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Zhou Z, Humphryes N, van Eijk P, Waters R, Yu S, Kraehenbuehl R, Hartsuiker E, Reed SH. UV induced ubiquitination of the yeast Rad4-Rad23 complex promotes survival by regulating cellular dNTP pools. Nucleic Acids Res 2015; 43:7360-70. [PMID: 26150418 PMCID: PMC4551923 DOI: 10.1093/nar/gkv680] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 06/22/2015] [Indexed: 11/13/2022] Open
Abstract
Regulating gene expression programmes is a central facet of the DNA damage response. The Dun1 kinase protein controls expression of many DNA damage induced genes, including the ribonucleotide reductase genes, which regulate cellular dNTP pools. Using a combination of gene expression profiling and chromatin immunoprecipitation, we demonstrate that in the absence of DNA damage the yeast Rad4–Rad23 nucleotide excision repair complex binds to the promoters of certain DNA damage response genes including DUN1, inhibiting their expression. UV radiation promotes the loss of occupancy of the Rad4–Rad23 complex from the regulatory regions of these genes, enabling their induction and thereby controlling the production of dNTPs. We demonstrate that this regulatory mechanism, which is dependent on the ubiquitination of Rad4 by the GG-NER E3 ligase, promotes UV survival in yeast cells. These results support an unanticipated regulatory mechanism that integrates ubiquitination of NER DNA repair factors with the regulation of the transcriptional response controlling dNTP production and cellular survival after UV damage.
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Affiliation(s)
- Zheng Zhou
- Institute of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK College of Biology, Hunan University, Changsha 410082, China
| | - Neil Humphryes
- Institute of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK New York University Department of Biology,1009 Silver Center, 100 Washington Square East, NY, USA
| | - Patrick van Eijk
- Institute of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Raymond Waters
- Institute of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Shirong Yu
- Institute of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK Cambridge Epigenetix, Jonas Webb Building, Babraham Campus, Cambridge, CB22 3AT, UK
| | - Rolf Kraehenbuehl
- North West Cancer Research Institute, Bangor University, Brambell Building, Bangor, LL57 2UW, UK
| | - Edgar Hartsuiker
- North West Cancer Research Institute, Bangor University, Brambell Building, Bangor, LL57 2UW, UK
| | - Simon H Reed
- Institute of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
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Qadri I, Fatima K, AbdeL-Hafiz H. Hepatitis B virus X protein impedes the DNA repair via its association with transcription factor, TFIIH. BMC Microbiol 2011; 11:48. [PMID: 21375739 PMCID: PMC3060106 DOI: 10.1186/1471-2180-11-48] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Accepted: 03/04/2011] [Indexed: 12/12/2022] Open
Abstract
Background Hepatitis B virus (HBV) infections play an important role in the development of hepatocellular carcinoma (HCC). HBV X protein (HBx) is a multifunctional protein that can modulate various cellular processes and plays a crucial role in the pathogenesis of HCC. HBx is known to interact with DNA helicase components of TFIIH, a basal transcriptional factor and an integral component of DNA excision repair. Results In this study, the functional relevance of this association was further investigated in the context to DNA repair. By site-directed mutagenesis HBx's critical residues for interaction with TFIIH were identified. Similarly, TFIIH mutants lacking ATPase domain and the conserved carboxyl-terminal domain failed to interact with HBx. Yeast and mammalian cells expressing HBxwt conferred hypersensitivity to UV irradiation, which is interpreted as a basic deficiency in nucleotide excision repair. HBxmut120 (Glu to Val) was defective in binding to TFIIH and failed to respond to UV. Conclusions We conclude that HBx may act as the promoting factor by inhibiting DNA repair causing DNA damage and accumulation of errors, thereby contributing to HCC development.
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Affiliation(s)
- Ishtiaq Qadri
- NUST Center of Virology and Immunology, National University of Science and Technology, Academic Block, Kashmir Highway, H-12 Islamabad, Pakistan.
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Boyd WA, Crocker TL, Rodriguez AM, Leung MCK, Lehmann DW, Freedman JH, Van Houten B, Meyer JN. Nucleotide excision repair genes are expressed at low levels and are not detectably inducible in Caenorhabditis elegans somatic tissues, but their function is required for normal adult life after UVC exposure. Mutat Res 2010; 683:57-67. [PMID: 19879883 PMCID: PMC2799044 DOI: 10.1016/j.mrfmmm.2009.10.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Revised: 10/06/2009] [Accepted: 10/16/2009] [Indexed: 04/09/2023]
Abstract
We performed experiments to characterize the inducibility of nucleotide excision repair (NER) in Caenorhabditis elegans, and to examine global gene expression in NER-deficient and -proficient strains as well as germline vs. somatic tissues, with and without genotoxic stress. We also carried out experiments to elucidate the importance of NER in the adult life of C. elegans under genotoxin-stressed and control conditions. Adult lifespan was not detectably different between wild-type and NER-deficient xpa-1 nematodes under control conditions. However, exposure to 6J/m(2)/day of ultraviolet C radiation (UVC) decreased lifespan in xpa-1 nematodes more than a dose of 100 J/m(2)/day in wild-type. Similar differential sensitivities were observed for adult size and feeding. Remarkably, global gene expression was nearly identical in young adult wild-type and xpa-1 nematodes, both in control conditions and 3h after exposure to 50 J/m(2) UVC. Neither NER genes nor repair activity were detectably inducible in young adults that lacked germ cells and developing embryos (glp-1 strain). However, expression levels of dozens of NER and other DNA damage response genes were much (5-30-fold) lower in adults lacking germ cells and developing embryos, suggesting that somatic and post-mitotic cells have a much lower DNA repair ability. Finally, we describe a refinement of our DNA damage assay that allows damage measurement in single nematodes.
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Affiliation(s)
- Windy A. Boyd
- Biomolecular Screening Branch, National Toxicology Program, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Tracey L. Crocker
- Nicholas School of the Environment, Duke University, Durham, NC 27708
| | - Ana M. Rodriguez
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | | | - D. Wade Lehmann
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Jonathan H. Freedman
- Laboratory of Molecular Toxicology, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Ben Van Houten
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Joel N. Meyer
- Nicholas School of the Environment, Duke University, Durham, NC 27708
- Address correspondence to: Joel N. Meyer
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Taschner M, Harreman M, Teng Y, Gill H, Anindya R, Maslen SL, Skehel JM, Waters R, Svejstrup JQ. A role for checkpoint kinase-dependent Rad26 phosphorylation in transcription-coupled DNA repair in Saccharomyces cerevisiae. Mol Cell Biol 2010; 30:436-46. [PMID: 19901073 PMCID: PMC2798469 DOI: 10.1128/mcb.00822-09] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Revised: 07/20/2009] [Accepted: 10/29/2009] [Indexed: 12/19/2022] Open
Abstract
Upon DNA damage, eukaryotic cells activate a conserved signal transduction cascade known as the DNA damage checkpoint (DDC). We investigated the influence of DDC kinases on nucleotide excision repair (NER) in Saccharomyces cerevisiae and found that repair of both strands of an active gene is affected by Mec1 but not by the downstream checkpoint kinases, Rad53 and Chk1. Repair of the nontranscribed strand (by global genome repair) requires new protein synthesis, possibly reflecting the involvement of Mec1 in the activation of repair genes. In contrast, repair of the transcribed strand by transcription-coupled NER (TC-NER) occurs in the absence of new protein synthesis, and DNA damage results in Mec1-dependent but Rad53-, Chk1-, Tel1-, and Dun1-independent phosphorylation of the TC-NER factor Rad26, a member of the Swi/Snf group of ATP-dependent translocases and yeast homologue of Cockayne syndrome B. Mutation of the Rad26 phosphorylation site results in a decrease in the rate of TC-NER, pointing to direct activation of Rad26 by Mec1 kinase. These findings establish a direct role for Mec1 kinase in transcription-coupled repair, at least partly via phosphorylation of Rad26, the main transcription-repair coupling factor.
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Affiliation(s)
- Michael Taschner
- Mechanisms of Transcription Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom, Pathology Department, Cardiff University, Heath Park CF14 4XN, United Kingdom, Protein Analysis and Proteomics Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom
| | - Michelle Harreman
- Mechanisms of Transcription Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom, Pathology Department, Cardiff University, Heath Park CF14 4XN, United Kingdom, Protein Analysis and Proteomics Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom
| | - Yumin Teng
- Mechanisms of Transcription Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom, Pathology Department, Cardiff University, Heath Park CF14 4XN, United Kingdom, Protein Analysis and Proteomics Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom
| | - Hefin Gill
- Mechanisms of Transcription Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom, Pathology Department, Cardiff University, Heath Park CF14 4XN, United Kingdom, Protein Analysis and Proteomics Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom
| | - Roy Anindya
- Mechanisms of Transcription Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom, Pathology Department, Cardiff University, Heath Park CF14 4XN, United Kingdom, Protein Analysis and Proteomics Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom
| | - Sarah L. Maslen
- Mechanisms of Transcription Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom, Pathology Department, Cardiff University, Heath Park CF14 4XN, United Kingdom, Protein Analysis and Proteomics Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom
| | - J. Mark Skehel
- Mechanisms of Transcription Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom, Pathology Department, Cardiff University, Heath Park CF14 4XN, United Kingdom, Protein Analysis and Proteomics Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom
| | - Raymond Waters
- Mechanisms of Transcription Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom, Pathology Department, Cardiff University, Heath Park CF14 4XN, United Kingdom, Protein Analysis and Proteomics Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom
| | - Jesper Q. Svejstrup
- Mechanisms of Transcription Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom, Pathology Department, Cardiff University, Heath Park CF14 4XN, United Kingdom, Protein Analysis and Proteomics Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom
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Al-Moghrabi NM, Al-Sharif IS, Aboussekhra A. The RAD9-dependent gene trans-activation is required for excision repair of active genes but not for repair of non-transcribed DNA. Mutat Res 2009; 663:60-8. [PMID: 19428371 DOI: 10.1016/j.mrfmmm.2009.01.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Revised: 01/20/2009] [Accepted: 01/26/2009] [Indexed: 10/21/2022]
Abstract
The Saccharomyces cerevisiae RAD9 and RAD24 are two cell cycle checkpoint genes required for UV-dependent up-regulation of a battery of genes involved in different metabolic pathways. RAD9 is also implicated in nucleotide excision repair (NER); however, its precise role is still unclear. For the present study, we made use of the high-resolution primer extension technique to show that the RAD9-deleted cells are deficient in the repair of both strands of the URA3 gene. Interestingly, this defect was suppressed by over-expressing the RAD24 gene, suggesting that the role of RAD9 in NER is indirect probably through the UV-dependent trans-activation of some NER factors. Accordingly, we present evidence that the inhibition of UV-related de novo protein synthesis by cycloheximide has no effect on the rad9Delta mutant while it suppresses the correcting effect of RAD24 over-expression. Importantly, we have also shown that RAD9 has no role in repair of transcriptionally inactive DNA sequences (URA3 promoter and transcriptionally silent GAL10 gene). Furthermore, de novo protein synthesis was not required for NER in the absence of transcription-coupled NER. This implies that RAD9-dependent gene up-regulation is required for NER only when this process is coupled to transcription.
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Affiliation(s)
- Nisreen M Al-Moghrabi
- King Faisal Specialist Hospital & Research Center, Department of Biological and Medical Research, Riyadh, Saudi Arabia
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Gillette TG, Yu S, Zhou Z, Waters R, Johnston SA, Reed SH. Distinct functions of the ubiquitin-proteasome pathway influence nucleotide excision repair. EMBO J 2006; 25:2529-38. [PMID: 16675952 PMCID: PMC1478203 DOI: 10.1038/sj.emboj.7601120] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2005] [Accepted: 04/06/2006] [Indexed: 01/15/2023] Open
Abstract
The Rad23/Rad4 nucleotide excision repair (NER) protein complex functions at an early stage of the NER reaction, possibly promoting the recognition of damaged DNA. Here we show that Rad4 protein is ubiquitinated and degraded in response to ultraviolet (UV) radiation, and identify a novel cullin-based E3 ubiquitin ligase required for this process. We also show that this novel ubiquitin ligase is required for optimal NER. Our results demonstrate that optimal NER correlates with the ubiquitination of Rad4 following UV radiation, but not its subsequent degradation. Furthermore, we show that the ubiquitin-proteasome pathway (UPP) regulates NER via two distinct mechanisms. The first occurs independently of de novo protein synthesis, and requires Rad23 and a nonproteolytic function of the 19S regulatory complex of the 26S proteasome. The second requires de novo protein synthesis, and relies on the activity of the newly identified E3 ubiquitin ligase. These studies reveal that, following UV radiation, NER is mediated by nonproteolytic activities of the UPP, via the ubiquitin-like domain of Rad23 and UV radiation-induced ubiquitination of Rad4.
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Affiliation(s)
- Thomas G Gillette
- The Center for Biomedical Inventions, Medicine and Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Shirong Yu
- Department of Pathology, School of Medicine, Cardiff University, Cardiff, UK
| | - Zheng Zhou
- Department of Pathology, School of Medicine, Cardiff University, Cardiff, UK
| | - Raymond Waters
- Department of Pathology, School of Medicine, Cardiff University, Cardiff, UK
| | - Stephen Albert Johnston
- The Center for Biomedical Inventions, Medicine and Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Simon H Reed
- Department of Pathology, School of Medicine, Cardiff University, Cardiff, UK
- Department of Pathology, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK. Tel.: +44 2920 745576; Fax: +44 2920 743496; E-mail:
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