetic integrity, ultraviolet light-induced photoproducts in DNA must be removed by the nucleotide excision repair (NER) pathway, which is initiated by damage recognition and dual incisions of the lesion-containing strand. We intended to detect the dual-incision step of cellular NER, by using a fluorescent probe. A 140-base pair linear duplex containing the (6-4) photoproduct and a fluorophore-quencher pair was prepared first. However, this type of DNA was found to be degraded rapidly by nucleases in cells. Next, a plasmid was used as a scaffold. In this case, the fluorophore and the quencher were attached to the same strand, and we expected that the dual-incision product containing them would be degraded in cells. At 3 h after transfection of HeLa cells with the plasmid-type probes, fluorescence emission was detected at the nuclei by fluorescence microscopy only when the probe contained the (6-4) photoproduct, and the results were confirmed by flow cytometry. Finally, XPA fibroblasts and the same cells expressing the XPA gene were transfected with the photoproduct-containing probe. Although the transfer of the probe into the cells was slow, fluorescence was detected depending on the NER ability of the cells.
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Affiliation(s)
- Tatsuya Toga
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Isao Kuraoka
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Shun Watanabe
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Eiji Nakano
- Division of Dermatology, Graduate School of Medicine, Kobe University, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
| | - Seiji Takeuchi
- Division of Dermatology, Graduate School of Medicine, Kobe University, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
| | - Chikako Nishigori
- Division of Dermatology, Graduate School of Medicine, Kobe University, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
| | - Kaoru Sugasawa
- Biosignal Research Center, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Shigenori Iwai
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
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10
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Wood RD. DNA damage tolerance and a web of connections with DNA repair at Yale. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2013; 86:507-16. [PMID: 24348215 PMCID: PMC3848105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
This short article summarizes some of the research carried out recently by my laboratory colleagues on the function of DNA polymerase zeta (polζ) in mammalian cells. Some personal background is also described, relevant to research associations with Yale University and its continuing influence. Polζ is involved in the bypass of many DNA lesions by translesion DNA synthesis and is responsible for the majority of DNA damage-induced point mutagenesis in mammalian cells (including human cells), as well as in yeast. We also found that the absence of this enzyme leads to gross chromosomal instability in mammalian cells and increased spontaneous tumorigenesis in mice. Recently, we discovered a further unexpectedly critical role for polζ: it plays an essential role in allowing continued rapid proliferation of cells and tissues. These observations and others indicate that polζ engages frequently during DNA replication to bypass and tolerate DNA lesions or unusual DNA structures that are barriers for the normal DNA replication machinery.
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11
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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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12
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Pines A, Vrouwe MG, Marteijn JA, Typas D, Luijsterburg MS, Cansoy M, Hensbergen P, Deelder A, de Groot A, Matsumoto S, Sugasawa K, Thoma N, Vermeulen W, Vrieling H, Mullenders L. PARP1 promotes nucleotide excision repair through DDB2 stabilization and recruitment of ALC1. ACTA ACUST UNITED AC 2012; 199:235-49. [PMID: 23045548 PMCID: PMC3471223 DOI: 10.1083/jcb.201112132] [Citation(s) in RCA: 186] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PARP1-mediated poly(ADP-ribosyl)ation of DDB2 prolongs its occupation on UV-damaged chromatin and promotes the recruitment of the chromatin remodeler ALC1. The WD40-repeat protein DDB2 is essential for efficient recognition and subsequent removal of ultraviolet (UV)-induced DNA lesions by nucleotide excision repair (NER). However, how DDB2 promotes NER in chromatin is poorly understood. Here, we identify poly(ADP-ribose) polymerase 1 (PARP1) as a novel DDB2-associated factor. We demonstrate that DDB2 facilitated poly(ADP-ribosyl)ation of UV-damaged chromatin through the activity of PARP1, resulting in the recruitment of the chromatin-remodeling enzyme ALC1. Depletion of ALC1 rendered cells sensitive to UV and impaired repair of UV-induced DNA lesions. Additionally, DDB2 itself was targeted by poly(ADP-ribosyl)ation, resulting in increased protein stability and a prolonged chromatin retention time. Our in vitro and in vivo data support a model in which poly(ADP-ribosyl)ation of DDB2 suppresses DDB2 ubiquitylation and outline a molecular mechanism for PARP1-mediated regulation of NER through DDB2 stabilization and recruitment of the chromatin remodeler ALC1.
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Affiliation(s)
- Alex Pines
- Department of Toxicogenetics, Leiden University Medical Center, Leiden, Netherlands
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13
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Sugasawa K. Multiple DNA damage recognition factors involved in mammalian nucleotide excision repair. BIOCHEMISTRY (MOSCOW) 2011; 76:16-23. [PMID: 21568836 DOI: 10.1134/s0006297911010044] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The nucleotide excision repair (NER) subpathway operating throughout the mammalian genome is a versatile DNA repair system that can remove a wide variety of helix-distorting base lesions. This system contributes to prevention of blockage of DNA replication by the lesions, thereby suppressing mutagenesis and carcinogenesis. Therefore, it is of fundamental significance to understand how the huge genome can be surveyed for occurrence of a small number of lesions. Recent studies have revealed that this difficult task seems to be accomplished through sequential actions of multiple DNA damage recognition factors, including UV-DDB, XPC, and TFIIH. Notably, these factors adopt completely different strategies to recognize DNA damage. XPC detects disruption and/or destabilization of the base pairing, which ensures a broad spectrum of substrate specificity for global genome NER. In contrast, UV-DDB directly recognizes particular types of lesions, such as UV-induced photoproducts, thereby vitally recruiting XPC as well as further extending the substrate specificity. After DNA binding by XPC, moreover, the helicase activity associated with TFIIH scans a DNA strand to make a final search for the presence of aberrant chemical modifications of DNA. The combination of these different strategies makes a crucial contribution to simultaneously achieving efficiency, accuracy, and versatility of the entire repair system.
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Affiliation(s)
- K Sugasawa
- Biosignal Research Center, Organization of Advanced Science and Technology, Kobe University, Hyogo, Japan.
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15
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Oh KS, Emmert S, Tamura D, DiGiovanna JJ, Kraemer KH. Multiple skin cancers in adults with mutations in the XP-E (DDB2) DNA repair gene. J Invest Dermatol 2011; 131:785-8. [PMID: 21107348 PMCID: PMC3471370 DOI: 10.1038/jid.2010.352] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Kyu-Seon Oh
- DNA Repair Section, Dermatology Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Steffen Emmert
- Department of Dermatology, Goettingen University, Goettingen, Germany
| | - Deborah Tamura
- DNA Repair Section, Dermatology Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - John J. DiGiovanna
- DNA Repair Section, Dermatology Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Kenneth H. Kraemer
- DNA Repair Section, Dermatology Branch, National Cancer Institute, Bethesda, Maryland, USA
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Guerrero-Santoro J, Levine AS, Rapić-Otrin V. Co-localization of DNA repair proteins with UV-induced DNA damage in locally irradiated cells. Methods Mol Biol 2011; 682:149-61. [PMID: 21057927 DOI: 10.1007/978-1-60327-409-8_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This chapter describes a technique in which indirect immunofluorescence is applied to visualize the process of nucleotide excision repair (NER) at the site of locally induced damage in DNA. UV-irradiation of cells through an isopore polycarbonate membrane filter generates cyclobutane pyrimidine dimers (CPD) and (6-4) photoproducts (6-4PP) on a subnuclear area, which corresponds to the size of a pore on the membrane. Specific antibodies to CPD and 6-4PP define the damaged spot. The NER components co-localize at the damaged-DNA subnuclear spot, where the proteins are stained with the appropriate fluorescent antibodies. This relatively simple and affordable method facilitates the examination of the sequential assembly of NER proteins in the chromatin-embedded DNA photoproducts. The method also enhances the identification of repair auxiliary proteins and complexes, such as ubiquitin E3 ligases, involved in the initiation of NER on non-transcribed DNA.
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Affiliation(s)
- Jennifer Guerrero-Santoro
- Department of Microbiology and Molecular Genetics, Hillman Cancer Center, University of Pittsburgh School of Medicine, and University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
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Grosskopf C, Schwerdtle T, Mullenders LHF, Hartwig A. Antimony impairs nucleotide excision repair: XPA and XPE as potential molecular targets. Chem Res Toxicol 2010; 23:1175-83. [PMID: 20509621 DOI: 10.1021/tx100106x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Trivalent antimony is a known genotoxic agent classified as a possible human carcinogen by the International Agency for Research on Cancer (IARC) and as an animal carcinogen by the German MAK Commission. Nevertheless, the underlying mechanism for its genotoxicity remains elusive. Because of the similarities between antimony and arsenic, the inhibition of DNA repair has been a promising hypothesis. Investigations on the removal of DNA lesions now revealed a damage specific impairment of nucleotide excision repair (NER). After irradiation of A549 human lung carcinoma cells with UVC, a higher number of cyclobutane pyrimidine dimers (CPD) remained in the presence of SbCl(3), whereas processing of the 6-4 photoproducts (6-4PP) and benzo[a]pyrene diol epoxide (BPDE)-induced DNA adducts was not impaired. Nevertheless, cell viability was reduced in a more than additive mode after combined treatment of SbCl(3) with UVC as well as with BPDE. In search of the molecular targets, a decrease in gene expression and protein level of XPE was found, which is known to be indispensable for the recognition of CPD. Moreover, trivalent antimony was shown to interact with the zinc finger domain of XPA, another NER protein, since SbCl(3) mediated a concentration dependent release of zinc from a peptide consistent with this domain. In the cellular system, association of XPA to and dissociation from damaged DNA was diminished in the presence of SbCl(3). These results show for the first time that trivalent antimony interferes with proteins involved in nucleotide excision repair and partly impairs this pathway, pointing to an indirect mechanism in the genotoxicity of trivalent antimony.
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Affiliation(s)
- Claudia Grosskopf
- Fachgebiet Lebensmittelchemie und Toxikologie, Institut fur Lebensmitteltechnologie und Lebensmittelchemie, Technische Universitat Berlin, Gustav-Meyer-Allee 25, Berlin, Germany
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18
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DDB2 complex-mediated ubiquitylation around DNA damage is oppositely regulated by XPC and Ku and contributes to the recruitment of XPA. Mol Cell Biol 2010; 30:2708-23. [PMID: 20368362 DOI: 10.1128/mcb.01460-09] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UV-damaged-DNA-binding protein (UV-DDB) is a heterodimer comprised of DDB1 and DDB2 and integrated in a complex that includes a ubiquitin ligase component, cullin 4A, and Roc1. Here we show that the ubiquitin ligase activity of the DDB2 complex is required for efficient global genome nucleotide excision repair (GG-NER) in chromatin. Mutant DDB2 proteins derived from xeroderma pigmentosum group E patients are not able to mediate ubiquitylation around damaged sites in chromatin. We also found that CSN, a negative regulator of cullin-based ubiquitin ligases, dissociates from the DDB2 complex when the complex binds to damaged DNA and that XPC and Ku oppositely regulate the ubiquitin ligase activity, especially around damaged sites. Furthermore, the DDB2 complex-mediated ubiquitylation plays a role in recruiting XPA to damaged sites. These findings shed some light on the early stages of GG-NER.
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19
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Scrima A, Koníčková R, Czyzewski BK, Kawasaki Y, Jeffrey PD, Groisman R, Nakatani Y, Iwai S, Pavletich NP, Thomä NH. Structural basis of UV DNA-damage recognition by the DDB1-DDB2 complex. Cell 2009; 135:1213-23. [PMID: 19109893 PMCID: PMC2676164 DOI: 10.1016/j.cell.2008.10.045] [Citation(s) in RCA: 322] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Revised: 09/25/2008] [Accepted: 10/31/2008] [Indexed: 11/18/2022]
Abstract
Ultraviolet (UV) light-induced pyrimidine photodimers are repaired by the nucleotide excision repair pathway. Photolesions have biophysical parameters closely resembling undamaged DNA, impeding discovery through damage surveillance proteins. The DDB1-DDB2 complex serves in the initial detection of UV lesions in vivo. Here we present the structures of the DDB1-DDB2 complex alone and bound to DNA containing either a 6-4 pyrimidine-pyrimidone photodimer (6-4PP) lesion or an abasic site. The structure shows that the lesion is held exclusively by the WD40 domain of DDB2. A DDB2 hairpin inserts into the minor groove, extrudes the photodimer into a binding pocket, and kinks the duplex by approximately 40 degrees. The tightly localized probing of the photolesions, combined with proofreading in the photodimer pocket, enables DDB2 to detect lesions refractory to detection by other damage surveillance proteins. The structure provides insights into damage recognition in chromatin and suggests a mechanism by which the DDB1-associated CUL4 ubiquitin ligase targets proteins surrounding the site of damage.
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Affiliation(s)
- Andrea Scrima
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH 4058, Basel, Switzerland
| | - Renata Koníčková
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH 4058, Basel, Switzerland
| | - Bryan K. Czyzewski
- Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA
| | - Yusuke Kawasaki
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Philip D. Jeffrey
- Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA
| | - Regina Groisman
- CNRS, FRE 2944, Institut Andre Lwoff, Univ Paris-Sud, Villejuif, F-94801
| | - Yoshihiro Nakatani
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115
| | - Shigenori Iwai
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Nikola P. Pavletich
- Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA
- Correspondence: Nicolas H. Thomä (E-mail: ), Nikola P. Pavletich (E-mail: )
| | - Nicolas H. Thomä
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH 4058, Basel, Switzerland
- Correspondence: Nicolas H. Thomä (E-mail: ), Nikola P. Pavletich (E-mail: )
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Chapter 6 Application of New Methods for Detection of DNA Damage and Repair. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2009; 277:217-51. [DOI: 10.1016/s1937-6448(09)77006-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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21
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Wakasugi M, Kasashima H, Fukase Y, Imura M, Imai R, Yamada S, Cleaver JE, Matsunaga T. Physical and functional interaction between DDB and XPA in nucleotide excision repair. Nucleic Acids Res 2008; 37:516-25. [PMID: 19056823 PMCID: PMC2632899 DOI: 10.1093/nar/gkn964] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Damaged DNA-binding protein (DDB), consisting of DDB1 and DDB2 subunits recognizes a wide spectrum of DNA lesions. DDB is dispensable for in vitro nucleotide excision repair (NER) reaction, but stimulates this reaction especially for cyclobutane pyrimidine dimer (CPD). Here we show that DDB directly interacts with XPA, one of core NER factors, mainly through DDB2 subunit and the amino-acid residues between 185 and 226 in XPA are important for the interaction. Interestingly, the point mutation causing the substitution from Arg-207 to Gly, which was previously identified in a XP-A revertant cell-line XP129, diminished the interaction with DDB in vitro and in vivo. In a defined system containing R207G mutant XPA and other core NER factors, DDB failed to stimulate the excision of CPD, although the mutant XPA was competent for the basal NER reaction. Moreover, in vivo experiments revealed that the mutant XPA is recruited to damaged DNA sites with much less efficiency compared with wild-type XPA and fails to support the enhancement of CPD repair by ectopic expression of DDB2 in SV40-transformed human cells. These results suggest that the physical interaction between DDB and XPA plays an important role in the DDB-mediated NER reaction.
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Affiliation(s)
- Mitsuo Wakasugi
- Laboratory of Human Molecular Genetics, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan
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22
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Pines A, Backendorf C, Alekseev S, Jansen JG, de Gruijl FR, Vrieling H, Mullenders LHF. Differential activity of UV-DDB in mouse keratinocytes and fibroblasts: impact on DNA repair and UV-induced skin cancer. DNA Repair (Amst) 2008; 8:153-61. [PMID: 18996499 DOI: 10.1016/j.dnarep.2008.09.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Revised: 09/15/2008] [Accepted: 09/29/2008] [Indexed: 10/21/2022]
Abstract
UV-damaged DNA-binding protein (UV-DDB) is essential for global genome nucleotide excision repair of UV-induced cyclobutane pyrimidine dimers (CPD) and accelerates repair of 6-4 photoproducts (6-4PP). The high UV-induced skin cancer susceptibility of mice compared to man has been attributed to low expression of the UV-DDB subunit DDB2 in mouse skin cells. However, DDB2 knockout mice exhibit enhanced UVB skin carcinogenesis indicating that DDB2 protects mice against UV-induced skin cancer. To resolve these apparent contradictory findings, we systematically investigated the NER capacity of mouse fibroblasts and keratinocytes. Compared to fibroblasts, keratinocytes exhibited an increased level of UV-DDB activity, contained significantly higher levels of other NER proteins (i.e. XPC and XPB) and displayed efficient repair of CPD. At low UVB dosages, the difference in skin cancer susceptibility between DDB2 KO and wild type mice was even much more pronounced than previously reported with high dose UVB exposures. Hence, our observations show that mouse keratinocytes express sufficient levels of UV-DDB for efficient repair of photolesions and efficient protection against UV-induced skin cancer at physiological relevant UV exposure.
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Affiliation(s)
- Alex Pines
- Department of Toxicogenetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
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23
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The Cullin 4B–Based UV-Damaged DNA-Binding Protein Ligase Binds to UV-Damaged Chromatin and Ubiquitinates Histone H2A. Cancer Res 2008; 68:5014-22. [DOI: 10.1158/0008-5472.can-07-6162] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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24
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Abstract
Chromatin structure plays a key role in most processes involving DNA metabolism. Chromatin modifications implicated in transcriptional regulation are relatively well characterized and are thought to be the result of a code on the histone proteins (histone code). This code, involving phosphorylation, ubiquitylation, sumoylation, acetylation and methylation, is believed to regulate chromatin accessibility either by disrupting chromatin contacts or by recruiting non-histone proteins to chromatin. Recent evidences suggest that such mechanisms are also involved in DNA damage detection and DNA repair. One of the most well-characterized modifications is caused by the formation of DNA double strand breaks (DSBs), resulting in phosphorylation of histone H2AX (the so-called gamma-H2AX) on the chromatin surrounding the DNA lesion. It is generally believed that histone H2AX phosphorylation is required for the concentration and stabilization of DNA repair proteins to the damaged chromatin. The phosphorylation of this histone seems to play a role in both non-homologous end-joining (NHEJ) and homologous recombination (HR) repair pathways. However, the choice of the repair pathway might depend on or induce additional post-translational modifications affecting other histone proteins necessary to the completion of the entire DNA repair process. Interestingly, even in the absence of DSBs, histone modifications occur. Indeed, following UV-exposure, histone acetylation takes place and is believed to facilitate the nucleotide excision repair (NER) process by promoting chromatin accessibility to the repair factors. This review focuses on recent data characterizing the function of histone modification in various repair processes and discusses if the combination of such modifications can be the trademark of a specific DNA repair pathway.
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25
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Li J, Wang QE, Zhu Q, El-Mahdy MA, Wani G, Praetorius-Ibba M, Wani AA. DNA damage binding protein component DDB1 participates in nucleotide excision repair through DDB2 DNA-binding and cullin 4A ubiquitin ligase activity. Cancer Res 2007; 66:8590-7. [PMID: 16951172 DOI: 10.1158/0008-5472.can-06-1115] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Functional defect in DNA damage binding (DDB) activity has a direct relationship to decreased nucleotide excision repair (NER) and increased susceptibility to cancer. DDB forms a complex with cullin 4A (Cul4A), which is now known to ubiquitylate DDB2, XPC, and histone H2A. However, the exact role of DDB1 in NER is unclear. In this study, we show that DDB1 knockdown in human cells impaired their ability to efficiently repair UV-induced cyclobutane pyrimidine dimers (CPD) but not 6-4 photoproducts (6-4PP). Extensive nuclear protein fractionation and chromatin association analysis revealed that upon irradiation, DDB1 protein is translocated from a loosely bound to a tightly bound in vivo chromatin fraction and the DDB1 translocation required the participation of functional DDB2 protein. DDB1 knockdown also affected the translocation of Cul4A component to the tightly bound form in UV-damaged chromatin in vivo as well as its recruitment to the locally damaged nuclear foci in situ. However, DDB1 knockdown had no effect on DNA damage binding capacity of DDB2. The data indicated that DDB2 can bind to damaged DNA in vivo as a monomer, whereas Cul4A recruitment to damage sites depends on the fully assembled complex. Our data also showed that DDB1 is required for the UV-induced DDB2 ubiquitylation and degradation. In summary, the results suggest that (a) DDB1 is critical for efficient NER of CPD; (b) DDB1 acts in bridging DDB2 and ubiquitin ligase Cul4A; and (c) DDB1 aids in recruiting the ubiquitin ligase activity to the damaged sites for successful commencement of lesion processing by NER.
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Affiliation(s)
- Jinyou Li
- Department of Radiology, The Ohio State University, Columbus, Ohio 43240, USA
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26
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The xeroderma pigmentosum group E gene product DDB2 activates nucleotide excision repair by regulating the level of p21Waf1/Cip1. Mol Cell Biol 2007; 28:177-87. [PMID: 17967871 DOI: 10.1128/mcb.00880-07] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The xeroderma pigmentosum group E gene product DDB2, a protein involved in nucleotide excision repair (NER), associates with the E3 ubiquitin ligase complex Cul4A-DDB1. But the precise role of these interactions in the NER activity of DDB2 is unclear. Several models, including DDB2-mediated ubiquitination of histones in UV-irradiated cells, have been proposed. But those models lack clear genetic evidence. Here we show that DDB2 participates in NER by regulating the cellular levels of p21(Waf1/Cip1). We show that DDB2 enhances nuclear accumulation of DDB1, which binds to a modified form of p53 containing phosphorylation at Ser18 (p53(S18P)) and targets it for degradation in low-dose-UV-irradiated cells. DDB2(-/-) mouse embryonic fibroblasts (MEFs), unlike wild-type MEFs, are deficient in the proteolysis of p53(S18P). Accumulation of p53(S18P) in DDB2(-/-) MEFs causes higher expression p21(Waf1/Cip1). We show that the increased expression of p21(Waf1/Cip1) is the cause NER deficiency in DDB2(-/-) cells because deletion or knockdown of p21(Waf1/Cip1) reverses their NER-deficient phenotype. p21(Waf1/Cip1) was shown to bind PCNA, which is required for both DNA replication and NER. Moreover, an increased level of p21(Waf1/Cip1) was shown to inhibit NER both in vitro and in vivo. Our results provide genetic evidence linking the regulation of p21(Waf1/Cip1) to the NER activity of DDB2.
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27
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Wang QE, Prætorius-Ibba M, Zhu Q, El-Mahdy MA, Wani G, Zhao Q, Qin S, Patnaik S, Wani AA. Ubiquitylation-independent degradation of Xeroderma pigmentosum group C protein is required for efficient nucleotide excision repair. Nucleic Acids Res 2007; 35:5338-50. [PMID: 17693435 PMCID: PMC2018625 DOI: 10.1093/nar/gkm550] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Xeroderma Pigmentosum group C (XPC) protein is indispensable to global genomic repair (GGR), a subpathway of nucleotide excision repair (NER), and plays an important role in the initial damage recognition. XPC can be modified by both ubiquitin and SUMO in response to UV irradiation of cells. Here, we show that XPC undergoes degradation upon UV irradiation, and this is independent of protein ubiquitylation. The subunits of DDB-Cul4A E3 ligase differentially regulate UV-induced XPC degradation, e.g DDB2 is required and promotes, whereas DDB1 and Cul4A protect the protein degradation. Mutation of XPC K655 to alanine abolishes both UV-induced XPC modification and degradation. XPC degradation is necessary for recruiting XPG and efficient NER. The overall results provide crucial insights regarding the fate and role of XPC protein in the initiation of excision repair.
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Affiliation(s)
- Qi-En Wang
- Department of Radiology, Department of Molecular and Cellular Biochemistry and Comprehensive Cancer Center, The Ohio State University, 460 W. 12th Ave, Columbus, OH 43210, USA
- *To whom correspondence should be addressed. +1 614 292 9015+1 614 293 0802;
| | - Mette Prætorius-Ibba
- Department of Radiology, Department of Molecular and Cellular Biochemistry and Comprehensive Cancer Center, The Ohio State University, 460 W. 12th Ave, Columbus, OH 43210, USA
| | - Qianzheng Zhu
- Department of Radiology, Department of Molecular and Cellular Biochemistry and Comprehensive Cancer Center, The Ohio State University, 460 W. 12th Ave, Columbus, OH 43210, USA
| | - Mohamed A. El-Mahdy
- Department of Radiology, Department of Molecular and Cellular Biochemistry and Comprehensive Cancer Center, The Ohio State University, 460 W. 12th Ave, Columbus, OH 43210, USA
| | - Gulzar Wani
- Department of Radiology, Department of Molecular and Cellular Biochemistry and Comprehensive Cancer Center, The Ohio State University, 460 W. 12th Ave, Columbus, OH 43210, USA
| | - Qun Zhao
- Department of Radiology, Department of Molecular and Cellular Biochemistry and Comprehensive Cancer Center, The Ohio State University, 460 W. 12th Ave, Columbus, OH 43210, USA
| | - Song Qin
- Department of Radiology, Department of Molecular and Cellular Biochemistry and Comprehensive Cancer Center, The Ohio State University, 460 W. 12th Ave, Columbus, OH 43210, USA
| | - Srinivas Patnaik
- Department of Radiology, Department of Molecular and Cellular Biochemistry and Comprehensive Cancer Center, The Ohio State University, 460 W. 12th Ave, Columbus, OH 43210, USA
| | - Altaf A. Wani
- Department of Radiology, Department of Molecular and Cellular Biochemistry and Comprehensive Cancer Center, The Ohio State University, 460 W. 12th Ave, Columbus, OH 43210, USA
- *To whom correspondence should be addressed. +1 614 292 9015+1 614 293 0802;
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28
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Tan L, Ehrlich E, Yu XF. DDB1 and Cul4A are required for human immunodeficiency virus type 1 Vpr-induced G2 arrest. J Virol 2007; 81:10822-30. [PMID: 17626091 PMCID: PMC2045451 DOI: 10.1128/jvi.01380-07] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Vpr-mediated induction of G2 cell cycle arrest has been postulated to be important for human immunodeficiency virus type 1 (HIV-1) replication, but the precise role of Vpr in this cell cycle arrest is unclear. In the present study, we have shown that HIV-1 Vpr interacts with damaged DNA binding protein 1 (DDB1) but not its partner DDB2. The interaction of Vpr with DDB1 was inhibited when DCAF1 (VprBP) expression was reduced by short interfering RNA (siRNA) treatment. The Vpr mutant (Q65R) that was defective for DCAF1 interaction also had a defect in DDB1 binding. However, Vpr binding to DDB1 was not sufficient to induce G2 arrest. A reduction in DDB1 or DDB2 expression in the absence of Vpr also did not induce G2 arrest. On the other hand, Vpr-induced G2 arrest was impaired when the intracellular level of DDB1 or Cullin 4A was reduced by siRNA treatment. Furthermore, Vpr-induced G2 arrest was largely abolished by a proteasome inhibitor. These data suggest that Vpr assembles with DDB1 through interaction with DCAF1 to form an E3 ubiquitin ligase that targets cellular substrates for proteasome-mediated degradation and G2 arrest.
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Affiliation(s)
- Lindi Tan
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
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29
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Shimanouchi K, Takata KI, Yamaguchi M, Murakami S, Ishikawa G, Takeuchi R, Kanai Y, Ruike T, Nakamura R, Abe Y, Sakaguchi K. Drosophila damaged DNA binding protein 1 contributes to genome stability in somatic cells. J Biochem 2007; 139:51-8. [PMID: 16428319 DOI: 10.1093/jb/mvj006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The damaged DNA-binding protein (DDB) complex consists of a heterodimer of p127 (DDB1) and p48 (DDB2) subunits and is believed to have a role in nucleotide excision repair (NER). We used the GAL4-UAS targeted expression system to knock down DDB1 in wing imaginal discs of Drosophila. The knock-down was achieved in transgenic flies using over-expression of inverted repeat RNA of the D-DDB1 gene [UAS-D-DDB1(650)-dsRNA]. As a consequence of RNA interference (RNAi), the fly had a shrunken wing phenotype. The wing spot test showed induced genome instability in transgenic flies with RNAi knock-down of D-DDB1 in wing imaginal discs. When Drosophila larvae with RNAi knock-down of D-DDB1 in wing imaginal discs were treated with the chemical mutagen methyl methanesulfonate (MMS), the frequency of flies with a severely shrunken wing phenotype increased compared to non-treated transgenic flies. These results suggested that DDB1 plays a role in the response to DNA damaged with MMS and in genome stability in Drosophila somatic cells.
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Affiliation(s)
- Kaori Shimanouchi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510
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30
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van der Wees C, Jansen J, Vrieling H, van der Laarse A, Van Zeeland A, Mullenders L. Nucleotide excision repair in differentiated cells. Mutat Res 2006; 614:16-23. [PMID: 16879838 DOI: 10.1016/j.mrfmmm.2006.06.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Nucleotide excision repair (NER) is the principal pathway for the removal of a wide range of DNA helix-distorting lesions and operates via two NER subpathways, i.e. global genome repair (GGR) and transcription-coupled repair (TCR). Although detailed information is available on expression and efficiency of NER in established mammalian cell lines, little is known about the expression of NER pathways in (terminally) differentiated cells. The majority of studies in differentiated cells have focused on repair of UV-induced cyclobutane pyrimidine dimers (CPD) and 6-4-photoproducts (6-4PP) because of the high frequency of photolesions at low level of toxicity and availability of sensitive technologies to determine photolesions in defined regions of the genome. The picture that emerges from these studies is blurred and rather complex. Fibroblasts and terminally differentiated myocytes of the rat heart display equally efficient GGR of 6-4PP but poor repair of CPD due to the absence of p48 expression. This repair phenotype is clearly different from human terminal differentiated neurons. Furthermore, both cell types were found to carry out TCR of CPD, thus mimicking the repair phenotype of established rodent cell lines. In contrast, in intact rat spermatogenic cells repair was very inefficient at the genome overall level and in transcriptionally active genes indicating that GGR and TCR are non-functional. Also, non-differentiated mouse embryonic stem (ES) cells exhibit low levels of NER after UV irradiation. However, the mechanisms that lead to low NER activity are clearly different: in differentiated spermatogenic cells differences in chromatin compaction and sequestering of NER proteins may underlie the lack of NER activity in pre-meiotic cells, whereas in non-differentiated ES cells NER is impaired by a strong apoptotic response.
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Affiliation(s)
- Caroline van der Wees
- Department of Toxicogenetics, Leiden University Medical Center, Leiden, The Netherlands
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31
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Gillet LCJ, Schärer OD. Molecular mechanisms of mammalian global genome nucleotide excision repair. Chem Rev 2006; 106:253-76. [PMID: 16464005 DOI: 10.1021/cr040483f] [Citation(s) in RCA: 464] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Ludovic C J Gillet
- Institute for Molecular Cancer Research, University of Zürich, Switzerland
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32
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Hu Z, Shao M, Yuan J, Xu L, Wang F, Wang Y, Yuan W, Qian J, Ma H, Wang Y, Liu H, Chen W, Yang L, Jin G, Huo X, Chen F, Jin L, Wei Q, Huang W, Lu D, Wu T, Shen H. Polymorphisms in DNA damage binding protein 2 (DDB2) and susceptibility of primary lung cancer in the Chinese: a case-control study. Carcinogenesis 2006; 27:1475-80. [PMID: 16522664 DOI: 10.1093/carcin/bgi350] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
DNA damage binding protein 2 (DDB2) is one of the major DNA repair proteins involved in the nucleotide excision repair (NER) pathway. Mutations in the DDB2 gene can cause a repair-deficiency syndrome xeroderma pigmentosum group E. Because tobacco carcinogens can cause DNA damage that is repaired by NER and suboptimal NER capacity is reported to be associated with lung cancer risk, we hypothesized that common variants in the DDB2 gene are associated with lung cancer risk. To test this hypothesis, we conducted a case-control study of 1010 patients with incident lung cancer and 1011 cancer-free controls and genotyped two DDB2 single nucleotide polymorphisms (SNPs) (rs830083 and rs3781620) that are in linkage disequilibrium with other untyped SNPs. We found that compared with the rs830083CC, subjects carrying the heterozygous rs830083CG genotype had a significantly 1.31-fold increased risk of lung cancer [95% confidence interval (CI) 1.08-1.60] and those carrying the homozygous rs830083GG genotype had a non-significantly 1.22-fold elevated risk (95% CI 0.89-1.67). In addition, effects of the combined rs830083CG/GG variant genotypes were more evident in young subjects, heavy smokers and subjects with a positive family history of cancer. These findings indicate, for the first time, that the DDB2 rs830083 polymorphism may contribute to the etiology of lung cancer. Further functional studies on this SNP and/or related variants are warranted to elucidate the underlying molecular mechanisms of the association.
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Affiliation(s)
- Zhibin Hu
- Department of Epidemiology and Biostatistics, Cancer Research Center of Nanjing Medical University, Nanjing 210029, China
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G. Kapetanaki M, Guerrero-Santoro J, Bisi DC, Hsieh CL, Rapić-Otrin V, Levine AS. The DDB1-CUL4ADDB2 ubiquitin ligase is deficient in xeroderma pigmentosum group E and targets histone H2A at UV-damaged DNA sites. Proc Natl Acad Sci U S A 2006; 103:2588-93. [PMID: 16473935 PMCID: PMC1413840 DOI: 10.1073/pnas.0511160103] [Citation(s) in RCA: 257] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Xeroderma pigmentosum (XP) is a heritable human disorder characterized by defects in nucleotide excision repair (NER) and the development of skin cancer. Cells from XP group E (XP-E) patients have a defect in the UV-damaged DNA-binding protein complex (UV-DDB), involved in the damage recognition step of NER. UV-DDB comprises two subunits, products of the DDB1 and DDB2 genes, respectively. Mutations in the DDB2 gene account for the underlying defect in XP-E. The UV-DDB complex is a component of the newly identified cullin 4A-based ubiquitin E3 ligase, DDB1-CUL4A(DDB2). The E3 ubiquitin ligases recognize specific substrates and mediate their ubiquitination to regulate protein activity or target proteins for degradation by the proteasomal pathway. In this study, we have addressed the role of the UV-DDB-based E3 in NER and sought a physiological substrate. We demonstrate that monoubiquitinated histone H2A in native chromatin coimmunoprecipitates with the endogenous DDB1-CUL4A(DDB2) complex in response to UV irradiation. Further, mutations in DDB2 alter the formation and binding activity of the DDB1-CUL4A(DDB2) ligase, accompanied by impaired monoubiquitination of H2A after UV treatment of XP-E cells, compared with repair-proficient cells. This finding indicates that DDB2, as the substrate receptor of the DDB1-CUL4A-based ligase, specifically targets histone H2A for monoubiquitination in a photolesion-binding-dependent manner. Given that the loss of monoubiquitinated histone H2A at the sites of UV-damaged DNA is associated with decreased global genome repair in XP-E cells, this study suggests that histone modification, mediated by the XPE factor, facilitates the initiation of NER.
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Affiliation(s)
- Maria G. Kapetanaki
- Department of Molecular Genetics and Biochemistry, School of Medicine, and Cancer Institute, University of Pittsburgh, Hillman Cancer Center, Research Pavilion, Suite 2.6, 5117 Centre Avenue, Pittsburgh, PA 15213
| | - Jennifer Guerrero-Santoro
- Department of Molecular Genetics and Biochemistry, School of Medicine, and Cancer Institute, University of Pittsburgh, Hillman Cancer Center, Research Pavilion, Suite 2.6, 5117 Centre Avenue, Pittsburgh, PA 15213
| | - Dawn C. Bisi
- Department of Molecular Genetics and Biochemistry, School of Medicine, and Cancer Institute, University of Pittsburgh, Hillman Cancer Center, Research Pavilion, Suite 2.6, 5117 Centre Avenue, Pittsburgh, PA 15213
| | - Ching L. Hsieh
- Department of Molecular Genetics and Biochemistry, School of Medicine, and Cancer Institute, University of Pittsburgh, Hillman Cancer Center, Research Pavilion, Suite 2.6, 5117 Centre Avenue, Pittsburgh, PA 15213
| | - Vesna Rapić-Otrin
- Department of Molecular Genetics and Biochemistry, School of Medicine, and Cancer Institute, University of Pittsburgh, Hillman Cancer Center, Research Pavilion, Suite 2.6, 5117 Centre Avenue, Pittsburgh, PA 15213
- To whom correspondence should be addressed. E-mail:
| | - Arthur S. Levine
- Department of Molecular Genetics and Biochemistry, School of Medicine, and Cancer Institute, University of Pittsburgh, Hillman Cancer Center, Research Pavilion, Suite 2.6, 5117 Centre Avenue, Pittsburgh, PA 15213
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Alekseev S, Kool H, Rebel H, Fousteri M, Moser J, Backendorf C, de Gruijl FR, Vrieling H, Mullenders LHF. Enhanced DDB2 expression protects mice from carcinogenic effects of chronic UV-B irradiation. Cancer Res 2006; 65:10298-306. [PMID: 16288018 DOI: 10.1158/0008-5472.can-05-2295] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
UV-damaged DNA-binding protein (UV-DDB) is essential for global genome repair (GGR) of UV-induced cyclobutane pyrimidine dimers (CPD). Unlike human cells, rodent epidermal cells are deficient in GGR of CPDs and express a subunit of UV-DDB, DDB2, at a low level. In this study, we generated mice (K14-DDB2) ectopically expressing mouse DDB2 at elevated levels. Enhanced expression of DDB2 both delayed the onset of squamous cell carcinoma and decreased the number of tumors per mouse in chronically UV-B light-exposed hairless mice. Enhanced expression of DDB2 improved repair of both CPDs and pyrimidine(6-4)pyrimidone photoproducts (6-4PP) in dermal fibroblasts. However, GGR of CPDs in K14-DDB2 mice did not reach the level of efficiency of human cells, suggesting that another repair protein may become rate limiting when DDB2 is abundantly present. To complement these studies, we generated mice in which the DDB2 gene was disrupted. DDB2-/- and DDB2+/- mice were found to be hypersensitive to UV-induced skin carcinogenesis. On the cellular level, we detected a delay in the repair of 6-4PPs in DDB2-/- dermal fibroblasts. Neither the absence nor the enhanced expression of DDB2 affected the levels of UV-induced apoptosis in epidermal keratinocytes or cultured dermal fibroblasts. Our results show an important role for DDB2 in the protection against UV-induced cancer and indicate that this protection is most likely mediated by accelerating the repair of photolesions.
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Affiliation(s)
- Sergey Alekseev
- Department of Toxicogenetics, Leiden University Medical Center, Leiden University, Leiden, the Netherlands
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35
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Kulaksiz G, Reardon JT, Sancar A. Xeroderma pigmentosum complementation group E protein (XPE/DDB2): purification of various complexes of XPE and analyses of their damaged DNA binding and putative DNA repair properties. Mol Cell Biol 2005; 25:9784-92. [PMID: 16260596 PMCID: PMC1280284 DOI: 10.1128/mcb.25.22.9784-9792.2005] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Xeroderma pigmentosum is characterized by increased sensitivity of the affected individuals to sunlight and light-induced skin cancers and, in some cases, to neurological abnormalities. The disease is caused by a mutation in genes XPA through XPG and the XP variant (XPV) gene. The proteins encoded by the XPA, -B, -C, -D, -F, and -G genes are required for nucleotide excision repair, and the XPV gene encodes DNA polymerase eta, which carries out translesion DNA synthesis. In contrast, the mechanism by which the XPE gene product prevents sunlight-induced cancers is not known. The gene (XPE/DDB2) encodes the small subunit of a heterodimeric DNA binding protein with high affinity to UV-damaged DNA (UV-damaged DNA binding protein [UV-DDB]). The DDB2 protein exists in at least four forms in the cell: monomeric DDB2, DDB1-DDB2 heterodimer (UV-DDB), and as a protein associated with both the Cullin 4A (CUL4A) complex and the COP9 signalosome. To better define the role of DDB2 in the cellular response to DNA damage, we purified all four forms of DDB2 and analyzed their DNA binding properties and their effects on mammalian nucleotide excision repair. We find that DDB2 has an intrinsic damaged DNA binding activity and that under our assay conditions neither DDB2 nor complexes that contain DDB2 (UV-DDB, CUL4A, and COP9) participate in nucleotide excision repair carried out by the six-factor human excision nuclease.
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Affiliation(s)
- Gülnihal Kulaksiz
- Biyokimya Anabilim Dali, Hacettepe Universitesi Tip Fakültesi, Ankara, Turkey
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36
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Pitsikas P, Francis MA, Rainbow AJ. Enhanced host cell reactivation of a UV-damaged reporter gene in pre-UV-treated cells is delayed in Cockayne syndrome cells. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2005; 81:89-97. [PMID: 16125967 DOI: 10.1016/j.jphotobiol.2005.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2004] [Revised: 05/31/2005] [Accepted: 06/07/2005] [Indexed: 12/15/2022]
Abstract
We have used a non-replicating recombinant adenovirus, Ad5HCMVlacZ, which expresses the beta-galactosidase (beta-gal) reporter gene, to examine the time course of UV-inducible repair of UV-damaged DNA in human fibroblasts. Host cell reactivation (HCR) of beta-gal activity for UV-irradiated Ad5HCMVlacZ was examined in non-irradiated and UV-irradiated nucleotide excision repair (NER) proficient normal human fibroblasts, xeroderma pigmentosum (XP) group C fibroblasts which are defective in the global genomic repair (GGR) pathway of NER and Cockayne syndrome (CS) fibroblasts which are defective in the transcription coupled repair (TCR) pathway of NER. HCR was deficient in untreated XP-C and CS cells indicating that both TCR and GGR are involved in removal of photolesions from the transcribed strand of the reporter gene in unirradiated human cells as reported previously. Prior UV-irradiation of cells with low UV fluences resulted in a transient enhancement of HCR in normal and XP-C fibroblasts that reached a maximum when cells were infected at 25-35 h after UV. In contrast, UV-enhanced HCR was delayed in CS-B cells, reaching levels similar to that in normal cells only when cells were infected between 40 and 60 h after UV exposure. These results are consistent with a UV-induced up-regulation of GGR through a TCR dependent pathway in CS cells.
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Affiliation(s)
- Photini Pitsikas
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ont., Canada L8S 4K1
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37
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Matsuda N, Azuma K, Saijo M, Iemura SI, Hioki Y, Natsume T, Chiba T, Tanaka K, Tanaka K. DDB2, the xeroderma pigmentosum group E gene product, is directly ubiquitylated by Cullin 4A-based ubiquitin ligase complex. DNA Repair (Amst) 2005; 4:537-45. [PMID: 15811626 DOI: 10.1016/j.dnarep.2004.12.012] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/17/2004] [Indexed: 11/27/2022]
Abstract
Xeroderma pigmentosum (XP) is a genetic disease characterized by hypersensitivity to UV irradiation and high incidence of skin cancer caused by inherited defects in DNA repair. Mutational malfunction of damaged-DNA binding protein 2 (DDB2) causes the XP complementation group E (XP-E). DDB2 together with DDB1 comprises a heterodimer called DDB complex, which is involved in damaged-DNA binding and nucleotide excision repair. Interestingly, by screening for a cellular protein(s) that interacts with Cullin 4A (Cul4A), a key component of the ubiquitin ligase complex, we identified DDB1. Immunoprecipitation confirmed that Cul4A interacts with DDB1 and also associates with DDB2. To date, it has been reported that DDB2 is rapidly degraded after UV irradiation and that overproduction of Cul4A stimulates the ubiquitylation of DDB2 in the cells. However, as biochemical analysis using pure Cul4A-containing E3 is missing, it is still unknown whether the Cul4A complex directly ubiquitylates DDB2 or not. We thus purified the Cul4A-containing E3 complex to near homogeneity and attempted to ubiquitylate DDB2 in vitro. The ubiquitylation of DDB2 was reconstituted using this pure E3 complex, indicating that DDB-Cul4A E3 complex in itself can ubiquitylate DDB2 directly. We also showed that an amino acid substitution, K244E, in DDB2 derived from a XP-E patient did not affect its ubiquitylation.
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Affiliation(s)
- Noriyuki Matsuda
- Department of Molecular Oncology, Tokyo Metropolitan Institute of Medical Science, 3-18-22 Honkomagome, Bunkyo-ku, Tokyo 113-8613, Japan
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38
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Moser J, Volker M, Kool H, Alekseev S, Vrieling H, Yasui A, van Zeeland AA, Mullenders LHF. The UV-damaged DNA binding protein mediates efficient targeting of the nucleotide excision repair complex to UV-induced photo lesions. DNA Repair (Amst) 2005; 4:571-82. [PMID: 15811629 DOI: 10.1016/j.dnarep.2005.01.001] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2004] [Revised: 01/04/2005] [Accepted: 01/05/2005] [Indexed: 11/17/2022]
Abstract
Previous studies point to the XPC-hHR23B complex as the principal initiator of global genome nucleotide excision repair (NER) pathway, responsible for the repair of UV-induced cyclobutane pyrimidine dimers (CPD) and 6-4 photoproducts (6-4PP) in human cells. However, the UV-damaged DNA binding protein (UV-DDB) has also been proposed as a damage recognition factor involved in repair of UV-photoproducts, especially CPD. Here, we show in human XP-E cells (UV-DDB deficient) that the incision complex formation at UV-induced lesions was severely diminished in locally damaged nuclear spots. Repair kinetics of CPD and 6-4PP in locally and globally UV-irradiated normal human and XP-E cells demonstrate that UV-DDB can mediate efficient targeting of XPC-hHR23B and other NER factors to 6-4PP. The data is consistent with a mechanism in which UV-DDB forms a stable complex when bound to a 6-4PP, allowing subsequent repair proteins--starting with XPC-hHR23B--to accumulate, and verify the lesion, resulting in efficient 6-4PP repair. These findings suggest that (i) UV-DDB accelerates repair of 6-4PP, and at later time points also CPD, (ii) the fraction of 6-4PP that can be bound by UV-DDB is limited due to its low cellular quantity and fast UV dependent degradation, and (iii) in the absence of UV-DDB a slow XPC-hHR23B dependent pathway is capable to repair 6-4PP, and to some extent also CPD.
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Affiliation(s)
- Jill Moser
- Department of Toxicogenetics, Leiden University Medical Center, Wassenaarseweg 72, 2333 AL Leiden, The Netherlands
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Reardon JT, Sancar A. Nucleotide Excision Repair. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2005; 79:183-235. [PMID: 16096029 DOI: 10.1016/s0079-6603(04)79004-2] [Citation(s) in RCA: 223] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Joyce T Reardon
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
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40
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Inoki T, Endo H, Inoki Y, Hamamoto T, Tsuru T, Mori T, Miyata K, Amano S, Yamagami S. Damaged DNA-binding protein 2 accelerates UV-damaged DNA repair in human corneal endothelium. Exp Eye Res 2004; 79:367-76. [PMID: 15336499 DOI: 10.1016/j.exer.2004.06.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2004] [Accepted: 06/08/2004] [Indexed: 11/24/2022]
Abstract
PURPOSE To determine damaged DNA-binding protein 2-gene expression levels in vitro and ex vivo, and the degree of DNA repair in damaged DNA-binding protein 2-overexpressing cultured human corneal endothelium after ultraviolet irradiation. METHODS Constitutive damaged DNA-binding protein 2-gene expression levels in various human tissues were determined by semi-quantitative reverse transcription-polymerase chain reactions. The dynamics of nucleotide excision repair-related gene expression in cultured human corneal endothelium were investigated in a ribonuclease protection assay after ultraviolet-irradiation. The effect of damaged DNA-binding protein 2 on DNA repair was studied after ultraviolet-irradiation in cultured human corneal endothelium infected with adenovirus carrying damaged DNA-binding protein 2. RESULTS Human corneal endothelium and epithelium in the donor cornea had the highest constitutive damaged DNA-binding protein 2-gene expression of the various human tissues studied. Gene expression level dynamics associated with nucleotide excision repair factors after ultraviolet-irradiation showed that the increase in the rate of damaged DNA-binding protein 2-gene expression in cultured human corneal endothelium was highest of the nucleotide excision repair-related genes studied. An in vivo DNA repair assay showed that DNA repair efficiency in damaged DNA-binding protein 2-overexpressing cultured human corneal endothelium after ultraviolet-irradiation was significantly improved as compared with that in the control human corneal endothelium. CONCLUSION The human corneal endothelium abundantly expresses the damaged DNA-binding protein 2-gene that is produced efficiently on ultraviolet exposure. This overexpressed damaged DNA-binding protein 2 in the human corneal endothelium contributes to the protection system against DNA damage after ultraviolet-irradiation. Our findings show a critical role for damaged DNA-binding protein 2 in DNA repair to maintain the human corneal endothelium function.
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Affiliation(s)
- Taeko Inoki
- Department of Ophthalmology, Jichi Medical School, Tochigi, Japan
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41
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van der Wees CGC, Vreeswijk MPG, Persoon M, van der Laarse A, van Zeeland AA, Mullenders LHF. Deficient global genome repair of UV-induced cyclobutane pyrimidine dimers in terminally differentiated myocytes and proliferating fibroblasts from the rat heart. DNA Repair (Amst) 2004; 2:1297-308. [PMID: 14642560 DOI: 10.1016/j.dnarep.2003.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Nucleotide excision repair (NER) is the principal pathway for the removal of a wide range of DNA helix-distorting lesions. Two NER subpathways have been identified, i.e. global genome repair (GGR) and transcription-coupled repair (TCR). Little is known about the expression of NER pathways in differentiated cells. We assessed the repair of UV-induced cyclobutane pyrimidine dimers (CPD) and 6-4-photoproducts (6-4 PP) in terminally differentiated myocytes and proliferating fibroblasts isolated from the hearts of neonatal rats. Myocytes and fibroblasts were found to carry out efficient removal of 6-4 PP but display poor repair of CPD by GGR. Furthermore, both cell types were found to carry out TCR of CPD, thus mimicking the repair phenotype of established rodent cell lines. The inefficient repair of CPD at the genome overall level occurs in the absence of massive apoptosis, but goes along with an undetectable level of transcription of the p48 gene, known to be mutated in xeroderma pigmentosum group E (XP-E) patients and recently proposed to be essential for repair of CPD in nonexpressed DNA. Taken together, the results suggest that primary non-dividing cardiac myocytes and proliferating fibroblasts from rat heart selectively remove CPD from the transcribed strand of transcriptionally active genes. GGR of CPD is poor due to the absence of p48 expression.
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Affiliation(s)
- Caroline G C van der Wees
- Department of Toxicogenetics, Leiden University Medical Center, Wassenaarseweg 72, 2333 AL, Leiden, The Netherlands
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Welsh C, Day R, McGurk C, Masters JRW, Wood RD, Köberle B. Reduced levels of XPA, ERCC1 and XPF DNA repair proteins in testis tumor cell lines. Int J Cancer 2004; 110:352-61. [PMID: 15095299 DOI: 10.1002/ijc.20134] [Citation(s) in RCA: 156] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Over 80% of patients with advanced metastatic testis tumors can be cured using cisplatin-based combination chemotherapy. This is unusual as metastatic cancer in adults is usually incurable. Cell lines derived from testis tumors retain sensitivity to cisplatin in vitro. We previously investigated 2 testis tumor cell lines with a low capacity to remove cisplatin-induced DNA damage and found that they had low levels of the DNA nucleotide excision repair proteins XPA, ERCC1 and XPF. To determine whether low levels of XPA, ERCC1 and XPF proteins are characteristic of testis tumor cell lines, we investigated 35 cell lines derived from cancers to determine whether groups of cell lines from diverse tissue origins differ from one another in constitutive levels of these NER proteins. Quantitative immunoblotting was used to compare groups of cell lines representing prostate, bladder, breast, lung, cervical, ovarian and testis cancers. Only the 6 testis tumor cell lines showed significantly lower mean levels of XPA (p = 0.001), XPF (p = 0.001) and ERCC1 (p = 0.004) proteins from the other groups. Our results encourage further investigation of the possibility that low levels of these nucleotide excision repair proteins could be related to the favorable response of testis tumors to cisplatin-based chemotherapy.
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Affiliation(s)
- Carey Welsh
- University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA 15213-1863, USA
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Inoki T, Yamagami S, Inoki Y, Tsuru T, Hamamoto T, Kagawa Y, Mori T, Endo H. Human DDB2 splicing variants are dominant negative inhibitors of UV-damaged DNA repair. Biochem Biophys Res Commun 2004; 314:1036-43. [PMID: 14751237 DOI: 10.1016/j.bbrc.2004.01.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Damaged DNA-binding protein (DDB) is a heterodimer (DDB1 and DDB2), which is implicated in the repair of UV-irradiated DNA damage. Here we have identified four DDB2 variants from HeLa cells (D1-D4) that are generated by alternative splicing. Analysis of tissue distribution by RT-PCR indicates that D1 is the most highly expressed in human brain and heart. A DNA repair assay revealed that both D1 and D2 are dominant negative inhibitors. Electrophoresis mobility shift assays indicated that D1 and D2 are not part of the damaged DNA-protein complex. Co-immunoprecipitation studies show that DDB2-WT interacts with D1 and itself. Nuclear import of DDB1 was less induced by transfection with D1 than WT. Based on these results, D1 and D2 are dominant negative inhibitors of DNA repair, which is probably due to disruption of complex formation between DDB1 and DDB2-WT and of DDB1 nuclear import.
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Affiliation(s)
- Taeko Inoki
- Department of Biochemistry, Jichi Medical School, Tochigi, Japan
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44
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Itoh T, Cado D, Kamide R, Linn S. DDB2 gene disruption leads to skin tumors and resistance to apoptosis after exposure to ultraviolet light but not a chemical carcinogen. Proc Natl Acad Sci U S A 2004; 101:2052-7. [PMID: 14769931 PMCID: PMC357050 DOI: 10.1073/pnas.0306551101] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2003] [Indexed: 11/18/2022] Open
Abstract
Mutations in the human DDB2 gene give rise to xeroderma pigmentosum group E, a disease characterized by increased skin tumorigenesis in response to UV-irradiation. Cell strains derived from xeroderma pigmentosum group E individuals also have enhanced resistance to UV-irradiation due to decreased p53-mediated apoptosis. To further address the precise function(s) of DDB2 and the consequence of non-naturally occurring DDB2 mutations, we generated mice with a disruption of the gene. The mice exhibited significantly enhanced skin carcinogenesis in response to UV-irradiation, and cells from the DDB2(-/-) mice were abnormally resistant to killing by the radiation and had diminished UV-induced, p53-mediated apoptosis. Notably, the cancer-prone phenotype and the resistance to cellular killing were not observed after exposure to the chemical carcinogen, 7,12-dimethylbenz[a]anthracene (DMBA), to which mice carrying defective nucleotide excision repair genes respond with enhanced tumors and cell killing. Although cells from heterozygous DDB2(+/-) mice appeared normal, these mice had enhanced skin carcinogenesis after UV-irradiation, so that XP-E heterozygotes might be at risk for carcinogenesis. In sum, these results demonstrate that DDB2 is well conserved between humans and mice and functions as a tumor suppressor, at least in part, by controlling p53-mediated apoptosis after UV-irradiation.
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Affiliation(s)
- Toshiki Itoh
- Divisions of Biochemistry and Molecular Biology, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA. toshiki@
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Wang QE, Zhu Q, Wani G, Chen J, Wani AA. UV radiation-induced XPC translocation within chromatin is mediated by damaged-DNA binding protein, DDB2. Carcinogenesis 2004; 25:1033-43. [PMID: 14742321 DOI: 10.1093/carcin/bgh085] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The tumor suppressor p53 protein has been established as an important factor in modulating the efficiency of global genomic repair. Our recent repair studies in human cells reported that p53 regulates the recruitment of XPC and TFIIH proteins to specific DNA damage sites. Here, we have examined the influence of p53 and damaged-DNA binding complex (DDB2) proteins on the distribution of XPC within damaged chromatin in vivo and the recruitment of XPC to DNA damage sites in situ. The results show that UV irradiation causes the translocation of XPC from a loosely bound form into a tight association with chromatin in vivo. The UV radiation-induced redistribution of XPC was equally compromised in p53-deficient, as well as DDB2-deficient, human cells. Similarly, rapid recruitment of XPC to DNA damage in situ was also impaired in both cell lines. Ectopic expression of DDB2 in p53-deficient cells overcame the requirement of p53 function for UV-induced translocation of XPC in vivo. Restoration of DDB2 function also enhanced the recruitment of XPC to DNA damage sites in situ and increased the global repair of cyclobutane pyrimidine dimer from the genome. These results indicate that DDB2 is a key downstream factor of p53 for regulating the movement of XPC to DNA damage in irradiated cells.
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Affiliation(s)
- Qi-En Wang
- Department of Radiology, The Ohio State University, Columbus, OH 43210, USA
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Bondar T, Ponomarev A, Raychaudhuri P. Ddb1 is required for the proteolysis of the Schizosaccharomyces pombe replication inhibitor Spd1 during S phase and after DNA damage. J Biol Chem 2003; 279:9937-43. [PMID: 14701809 DOI: 10.1074/jbc.m312570200] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recently we showed that the Schizosaccharomyces pombe ddb1 gene plays a role in S phase progression. A mutant S. pombe strain lacking expression of the ddb1 gene exhibited slow replication through both early and late regions causing a slow S phase phenotype. We attributed the phenotypes in the ddb1 strain to an increased activity of the replication checkpoint kinase Cds1. However, the basis for a high basal Cds1 activity in the ddb1 strain was not clear. It was shown that Ddb1 associates with the Cop9/signalosome. Moreover, the phenotypes of the Deltaddb1 strain are remarkably similar to the Deltacsn1 (or Deltacsn2) strain that lacks expression of the Csn1 (or Csn2) subunit of the Cop9/signalosome. Cop9/signalosome cooperates with Pcu4 to induce proteolysis of Spd1, which inhibits DNA replication by inhibiting ribonucleotide reductase. Therefore, we investigated whether Ddb1 is required for the proteolysis of Spd1. Here we show that a S. pombe strain lacking expression of Ddb1 fails to induce proteolysis of Spd1 in S phase and after DNA damage. Moreover, deletion of the spd1 gene attenuates the Cds1 kinase activity in cells lacking the expression of ddb1, suggesting that an accumulation of Spd1 results in the increase of Cds1 activity in the Deltaddb1 strain. In addition, the double mutant lacking spd1 and ddb1 no longer exhibits the growth defects and DNA damage sensitivity observed in the Deltaddb1 strain. Our results establish an essential role of Ddb1 in the proteolysis of Spd1. In addition, the observation provides evidence for a functional link between Ddb1 and the Cop9/signalosome.
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Affiliation(s)
- Tanya Bondar
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607, USA
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Reardon JT, Sancar A. Recognition and repair of the cyclobutane thymine dimer, a major cause of skin cancers, by the human excision nuclease. Genes Dev 2003; 17:2539-51. [PMID: 14522951 PMCID: PMC218148 DOI: 10.1101/gad.1131003] [Citation(s) in RCA: 146] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The cyclobutane thymine dimer is the major DNA lesion induced in human skin by sunlight and is a primary cause of skin cancer, the most prevalent form of cancer in the Northern Hemisphere. In humans, the only known cellular repair mechanism for eliminating the dimer from DNA is nucleotide excision repair. Yet the mechanism by which the dimer is recognized and removed by this repair system is not known. Here we demonstrate that the six-factor human excision nuclease recognizes and removes the dimer at a rate consistent with the in vivo rate of removal of this lesion, even though none of the six factors alone is capable of efficiently discriminating the dimer from undamaged DNA. We propose a recognition mechanism by which the low-specificity recognition factors, RPA, XPA, and XPC, act in a cooperative manner to locate the lesion and, aided by the kinetic proofreading provided by TFIIH, form a high-specificity complex at the damage site that initiates removal of thymine dimers at a physiologically relevant rate and specificity.
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Affiliation(s)
- Joyce T Reardon
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
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Bondar T, Mirkin EV, Ucker DS, Walden WE, Mirkin SM, Raychaudhuri P. Schizosaccharomyces pombe Ddb1 is functionally linked to the replication checkpoint pathway. J Biol Chem 2003; 278:37006-14. [PMID: 12857752 DOI: 10.1074/jbc.m303003200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Schizosaccharomyces pombe Ddb1 is homologous to the mammalian DDB1 protein, which has been implicated in damaged-DNA recognition and global genomic repair. However, a recent study suggested that the S. pombe Ddb1 is involved in cell division and chromosomal segregation. Here, we provide evidence that the S. pombe Ddb1 is functionally linked to the replication checkpoint control gene cds1. We show that the S. pombe strain lacking ddb1 has slow growth due to delayed replication progression. Flow cytometric analysis shows an extensive heterogeneity in DNA content. Furthermore, the Deltaddb1 strain is hypersensitive to UV irradiation in S phase and is unable to tolerate a prolonged replication block imposed by hydroxyurea. Interestingly, the Deltaddb1 strain exhibits a high level of the Cds1 kinase activity during passage through S phase. Moreover, mutation of the cds1 gene relieves the defects observed in Deltaddb1 strain. The results suggest that many of the defects observed in Deltaddb1 cells are linked to an aberrant activation of Cds1, and that Ddb1 is functionally linked to Cds1.
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Affiliation(s)
- Tanya Bondar
- Department of Biochemistry, University of Illinois, Chicago, Illinois 60612, USA
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Abstract
A group of recent publications contribute new insights concerning the role of the DNA damage-binding protein complex (DDB) in DNA repair. Mutations in the 48kDa DDB2 subunit are now found in all confirmed cases of xeroderma pigmentosum complementation group E. Several studies have reported a connection between the 127kDa DDB1 subunit and proteins involved in ubiquitin-mediated proteolysis. One such multiprotein complex containing DDB1 and DDB2 is closely related to a complex containing DDB1 and the Cockayne syndrome group A (CSA) protein. There is accumulating evidence for several levels of cellular regulation of DDB, including translocation to the nucleus, proteolytic degradation of DDB2 protein, and transcriptional induction of DDB2 mRNA. Although the mechanism is not yet known, it appears that DDB assists in nucleotide excision repair in chromatin.
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Affiliation(s)
- Birgitte Ø Wittschieben
- Research Pavilion, Hillman Cancer Center, University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Suite 2.6, Pittsburgh, PA 15213, USA
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Abstract
In response to a variety of types of DNA damage, the p53 tumor suppressor gene product is activated and regulates a number of downstream cellular processes such as cell cycle arrest, apoptosis and DNA repair. Recent discoveries concerning the regulation of DNA repair processes by p53, such as nucleotide excision repair (NER) and base excision repair (BER) have paved the way for studies to understand the mechanisms governing p53-dependent DNA repair. Although several theories have been proposed, accumulating evidence points to a transcriptional regulatory role for p53 in NER, mediating expression of the global genomic repair (GGR)-specific damage recognition genes, DDB2 and XPC. In BER, a more direct role for p53 has been proposed, potentially acting through protein-protein interactions with BER specific factors. These advances have greatly enhanced our understanding of the role of p53 in DNA repair and this review comprehensively summarizes current opinions on the mechanisms of p53-dependent DNA repair.
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Affiliation(s)
- Shanthi Adimoolam
- Department of Medicine (Oncology), Stanford University School of Medicine, 1115 CCSR Building, 269 Campus Drive, Stanford, CA 94305, USA
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