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Luo XC, Yu L, Xu SY, Ying SH, Feng MG. Photoreactivation Activities of Rad5, Rad16A and Rad16B Help Beauveria bassiana to Recover from Solar Ultraviolet Damage. J Fungi (Basel) 2024; 10:420. [PMID: 38921406 PMCID: PMC11205155 DOI: 10.3390/jof10060420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/02/2024] [Accepted: 06/12/2024] [Indexed: 06/27/2024] Open
Abstract
In budding yeast, Rad5 and Rad7-Rad16 play respective roles in the error-free post-replication repair and nucleotide excision repair of ultraviolet-induced DNA damage; however, their homologs have not yet been studied in non-yeast fungi. In the fungus Beauveria bassiana, a deficiency in the Rad7 homolog, Rad5 ortholog and two Rad16 paralogs (Rad16A/B) instituted an ability to help the insect-pathogenic fungus to recover from solar UVB damage through photoreactivation. The fungal lifecycle-related phenotypes were not altered in the absence of rad5, rad16A or rad16B, while severe defects in growth and conidiation were caused by the double deletion of rad16A and rad16B. Compared with the wild-type and complemented strains, the mutants showed differentially reduced activities regarding the resilience of UVB-impaired conidia at 25 °C through a 12-h incubation in a regime of visible light plus dark (L/D 3:9 h or 5:7 h for photoreactivation) or of full darkness (dark reactivation) mimicking a natural nighttime. The estimates of the median lethal UVB dose LD50 from the dark and L/D treatments revealed greater activities of Rad5 and Rad16B than of Rad16A and additive activities of Rad16A and Rad16B in either NER-dependent dark reactivation or photorepair-dependent photoreactivation. However, their dark reactivation activities were limited to recovering low UVB dose-impaired conidia but were unable to recover conidia impaired by sublethal and lethal UVB doses as did their photoreactivation activities at L/D 3:9 or 5:7, unless the night/dark time was doubled or further prolonged. Therefore, the anti-UV effects of Rad5, Rad16A and Rad16B in B. bassiana depend primarily on photoreactivation and are mechanistically distinct from those for their yeast homologs.
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Affiliation(s)
| | | | | | | | - Ming-Guang Feng
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (X.-C.L.); (L.Y.); (S.-Y.X.); (S.-H.Y.)
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2
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Gong W, Li S. Rpb7 represses transcription-coupled nucleotide excision repair. J Biol Chem 2023; 299:104969. [PMID: 37380080 PMCID: PMC10382679 DOI: 10.1016/j.jbc.2023.104969] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/30/2023] Open
Abstract
Transcription-coupled repair (TCR) is a subpathway of nucleotide excision repair (NER) that is regulated by multiple facilitators, such as Rad26, and repressors, such as Rpb4 and Spt4/Spt5. How these factors interplay with each other and with core RNA polymerase II (RNAPII) remains largely unknown. In this study, we identified Rpb7, an essential RNAPII subunit, as another TCR repressor and characterized its repression of TCR in the AGP2, RPB2, and YEF3 genes, which are transcribed at low, moderate, and high rates, respectively. The Rpb7 region that interacts with the KOW3 domain of Spt5 represses TCR largely through the same common mechanism as Spt4/Spt5, as mutations in this region mildly enhance the derepression of TCR by spt4Δ only in the YEF3 gene but not in the AGP2 or RPB2 gene. The Rpb7 regions that interact with Rpb4 and/or the core RNAPII repress TCR largely independently of Spt4/Spt5, as mutations in these regions synergistically enhance the derepression of TCR by spt4Δ in all the genes analyzed. The Rpb7 regions that interact with Rpb4 and/or the core RNAPII may also play positive roles in other (non-NER) DNA damage repair and/or tolerance mechanisms, as mutations in these regions can cause UV sensitivity that cannot be attributed to derepression of TCR. Our study reveals a novel function of Rpb7 in TCR regulation and suggests that this RNAPII subunit may have broader roles in DNA damage response beyond its known function in transcription.
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Affiliation(s)
- Wenzhi Gong
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Shisheng Li
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA.
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3
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Alrayes L, Stout J, Schroeder D. Arabidopsis RAD16 Homologues Are Involved in UV Tolerance and Growth. Genes (Basel) 2023; 14:1552. [PMID: 37628604 PMCID: PMC10454142 DOI: 10.3390/genes14081552] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
In plants, prolonged exposure to ultraviolet (UV) radiation causes harmful DNA lesions. Nucleotide excision repair (NER) is an important DNA repair mechanism that operates via two pathways: transcription coupled repair (TC-NER) and global genomic repair (GG-NER). In plants and mammals, TC-NER is initiated by the Cockayne Syndrome A and B (CSA/CSB) complex, whereas GG-NER is initiated by the Damaged DNA Binding protein 1/2 (DDB1/2) complex. In the yeast Saccharomyces cerevisiae (S. cerevisiae), GG-NER is initiated by the Radiation Sensitive 7 and 16, (RAD7/16) complex. Arabidopsis thaliana has two homologues of yeast RAD16, At1g05120 and At1g02670, which we named AtRAD16 and AtRAD16b, respectively. In this study, we characterized the roles of AtRAD16 and AtRAD16b. Arabidopsis rad16 and rad16b null mutants exhibited increased UV sensitivity. Moreover, AtRAD16 overexpression increased plant UV tolerance. Thus, AtRAD16 and AtRAD16b contribute to plant UV tolerance and growth. Additionally, we found physical interaction between AtRAD16 and AtRAD7. Thus, the Arabidopsis RAD7/16 complex is functional in plant NER. Furthermore, AtRAD16 makes a significant contribution to Arabidopsis UV tolerance compared to the DDB1/2 and the CSB pathways. This is the first time the role and interaction of DDB1/2, RAD7/16, and CSA/CSB components in a single system have been studied.
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Affiliation(s)
- Linda Alrayes
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (J.S.); (D.S.)
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Hrq1/RECQL4 regulation is critical for preventing aberrant recombination during DNA intrastrand crosslink repair and is upregulated in breast cancer. PLoS Genet 2022; 18:e1010122. [PMID: 36126066 PMCID: PMC9488787 DOI: 10.1371/journal.pgen.1010122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 08/18/2022] [Indexed: 11/19/2022] Open
Abstract
Human RECQL4 is a member of the RecQ family of DNA helicases and functions during DNA replication and repair. RECQL4 mutations are associated with developmental defects and cancer. Although RECQL4 mutations lead to disease, RECQL4 overexpression is also observed in cancer, including breast and prostate. Thus, tight regulation of RECQL4 protein levels is crucial for genome stability. Because mammalian RECQL4 is essential, how cells regulate RECQL4 protein levels is largely unknown. Utilizing budding yeast, we investigated the RECQL4 homolog, HRQ1, during DNA crosslink repair. We find that Hrq1 functions in the error-free template switching pathway to mediate DNA intrastrand crosslink repair. Although Hrq1 mediates repair of cisplatin-induced lesions, it is paradoxically degraded by the proteasome following cisplatin treatment. By identifying the targeted lysine residues, we show that preventing Hrq1 degradation results in increased recombination and mutagenesis. Like yeast, human RECQL4 is similarly degraded upon exposure to crosslinking agents. Furthermore, over-expression of RECQL4 results in increased RAD51 foci, which is dependent on its helicase activity. Using bioinformatic analysis, we observe that RECQL4 overexpression correlates with increased recombination and mutations. Overall, our study uncovers a role for Hrq1/RECQL4 in DNA intrastrand crosslink repair and provides further insight how misregulation of RECQL4 can promote genomic instability, a cancer hallmark. RECQL4 is a DNA helicase and functions during DNA replication and repair. While loss-of-function RECQL4 mutations are found in diseases characterized by developmental defects and cancer, such as Rothmund-Thomson syndrome, over-expression of RECQL4 is also observed in cancer, such as breast cancer. Therefore, RECQL4 protein expression must be tightly regulated. Here we used the budding yeast homolog of RECQL4, Hrq1, and discovered that overexpression of Hrq1 protein levels result in increased recombination and mutations, both cancer hallmarks. We find that Hrq1 functions to mediate repair of a specific type of DNA damage, intrastrand crosslinks, which occur when DNA nucleotides on the same strand are chemically linked together. These findings are also conserved in humans suggesting a common mechanism between yeast Hrq1 and human RECQL4. Overall, our study identifies a conserved role for RECQL4 in DNA intrastrand crosslink repair and provides insights into how its misregulation could promote cancer development.
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Crystal structure of the yeast Rad7-Elc1 complex and assembly of the Rad7-Rad16-Elc1-Cul3 complex. DNA Repair (Amst) 2019; 77:1-9. [PMID: 30840920 DOI: 10.1016/j.dnarep.2019.02.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 01/30/2019] [Accepted: 02/21/2019] [Indexed: 11/20/2022]
Abstract
Nucleotide excision repair (NER) is a versatile system that deals with various bulky and helix-distorting DNA lesions caused by UV and environmental mutagens. Based on how lesion recognition occurs, NER has been separated into global genome repair (GGR) and transcription-coupled repair (TCR). The yeast Rad7-Rad16 complex is indispensable for the GGR sub-pathway. Rad7-Rad16 binds to UV-damaged DNA in a synergistic fashion with Rad4, the main lesion recognizer, to achieve efficient recognition of lesions. In addition, Rad7-Rad16 associates with Elc1 and Cul3 to form an EloC-Cul-SOCS-box (ECS)-type E3 ubiquitin ligase complex that ubiquitinates Rad4 in response to UV radiation. However, the structure and architecture of the Rad7-Rad16-Elc1-Cul3 complex remain unsolved. Here, we determined the structure of the Rad7-Elc1 complex and revealed key interaction regions responsible for the formation of the Rad7-Rad16-Elc1-Cul3 complex. These results provide new insights into the assembly of the Rad7-Rad16-Elc1-Cul3 complex and structural framework for further studies.
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van Eijk P, Nandi SP, Yu S, Bennett M, Leadbitter M, Teng Y, Reed SH. Nucleosome remodeling at origins of global genome-nucleotide excision repair occurs at the boundaries of higher-order chromatin structure. Genome Res 2018; 29:74-84. [PMID: 30552104 PMCID: PMC6314166 DOI: 10.1101/gr.237198.118] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 11/07/2018] [Indexed: 11/24/2022]
Abstract
Repair of UV-induced DNA damage requires chromatin remodeling. How repair is initiated in chromatin remains largely unknown. We recently demonstrated that global genome–nucleotide excision repair (GG-NER) in chromatin is organized into domains in relation to open reading frames. Here, we define these domains, identifying the genomic locations from which repair is initiated. By examining DNA damage–induced changes in the linear structure of nucleosomes at these sites, we demonstrate how chromatin remodeling is initiated during GG-NER. In undamaged cells, we show that the GG-NER complex occupies chromatin, establishing the nucleosome structure at these genomic locations, which we refer to as GG-NER complex binding sites (GCBSs). We demonstrate that these sites are frequently located at genomic boundaries that delineate chromosomally interacting domains (CIDs). These boundaries define domains of higher-order nucleosome–nucleosome interaction. We demonstrate that initiation of GG-NER in chromatin is accompanied by the disruption of dynamic nucleosomes that flank GCBSs by the GG-NER complex.
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Affiliation(s)
- Patrick van Eijk
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Shuvro Prokash Nandi
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Shirong Yu
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Mark Bennett
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Matthew Leadbitter
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Yumin Teng
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Simon H Reed
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
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7
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Regulation of DNA Repair Mechanisms: How the Chromatin Environment Regulates the DNA Damage Response. Int J Mol Sci 2017; 18:ijms18081715. [PMID: 28783053 PMCID: PMC5578105 DOI: 10.3390/ijms18081715] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/17/2017] [Accepted: 08/02/2017] [Indexed: 01/21/2023] Open
Abstract
Cellular DNA is constantly challenged by damage-inducing factors derived from exogenous or endogenous sources. In order to maintain genome stability and integrity, cells have evolved a wide variety of DNA repair pathways which counteract different types of DNA lesions, also referred to as the DNA damage response (DDR). However, DNA in eukaryotes is highly organized and compacted into chromatin representing major constraints for all cellular pathways, including DNA repair pathways, which require DNA as their substrate. Therefore, the chromatin configuration surrounding the lesion site undergoes dramatic remodeling to facilitate access of DNA repair factors and subsequent removal of the DNA lesion. In this review, we focus on the question of how the cellular DNA repair pathways overcome the chromatin barrier, how the chromatin environment is rearranged to facilitate efficient DNA repair, which proteins mediate this re-organization process and, consequently, how the altered chromatin landscape is involved in the regulation of DNA damage responses.
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8
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Yu S, Evans K, van Eijk P, Bennett M, Webster RM, Leadbitter M, Teng Y, Waters R, Jackson SP, Reed SH. Global genome nucleotide excision repair is organized into domains that promote efficient DNA repair in chromatin. Genome Res 2016; 26:1376-1387. [PMID: 27470111 PMCID: PMC5052058 DOI: 10.1101/gr.209106.116] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 07/27/2016] [Indexed: 01/08/2023]
Abstract
The rates at which lesions are removed by DNA repair can vary widely throughout the genome, with important implications for genomic stability. To study this, we measured the distribution of nucleotide excision repair (NER) rates for UV-induced lesions throughout the budding yeast genome. By plotting these repair rates in relation to genes and their associated flanking sequences, we reveal that, in normal cells, genomic repair rates display a distinctive pattern, suggesting that DNA repair is highly organized within the genome. Furthermore, by comparing genome-wide DNA repair rates in wild-type cells and cells defective in the global genome-NER (GG-NER) subpathway, we establish how this alters the distribution of NER rates throughout the genome. We also examined the genomic locations of GG-NER factor binding to chromatin before and after UV irradiation, revealing that GG-NER is organized and initiated from specific genomic locations. At these sites, chromatin occupancy of the histone acetyl-transferase Gcn5 is controlled by the GG-NER complex, which regulates histone H3 acetylation and chromatin structure, thereby promoting efficient DNA repair of UV-induced lesions. Chromatin remodeling during the GG-NER process is therefore organized into these genomic domains. Importantly, loss of Gcn5 significantly alters the genomic distribution of NER rates; this has implications for the effects of chromatin modifiers on the distribution of mutations that arise throughout the genome.
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Affiliation(s)
- Shirong Yu
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, United Kingdom
| | - Katie Evans
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, United Kingdom
| | - Patrick van Eijk
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, United Kingdom
| | - Mark Bennett
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, United Kingdom
| | - Richard M Webster
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, United Kingdom
| | - Matthew Leadbitter
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, United Kingdom
| | - Yumin Teng
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, United Kingdom
| | - Raymond Waters
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, United Kingdom
| | - Stephen P Jackson
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, United Kingdom
| | - Simon H Reed
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, United Kingdom
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9
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Brock KP, Abraham AC, Amen T, Kaganovich D, England JL. Structural Basis for Modulation of Quality Control Fate in a Marginally Stable Protein. Structure 2015; 23:1169-78. [PMID: 26027734 PMCID: PMC4509718 DOI: 10.1016/j.str.2015.04.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 04/09/2015] [Accepted: 04/18/2015] [Indexed: 11/25/2022]
Abstract
The human von Hippel-Lindau (VHL) tumor suppressor is a marginally stable protein previously used as a model substrate of eukaryotic refolding and degradation pathways. When expressed in the absence of its cofactors, VHL cannot fold and is quickly degraded by the quality control machinery of the cell. We combined computational methods with in vivo experiments to examine the basis of the misfolding propensity of VHL. By expressing a set of randomly mutated VHL sequences in yeast, we discovered a more stable mutant form. Subsequent modeling suggested the mutation had caused a conformational change affecting cofactor and chaperone interaction, and this hypothesis was then confirmed by additional knockout and overexpression experiments targeting a yeast cofactor homolog. These findings offer a detailed structural basis for the modulation of quality control fate in a model misfolded protein and highlight burial mode modeling as a rapid means to detect functionally important conformational changes in marginally stable globular domains.
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Affiliation(s)
- Kelly P Brock
- Computational and Systems Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Ayelet-chen Abraham
- Department of Cell and Developmental Biology, Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Triana Amen
- Department of Cell and Developmental Biology, Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel; Alexander Grass Center for Bioengineering, Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Daniel Kaganovich
- Department of Cell and Developmental Biology, Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel.
| | - Jeremy L England
- Physics of Living Systems Group, Department of Physics, Massachusetts Institute of Technology, 400 Tech Square, Cambridge, MA 02139, USA.
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10
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House NCM, Koch MR, Freudenreich CH. Chromatin modifications and DNA repair: beyond double-strand breaks. Front Genet 2014; 5:296. [PMID: 25250043 PMCID: PMC4155812 DOI: 10.3389/fgene.2014.00296] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 08/08/2014] [Indexed: 12/28/2022] Open
Abstract
DNA repair must take place in the context of chromatin, and chromatin modifications and DNA repair are intimately linked. The study of double-strand break repair has revealed numerous histone modifications that occur after induction of a DSB, and modification of the repair factors themselves can also occur. In some cases the function of the modification is at least partially understood, but in many cases it is not yet clear. Although DSB repair is a crucial activity for cell survival, DSBs account for only a small percentage of the DNA lesions that occur over the lifetime of a cell. Repair of single-strand gaps, nicks, stalled forks, alternative DNA structures, and base lesions must also occur in a chromatin context. There is increasing evidence that these repair pathways are also regulated by histone modifications and chromatin remodeling. In this review, we will summarize the current state of knowledge of chromatin modifications that occur during non-DSB repair, highlighting similarities and differences to DSB repair as well as remaining questions.
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Affiliation(s)
| | - Melissa R Koch
- Department of Biology, Tufts University Medford, MA, USA
| | - Catherine H Freudenreich
- Department of Biology, Tufts University Medford, MA, USA ; Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University Boston, MA, USA
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11
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Zhu M, Chen Y, Ding XS, Webb SL, Zhou T, Nelson RS, Fan Z. Maize Elongin C interacts with the viral genome-linked protein, VPg, of Sugarcane mosaic virus and facilitates virus infection. THE NEW PHYTOLOGIST 2014; 203:1291-1304. [PMID: 24954157 PMCID: PMC4143955 DOI: 10.1111/nph.12890] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 05/08/2014] [Indexed: 05/18/2023]
Abstract
The viral genome-linked protein, VPg, of potyviruses is involved in viral genome replication and translation. To determine host proteins that interact with Sugarcane mosaic virus (SCMV) VPg, a yeast two-hybrid screen was used and a maize (Zea mays) Elongin C (ZmElc) protein was identified. ZmELC transcript was observed in all maize organs, but most highly in leaves and pistil extracts, and ZmElc was present in the cytoplasm and nucleus of maize cells in the presence or absence of SCMV. ZmELC expression was increased in maize tissue at 4 and 6 d post SCMV inoculation. When ZmELC was transiently overexpressed in maize protoplasts the accumulation of SCMV RNA was approximately doubled compared with the amount of virus in control protoplasts. Silencing ZmELC expression using a Brome mosaic virus-based gene silencing vector (virus-induced gene silencing) did not influence maize plant growth and development, but did decrease RNA accumulation of two isolates of SCMV and host transcript encoding ZmeIF4E during SCMV infection. Interestingly, Maize chlorotic mottle virus, from outside the Potyviridae, was increased in accumulation after silencing ZmELC expression. Our results describe both the location of ZmElc expression in maize and a new activity associated with an Elc: support of potyvirus accumulation.
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Affiliation(s)
- Min Zhu
- State Key Laboratory of Agro-biotechnology and Key Laboratory for Plant Pathology – Ministry of Agriculture, China Agricultural UniversityBeijing, 100193, China
| | - Yuting Chen
- State Key Laboratory of Agro-biotechnology and Key Laboratory for Plant Pathology – Ministry of Agriculture, China Agricultural UniversityBeijing, 100193, China
| | - Xin Shun Ding
- Plant Biology Division, The Samuel Roberts Noble Foundation, Inc.2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Stephen L Webb
- Department of Computing Services, The Samuel Roberts Noble Foundation Inc.2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Tao Zhou
- State Key Laboratory of Agro-biotechnology and Key Laboratory for Plant Pathology – Ministry of Agriculture, China Agricultural UniversityBeijing, 100193, China
| | - Richard S Nelson
- Plant Biology Division, The Samuel Roberts Noble Foundation, Inc.2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Zaifeng Fan
- State Key Laboratory of Agro-biotechnology and Key Laboratory for Plant Pathology – Ministry of Agriculture, China Agricultural UniversityBeijing, 100193, China
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12
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Guionet A, Joubert-Durigneux V, Packan D, Cheype C, Garnier JP, David F, Zaepffel C, Leroux RM, Teissié J, Blanckaert V. Effect of nanosecond pulsed electric field on Escherichia coli
in water: inactivation and impact on protein changes. J Appl Microbiol 2014; 117:721-8. [DOI: 10.1111/jam.12558] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 05/23/2014] [Accepted: 05/29/2014] [Indexed: 11/29/2022]
Affiliation(s)
- A. Guionet
- VERI; Chemin de la Digue; Maisons Lafitte France
- CNRS UMR5089 - IPBS (Institut de Pharmacologie et de Biologie Structurale); Toulouse France
- Université de Toulouse; UPS; IPBS; Toulouse France
| | | | - D. Packan
- ONERA; DMPH; Chemin de la Hunière; Palaiseau France
| | - C. Cheype
- CERPEM; Laval Mayenne Technopole; Laval France
| | | | - F. David
- VERI; Chemin de la Digue; Maisons Lafitte France
| | - C. Zaepffel
- ONERA; DMPH; Chemin de la Hunière; Palaiseau France
| | - R.-M. Leroux
- Mer, Molécules, Santé; IUML-FR 3473 CNRS, Université du Maine; IUT de Laval; Département Génie Biologique, Laval France
| | - J. Teissié
- CNRS UMR5089 - IPBS (Institut de Pharmacologie et de Biologie Structurale); Toulouse France
- Université de Toulouse; UPS; IPBS; Toulouse France
| | - V. Blanckaert
- Mer, Molécules, Santé; IUML-FR 3473 CNRS, Université du Maine; IUT de Laval; Département Génie Biologique, Laval France
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13
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Abstract
DNA repair mechanisms are critical for maintaining the integrity of genomic DNA, and their loss is associated with cancer predisposition syndromes. Studies in Saccharomyces cerevisiae have played a central role in elucidating the highly conserved mechanisms that promote eukaryotic genome stability. This review will focus on repair mechanisms that involve excision of a single strand from duplex DNA with the intact, complementary strand serving as a template to fill the resulting gap. These mechanisms are of two general types: those that remove damage from DNA and those that repair errors made during DNA synthesis. The major DNA-damage repair pathways are base excision repair and nucleotide excision repair, which, in the most simple terms, are distinguished by the extent of single-strand DNA removed together with the lesion. Mistakes made by DNA polymerases are corrected by the mismatch repair pathway, which also corrects mismatches generated when single strands of non-identical duplexes are exchanged during homologous recombination. In addition to the true repair pathways, the postreplication repair pathway allows lesions or structural aberrations that block replicative DNA polymerases to be tolerated. There are two bypass mechanisms: an error-free mechanism that involves a switch to an undamaged template for synthesis past the lesion and an error-prone mechanism that utilizes specialized translesion synthesis DNA polymerases to directly synthesize DNA across the lesion. A high level of functional redundancy exists among the pathways that deal with lesions, which minimizes the detrimental effects of endogenous and exogenous DNA damage.
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14
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Richardson A, Gardner RG, Prelich G. Physical and genetic associations of the Irc20 ubiquitin ligase with Cdc48 and SUMO. PLoS One 2013; 8:e76424. [PMID: 24155900 PMCID: PMC3796546 DOI: 10.1371/journal.pone.0076424] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 08/29/2013] [Indexed: 11/30/2022] Open
Abstract
A considerable percentage of the genome is dedicated to the ubiquitin-proteasome system, with the yeast genome predicted to encode approximately 100 ubiquitin ligases (or E3s), and the human genome predicted to encode more than 600 E3s. The most abundant class of E3s consists of RING finger-containing proteins. Although many insights have been obtained regarding the structure and catalytic mechanism of the E3s, much remains to be learned about the function of the individual E3s. Here we characterize IRC20, which encodes a dual RING- and Snf/Swi family ATPase domain-containing protein in yeast that has been implicated in DNA repair. We found that overexpression of IRC20 causes two transcription-associated phenotypes and demonstrate that the Irc20 RING domain possesses ubiquitin E3 activity in vitro. Two mass spectrometry approaches were undertaken to identify Irc20-associated proteins. Wild-type Irc20 associated with Cdc48, a AAA-ATPase that serves as an intermediary in the ubiquitin-proteasome system. A second approach using a RING mutant derivative of Irc20 detected increased association of the Irc20 mutant with SUMO. These findings provide a foundation for understanding the roles of Irc20 in transcription and DNA repair.
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Affiliation(s)
- Aaron Richardson
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Richard G. Gardner
- Department of Pharmacology, University of Washington, Seattle, Washington, United States of America
| | - Gregory Prelich
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail:
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15
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Li J, Bhat A, Xiao W. Regulation of nucleotide excision repair through ubiquitination. Acta Biochim Biophys Sin (Shanghai) 2011; 43:919-29. [PMID: 21986915 DOI: 10.1093/abbs/gmr088] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nucleotide excision repair (NER) is the most versatile DNA-repair pathway in all organisms. While bacteria require only three proteins to complete the incision step of NER, eukaryotes employ about 30 proteins to complete the same step. Here we summarize recent studies demonstrating that ubiquitination, a post-translational modification, plays critical roles in regulating the NER activity either dependent on or independent of ubiquitin-proteolysis. Several NER components have been shown as targets of ubiquitination while others are actively involved in the ubiquitination process. We argue through this analysis that ubiquitination serves to coordinate various steps of NER and meanwhile connect NER with other related pathways to achieve the efficient global DNA-damage response.
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Affiliation(s)
- Jia Li
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada
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16
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A role for SUMO in nucleotide excision repair. DNA Repair (Amst) 2011; 10:1243-51. [PMID: 21968059 DOI: 10.1016/j.dnarep.2011.09.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 09/13/2011] [Accepted: 09/14/2011] [Indexed: 01/01/2023]
Abstract
The two Siz/PIAS SUMO E3 ligases Siz1 and Siz2 are responsible for the vast majority of sumoylation in Saccharomyces cerevisiae. We found that siz1Δ siz2Δ mutants are sensitive to ultra-violet (UV) light. Epistasis analysis showed that the SIZ genes act in the nucleotide excision repair (NER) pathway, and suggested that they participate both in global genome repair (GGR) and in the Rpb9-dependent subpathway of transcription-coupled repair (TCR), but have minimal role in Rad26-dependent TCR. Quantitative analysis of NER at the single-nucleotide level showed that siz1Δ siz2Δ is deficient in repair of both the transcribed and non-transcribed strands of the DNA. These experiments confirmed that the SIZ genes participate in GGR. Their role in TCR remains unclear. It has been reported previously that mutants deficient for the SUMO conjugating enzyme Ubc9 contain reduced levels of Rad4, the yeast homolog of human XPC. However, our experiments do not support the conclusion that SUMO conjugation affects Rad4 levels. We found that several factors that participate in NER are sumoylated, including Rad4, Rad16, Rad7, Rad1, Rad10, Ssl2, Rad3, and Rpb4. Although Rad16 was heavily sumoylated, elimination of the major SUMO attachment sites in Rad16 had no detectable effect on UV resistance or removal of DNA lesions. SUMO attachment to most of these NER factors was significantly increased by DNA damage. Furthermore, SUMO-modified Rad4 accumulated in NER mutants that block the pathway downstream of Rad4, suggesting that SUMO becomes attached to Rad4 at a specific point during its functional cycle. Collectively, these results suggest that SIZ-dependent sumoylation may modulate the activity of multiple proteins to promote efficient NER.
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17
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Yu S, Teng Y, Waters R, Reed SH. How chromatin is remodelled during DNA repair of UV-induced DNA damage in Saccharomyces cerevisiae. PLoS Genet 2011; 7:e1002124. [PMID: 21698136 PMCID: PMC3116912 DOI: 10.1371/journal.pgen.1002124] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 04/21/2011] [Indexed: 11/19/2022] Open
Abstract
Global genome nucleotide excision repair removes DNA damage from transcriptionally silent regions of the genome. Relatively little is known about the molecular events that initiate and regulate this process in the context of chromatin. We've shown that, in response to UV radiation–induced DNA damage, increased histone H3 acetylation at lysine 9 and 14 correlates with changes in chromatin structure, and these alterations are associated with efficient global genome nucleotide excision repair in yeast. These changes depend on the presence of the Rad16 protein. Remarkably, constitutive hyperacetylation of histone H3 can suppress the requirement for Rad7 and Rad16, two components of a global genome repair complex, during repair. This reveals the connection between histone H3 acetylation and DNA repair. Here, we investigate how chromatin structure is modified following UV irradiation to facilitate DNA repair in yeast. Using a combination of chromatin immunoprecipitation to measure histone acetylation levels, histone acetylase occupancy in chromatin, MNase digestion, or restriction enzyme endonuclease accessibility assays to analyse chromatin structure, and finally nucleotide excision repair assays to examine DNA repair, we demonstrate that global genome nucleotide excision repair drives UV-induced chromatin remodelling by controlling histone H3 acetylation levels in chromatin. The concerted action of the ATPase and C3HC4 RING domains of Rad16 combine to regulate the occupancy of the histone acetyl transferase Gcn5 on chromatin in response to UV damage. We conclude that the global genome repair complex in yeast regulates UV-induced histone H3 acetylation by controlling the accessibility of the histone acetyl transferase Gcn5 in chromatin. The resultant changes in histone H3 acetylation promote chromatin remodelling necessary for efficient repair of DNA damage. Recent evidence suggests that GCN5 plays a role in NER in human cells. Our work provides important insight into how GG-NER operates in chromatin. Protection against genotoxic insult requires a network of DNA damage responses, including DNA repair. Inherited DNA repair defects cause severe clinical consequences including extreme cancer susceptibility. Despite detailed mechanistic understanding of the core reactions, little is known about the molecular events that initiate and regulate these processes as they occur in chromatin. We study the conserved nucleotide excision repair pathway in Saccharomyces cerevisiae. This pathway removes a broad spectrum of DNA damages including UV radiation–induced damage. Patients with mutations in genes involved in this process suffer dramatically elevated levels of skin and other cancers. Here we demonstrate how a group of genes involved in repair of transcriptionally silent regions of the genome, a process called global genome repair, modifies chromatin structure following UV irradiation to promote efficient removal of DNA damage from the genome. We show that the concerted action of global genome repair genes combine to regulate histone acetyl transferase accessibility to the chromatin in response to UV damage. In this way, global genome repair regulates histone H3 acetylation status, which ultimately regulates chromatin structure promoting efficient DNA repair in the genome. Our results contribute a significant advance in our understanding of how chromatin is processed during DNA repair.
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Affiliation(s)
- Shirong Yu
- Department of Medical Genetics, Haematology, and Pathology, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Yumin Teng
- Department of Medical Genetics, Haematology, and Pathology, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Raymond Waters
- Department of Medical Genetics, Haematology, and Pathology, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Simon H. Reed
- Department of Medical Genetics, Haematology, and Pathology, School of Medicine, Cardiff University, Cardiff, United Kingdom
- * E-mail:
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18
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Reed SH. Nucleotide excision repair in chromatin: damage removal at the drop of a HAT. DNA Repair (Amst) 2011; 10:734-42. [PMID: 21600858 DOI: 10.1016/j.dnarep.2011.04.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In an earlier review of our understanding of the mechanism of nucleotide excision repair (NER) we examined the process with respect to how it occurs in chromatin [1]. We described how much of our mechanistic understanding of NER was derived from biochemical studies that analysed the repair reaction in DNA substrates not representative of that which exists in the living cell. We pointed out that our efforts to understand how NER operates in chromatin had been hampered in part because of the well-known inhibition of NER that occurs when DNA is assembled into nucleosomes and used as the substrate to examine the repair reaction in vitro. Despite this technical bottleneck, we summarized the biochemical, genetic and cell-based studies which have provided insights into the molecular mechanism of NER in the cellular context. More recently, we revisited the topic of how UV induced DNA damage is repaired in chromatin. In this review we examined the commonly held view that depicts a struggle in which the DNA repair machinery battles to overcome the inhibitory effect of chromatin during the repair process. We suggested that in this interpretation of events, the DNA repair mechanisms might be described as 'tilting at windmills': fighting an imaginary foe [2]. We surmised that this scenario was overly simplistic, and we described an emerging picture in which the DNA repair process and chromatin remodeling were mechanistically linked and were in fact functioning cooperatively to organize the efficient removal of DNA damage from the genome. Here we discuss the latest findings, which contribute to the idea that DNA damage induced changes to chromatin represent an important way in which the DNA repair process is initiated and organized throughout the genome to promote the efficient removal of damage in response to UV radiation.
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Affiliation(s)
- Simon H Reed
- Department of Medical Genetics, Haematology and Pathology, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.
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19
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Verma R, Oania R, Fang R, Smith GT, Deshaies RJ. Cdc48/p97 mediates UV-dependent turnover of RNA Pol II. Mol Cell 2011; 41:82-92. [PMID: 21211725 PMCID: PMC3063307 DOI: 10.1016/j.molcel.2010.12.017] [Citation(s) in RCA: 163] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Revised: 10/09/2010] [Accepted: 12/10/2010] [Indexed: 12/13/2022]
Abstract
Cdc48/p97 is an essential ATPase whose role in targeting substrates to the ubiquitin-proteasome system (UPS) remains unclear. Existing models posit that Cdc48 acts upstream of UPS receptors. To address this hypothesis, we examined the association of ubiquitin (Ub) conjugates with 26S proteasomes. Unexpectedly, proteasomes isolated from cdc48 mutants contain high levels of Ub conjugates, and mass spectrometry identified numerous nonproteasomal proteins, including Rpb1, the largest subunit of RNA Pol II. UV-induced turnover of Rpb1 depends upon Cdc48-Ufd1-Npl4, Ubx4, and the uncharacterized adaptor Ubx5. Ubiquitinated Rpb1, proteasomes, and Cdc48 accumulate on chromatin in UV-treated wild-type cells, and the former two accumulate to higher levels in mutant cells, suggesting that degradation of Rpb1 is facilitated by Cdc48 at sites of stalled transcription. These data reveal an intimate coupling of function between proteasomes and Cdc48 that we suggest is necessary to sustain processive degradation of unstable subunits of some macromolecular protein complexes.
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Affiliation(s)
- Rati Verma
- California Institute of Technology, Pasadena, CA 91125, USA.
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20
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Jones KL, Zhang L, Seldeen KL, Gong F. Detection of bulky DNA lesions: DDB2 at the interface of chromatin and DNA repair in eukaryotes. IUBMB Life 2010; 62:803-11. [DOI: 10.1002/iub.391] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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21
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Heidenreich E, Eisler H, Lengheimer T, Dorninger P, Steinboeck F. A mutation-promotive role of nucleotide excision repair in cell cycle-arrested cell populations following UV irradiation. DNA Repair (Amst) 2010; 9:96-100. [DOI: 10.1016/j.dnarep.2009.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2009] [Revised: 09/22/2009] [Accepted: 10/13/2009] [Indexed: 11/29/2022]
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22
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Ding B, LeJeune D, Li S. The C-terminal repeat domain of Spt5 plays an important role in suppression of Rad26-independent transcription coupled repair. J Biol Chem 2009; 285:5317-26. [PMID: 20042611 DOI: 10.1074/jbc.m109.082818] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
In eukaryotic cells, transcription coupled nucleotide excision repair (TCR) is believed to be initiated by RNA polymerase II (Pol II) stalled at a lesion in the transcribed strand of a gene. Rad26, the yeast homolog of the human Cockayne syndrome group B (CSB) protein, plays an important role in TCR. Spt4, a transcription elongation factor that forms a complex with Spt5, has been shown to suppress TCR in rad26Delta cells. Here we present evidence that Spt4 indirectly suppresses Rad26-independent TCR by protecting Spt5 from degradation and stabilizing the interaction of Spt5 with Pol II. We further found that the C-terminal repeat (CTR) domain of Spt5, which is dispensable for cell viability and is not involved in interactions with Spt4 and Pol II, plays an important role in the suppression. The Spt5 CTR is phosphorylated by the Bur kinase. Inactivation of the Bur kinase partially alleviates TCR in rad26Delta cells. We propose that the Spt5 CTR suppresses Rad26-independent TCR by serving as a platform for assembly of a multiple protein suppressor complex that is associated with Pol II. Phosphorylation of the Spt5 CTR by the Bur kinase may facilitate the assembly of the suppressor complex.
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Affiliation(s)
- Baojin Ding
- Department of Comparative Biomedical Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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23
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Distinct ubiquitin ligases act sequentially for RNA polymerase II polyubiquitylation. Proc Natl Acad Sci U S A 2009; 106:20705-10. [PMID: 19920177 DOI: 10.1073/pnas.0907052106] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The proteasome degrades proteins modified by polyubiquitylation, so correctly controlled ubiquitylation is crucial to avoid unscheduled proteolysis of essential proteins. The mechanism regulating proteolysis of RNAPII has been controversial since two distinct ubiquitin ligases (E3s), Rsp5 (and its human homologue NEDD4) and Elongin-Cullin complex, have both been shown to be required for its DNA-damage-induced polyubiquitylation. Here we show that these E3s work sequentially in a two-step mechanism. First, Rsp5 adds mono-ubiquitin, or sometimes a ubiquitin chain linked via ubiquitin lysine 63 that does not trigger proteolysis. When produced, the K63 chain can be trimmed to mono-ubiquitylation by an Rsp5-associated ubiquitin protease, Ubp2. Based on this mono-ubiquitin moiety on RNAPII, an Elc1/Cul3 complex then produces a ubiquitin chain linked via lysine 48, which can trigger proteolysis. Likewise, for correct polyubiquitylation of human RNAPII, NEDD4 cooperates with the ElonginA/B/C-Cullin 5 complex. These data indicate that RNAPII polyubiquitylation requires cooperation between distinct, sequentially acting ubiquitin ligases, and raise the intriguing possibility that other members of the large and functionally diverse family of NEDD4-like ubiquitin ligases also require the assistance of a second E3 when targeting proteins for degradation.
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24
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The Snf1 kinase and proteasome-associated Rad23 regulate UV-responsive gene expression. EMBO J 2009; 28:2919-31. [PMID: 19680226 DOI: 10.1038/emboj.2009.229] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Accepted: 07/16/2009] [Indexed: 01/13/2023] Open
Abstract
The transcriptional response to damaging agents is of fundamental significance for understanding mechanisms responsible for cell survival and genome maintenance. However, how damage signals are transmitted to the transcriptional apparatus is poorly understood. Here we identify two new regulators of the UV response transcriptome: Snf1, a nutrient-sensing kinase, and Rad23, a nucleotide excision repair factor with no previously known function in transcriptional control. Over half of all UV-responsive genes are dependent on Snf1 or Rad23 for proper regulation. After irradiation, Snf1 targets the Mig3 repressor, a new effector of the UV response. Snf1 and Rad23 are both required for the displacement of Mig3 from the UV-activated HUG1 promoter, and Rad23's activity is functionally linked to the proteasome 19S regulatory particle. Our data reveal overlapping functions for Snf1 and Rad23 in UV-responsive transcriptional regulation and provide mechanistic insight into the action of these factors at a UV-activated promoter. These results also highlight how diverse environmental stimuli are processed by a limited repertoire of signalling molecules to result in tailored patterns of gene expression.
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25
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Zhang L, Jones K, Gong F. The molecular basis of chromatin dynamics during nucleotide excision repair. Biochem Cell Biol 2009; 87:265-72. [PMID: 19234540 DOI: 10.1139/o08-101] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The assembly of DNA into chromatin in eukaryotic cells affects all DNA-related cellular activities, such as replication, transcription, recombination, and repair. Rearrangement of chromatin structure during nucleotide excision repair (NER) was discovered more than 2 decades ago. However, the molecular basis of chromatin dynamics during NER remains undefined. Pioneering studies in the field of gene transcription have shown that ATP-dependent chromatin-remodeling complexes and histone-modifying enzymes play a critical role in chromatin dynamics during transcription. Similarly, recent studies have demonstrated that the SWI/SNF chromatin-remodeling complex facilitates NER both in vitro and in vivo. Additionally, histone acetylation has also been linked to the NER of ultraviolet light damage. In this article, we will discuss the role of these identified chromatin-modifying activities in NER.
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Affiliation(s)
- Ling Zhang
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33156, USA
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26
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Dantuma NP, Heinen C, Hoogstraten D. The ubiquitin receptor Rad23: at the crossroads of nucleotide excision repair and proteasomal degradation. DNA Repair (Amst) 2009; 8:449-60. [PMID: 19223247 DOI: 10.1016/j.dnarep.2009.01.005] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A protein that exemplifies the intimate link between the ubiquitin/proteasome system (UPS) and DNA repair is the yeast nucleotide excision repair (NER) protein Rad23 and its human orthologs hHR23A and hHR23B. Rad23, which was originally identified as an important factor involved in the recognition of DNA lesions, also plays a central role in targeting ubiquitylated proteins for proteasomal degradation, an activity that it shares with other ubiquitin receptors like Dsk2 and Ddi1. Although the finding that Rad23 serves as a ubiquitin receptor explains to a large extent its importance in proteasomal degradation, the precise mode of action of Rad23 in NER and the possible link with the UPS is less clear. In this review, we discuss our present knowledge on the functions of Rad23 in protein degradation and DNA repair and speculate on the importance of the dual roles of Rad23 for the cell's ability to cope with stress conditions.
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Affiliation(s)
- Nico P Dantuma
- Department of Cell and Molecular Biology, The Medical Nobel Institute, Karolinska Institutet, Von Eulers väg 3, S-17177 Stockholm, Sweden.
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27
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Tran N, Qu PP, Simpson DA, Lindsey-Boltz L, Guan X, Schmitt CP, Ibrahim JG, Kaufmann WK. In silico construction of a protein interaction landscape for nucleotide excision repair. Cell Biochem Biophys 2009; 53:101-14. [PMID: 19156361 DOI: 10.1007/s12013-009-9042-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To obtain a systems-level perspective on the topological and functional relationships among proteins contributing to nucleotide excision repair (NER) in Saccharomyces cerevisiae, we built two models to analyze protein-protein physical interactions. A recursive computational model based on set theory systematically computed overlaps among protein interaction neighborhoods. A statistical model scored computation results to detect significant overlaps which exposed protein modules and hubs concurrently. We used these protein entities to guide the construction of a multi-resolution landscape which showed relationships among NER, transcription, DNA replication, chromatin remodeling, and cell cycle regulation. Literature curation was used to support the biological significance of identified modules and hubs. The NER landscape revealed a hierarchical topology and a recurrent pattern of kernel modules coupling a variety of proteins in structures that provide diverse functions. Our analysis offers a computational framework that can be applied to construct landscapes for other biological processes.
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Affiliation(s)
- Nancy Tran
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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28
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LeJeune D, Chen X, Ruggiero C, Berryhill S, Ding B, Li S. Yeast Elc1 plays an important role in global genomic repair but not in transcription coupled repair. DNA Repair (Amst) 2009; 8:40-50. [DOI: 10.1016/j.dnarep.2008.08.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Revised: 08/28/2008] [Accepted: 08/28/2008] [Indexed: 11/16/2022]
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29
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Momcilovic M, Iram SH, Liu Y, Carlson M. Roles of the glycogen-binding domain and Snf4 in glucose inhibition of SNF1 protein kinase. J Biol Chem 2008; 283:19521-9. [PMID: 18474591 DOI: 10.1074/jbc.m803624200] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The SNF1/AMP-activated protein kinase (AMPK) family is required for adaptation to metabolic stress and energy homeostasis. The gamma subunit of AMPK binds AMP and ATP, and mutations that affect binding cause human disease. We have here addressed the role of the Snf4 (gamma) subunit in regulating SNF1 protein kinase in response to glucose availability in Saccharomyces cerevisiae. Previous studies of mutant cells lacking Snf4 suggested that Snf4 counteracts autoinhibition by the C-terminal sequence of the Snf1 catalytic subunit but is dispensable for glucose regulation, and AMP does not activate SNF1 in vitro. We first introduced substitutions at sites that, in AMPK, contribute to nucleotide binding and regulation. Mutations at several sites relieved glucose inhibition of SNF1, as judged by catalytic activity, phosphorylation of the activation-loop Thr-210, and growth assays, although analogs of the severe human mutations R531G/Q had little effect. We further showed that alterations of Snf4 residues that interact with the glycogen-binding domain (GBD) of the beta subunit strongly relieved glucose inhibition. Finally, substitutions in the GBD of the Gal83 beta subunit that are predicted to disrupt interactions with Snf4 and also complete deletion of the GBD similarly relieved glucose inhibition of SNF1. Analysis of mutant cells lacking glycogen synthase showed that regulation of SNF1 is normal in the absence of glycogen. These findings reveal novel roles for Snf4 and the GBD in regulation of SNF1.
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Affiliation(s)
- Milica Momcilovic
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
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30
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den Dulk B, van Eijk P, de Ruijter M, Brandsma JA, Brouwer J. The NER protein Rad33 shows functional homology to human Centrin2 and is involved in modification of Rad4. DNA Repair (Amst) 2008; 7:858-68. [PMID: 18387345 DOI: 10.1016/j.dnarep.2008.02.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2007] [Revised: 02/03/2008] [Accepted: 02/12/2008] [Indexed: 11/25/2022]
Abstract
In the yeast Saccharomyces cerevisiae the Rad4-Rad23 complex is implicated in the initial damage recognition of the Nucleotide Excision Repair (NER) pathway. NER removes a variety of lesions via two subpathways: Transcription Coupled Repair (TCR) and Global Genome Repair (GGR). We previously showed that the new NER protein Rad33 is involved in both NER subpathways TCR and GGR. In the present study we show UV induced modification of Rad4 that is strongly increased in cells deleted for RAD33. Modification of Rad4 in rad33 cells does not require the incision reaction but is dependent on the TCR factor Rad26. The predicted structure of Rad33 shows resemblance to the Centrin homologue Cdc31. In human cells, Centrin2 binds to XPC and is involved in NER. We demonstrate that Rad4 binds Rad33 directly and via the same conserved amino acids required for the interaction of XPC with Centrin2. Disruption of the Rad4-Rad33 interaction is sufficient to enhance the modification of Rad4 and results in a repair defect similar to that of a rad33 mutant. The current study suggests that the role of Rad33 in the Rad4-Rad23 complex might have parallels with the role of Centrin2 in the XPC-HHR23B complex.
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Affiliation(s)
- Ben den Dulk
- MGC Department of Molecular Genetics, Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
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31
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Lettieri T, Kraehenbuehl R, Capiaghi C, Livingstone-Zatchej M, Thoma F. Functionally distinct nucleosome-free regions in yeast require Rad7 and Rad16 for nucleotide excision repair. DNA Repair (Amst) 2008; 7:734-43. [PMID: 18329964 DOI: 10.1016/j.dnarep.2008.01.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2008] [Accepted: 01/23/2008] [Indexed: 11/16/2022]
Abstract
In yeast, Rad7 and Rad16 are two proteins required for nucleotide excision repair (NER) of non-transcribed chromatin. They have roles in damage recognition, in the postincision steps of NER, and in ultraviolet-light-dependent histone H3 acetylation. Moreover, Rad16 is an ATP-ase of the SNF2 superfamily and therefore might facilitate chromatin repair by nucleosome remodelling. Here, we used yeast rad7 Delta rad16 Delta mutants and show that Rad7-Rad16 is also required for NER of UV-lesions in three functionally distinct nucleosome-free regions (NFRs), the promoter and 3'-end of the URA3 gene and the ARS1 origin of replication. Moreover, rapid repair of UV-lesions by photolyase confirmed that nucleosomes were absent and that neither UV-damage formation nor rad7 Delta rad16 Delta mutations altered chromatin accessibility in NFRs. The data are consistent with a role of Rad7-Rad16 in damage recognition and processing in absence of nucleosomes. An additional role in nucleosome remodelling is discussed.
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Affiliation(s)
- Teresa Lettieri
- Institute of Cell Biology, ETH Zurich, Schafmattstrasse 18, CH-8093 Zurich, Switzerland.
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32
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McIntyre J, Baranowska H, Skoneczna A, Halas A, Sledziewska-Gojska E. The spectrum of spontaneous mutations caused by deficiency in proteasome maturase Ump1 in Saccharomyces cerevisiae. Curr Genet 2007; 52:221-8. [PMID: 17909815 DOI: 10.1007/s00294-007-0156-8] [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: 07/09/2007] [Revised: 09/17/2007] [Accepted: 09/18/2007] [Indexed: 12/16/2022]
Abstract
Ump1 is responsible for maturation of the catalytic core of the 26S proteasome. Dysfunction of Ump1 causes an increase in the frequency of spontaneous mutations in Saccharomyces cerevisiae. In this study we analyze the spectrum of mutations occurring spontaneously in yeast deficient in Ump1 by use of the SUP4-o system. Single base substitutions predominate among the mutations analyzed (73 of the 91 alterations examined). Two major classes are GC to TA transversions and GC to AT transitions ( approximately 50 and approximately 30% of base substitutions, respectively). Besides base substitutions, almost all the major types of sequence alterations are represented. The specificity and distribution of mutations occurring in the ump1 strain are unique compared to the spectra previously established for other yeast mutators. However, the profile of mutations arising in this strain is similar to that observed in wild type. The same similarity has previously been reported for yeast deficient in Mms2, a protein involved in Rad6-dependent postreplication DNA repair (PRR). The specificity of the mutator effect caused by ump1 is discussed in light of the proposed role of the proteasome activity in the regulation of the PRR mechanisms.
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Affiliation(s)
- Justyna McIntyre
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawinskiego 5A, 02-106, Warsaw, Poland
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Silva CS, Silva SH, Pereira-Júnior OS, Cabral FJ, Costa-Cruz JM, Rodrigues V. Schistosoma mansoni: gene expression of the nucleotide excision repair factor 2 (NEF2) during the parasite life cycle, and in adult worms after exposure to different DNA-damaging agents. Acta Trop 2007; 104:52-62. [PMID: 17850756 DOI: 10.1016/j.actatropica.2007.07.006] [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: 07/26/2006] [Revised: 07/06/2007] [Accepted: 07/26/2007] [Indexed: 01/16/2023]
Abstract
DNA is often damaged by many environmental agents, which lead to the up-regulation of several genes involved in different repair pathways. Schistosoma mansoni has a complex life cycle, being exposed to a subset of DNA-damaging agents, such as those present in the environment and host immune response. Recently, studies showed that nucleotide excision repair (NER) is an indispensable mechanism for removing a broad spectrum of different DNA lesions. In the present report, we showed the gene expression of nucleotide excision repair factor 2 (NEF2) SmRad23 and SmRad4, in different developmental stages of S. mansoni, as well as the differential expression of these genes in S. mansoni adult worms treated with DNA-damaging agents. Furthermore, it was revealed the correlation of these genes with their orthologues in other eukaryotes. Our reports suggest that NER is an important repair pathway during the complex life cycle of S. mansoni.
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Affiliation(s)
- Camila S Silva
- Department of Biochemistry and Immunology, School of Medicine, University of São Paulo, Av. Bandeirantes 3900, 14049-900, Ribeirão Preto, SP, Brazil
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Ding B, Ruggiero C, Chen X, Li S. Tfb5 is partially dispensable for Rad26 mediated transcription coupled nucleotide excision repair in yeast. DNA Repair (Amst) 2007; 6:1661-9. [PMID: 17644494 PMCID: PMC2096704 DOI: 10.1016/j.dnarep.2007.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2007] [Accepted: 06/08/2007] [Indexed: 11/18/2022]
Abstract
Nucleotide excision repair (NER) is a conserved DNA repair mechanism capable of removing a variety of helix-distorting DNA lesions. A specialized NER pathway, called transcription coupled NER (TC-NER), refers to preferential repair in the transcribed strand of an actively transcribed gene. To be distinguished from TCR-NER, the genome-wide NER process is termed as global genomic NER (GG-NER). In Saccharomyces cerevisiae, GG-NER is dependent on Rad7, whereas TC-NER is mediated by Rad26, the homolog of the human Cockayne syndrome group B protein, and by Rpb9, a non-essential subunit of RNA polymerase II. Tfb5, the tenth subunit of the transcription/repair factor TFIIH, is implicated in one group of the human syndrome trichothiodystrophy. Here, we show that Tfb5 plays different roles in different NER pathways in yeast. No repair takes place in the non-transcribed strand of a gene in tfb5 cells, or in both strands of a gene in rad26 rpb9 tfb5 cells, indicating that Tfb5 is essential for GG-NER. However, residual repair occurs in the transcribed strand of a gene in tfb5 cells, suggesting that Tfb5 is important, but not absolutely required for TC-NER. Interestingly, substantial repair occurs in the transcribed strand of a gene in rad7 tfb5 and rad7 rpb9 tfb5 cells, indicating that, in the absence of GG-NER, Tfb5 is largely dispensable for Rad26 mediated TC-NER. Furthermore, we show that no repair takes place in the transcribed strand of a gene in rad7 rad26 tfb5 cells, suggesting that Tfb5 is required for Rpb9 mediated TC-NER. Taken together, our results indicate that Tfb5 is partially dispensable for Rad26 mediated TC-NER, especially in GG-NER deficient cells. However, this TFIIH subunit is required for other NER pathways.
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Affiliation(s)
| | | | | | - Shisheng Li
- *Corresponding Author [225-578-9102(Phone)/225-578-9895(FAX)/ ]
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Li S, Ding B, LeJeune D, Ruggiero C, Chen X, Smerdon MJ. The roles of Rad16 and Rad26 in repairing repressed and actively transcribed genes in yeast. DNA Repair (Amst) 2007; 6:1596-606. [PMID: 17611170 PMCID: PMC2095784 DOI: 10.1016/j.dnarep.2007.05.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2007] [Revised: 05/11/2007] [Accepted: 05/16/2007] [Indexed: 11/17/2022]
Abstract
Nucleotide excision repair (NER) is a conserved DNA repair mechanism capable of removing a variety of helix-distorting DNA lesions. Rad26, a member of the Swi2/Snf2 superfamily of proteins, has been shown to be involved in a specialized NER process called transcription coupled NER. Rad16, another member of the same protein superfamily, has been shown to be required for genome-wide NER. Here we show that Rad16 and Rad26 play different roles in repairing repressed and actively transcribed genes in yeast. Rad16 is partially dispensable, and Rad26 plays a significant role in repairing certain regions of the repressed GAL1-10, PHO5 and ADH2 genes, especially in the core DNA of well-positioned nucleosomes. Simultaneous elimination of Rad16 and Rad26 results in no detectable repair in these regions of the repressed genes. Transcriptional induction of the GAL1-10 genes abolishes the role of Rad26, but does not affect the role of Rad16 in repairing the nontranscribed strand of the genes. Interestingly, when the transcription activator Gal4 is eliminated from the cells, Rad16 becomes partially dispensable and Rad26 plays a significant role in repairing both strands of the GAL1-10 genes even under inducing conditions. Our results suggest that Rad16 and Rad26 play different and, to some extent, complementary roles in repairing both strands of repressed genes, although the relative contributions of the two proteins can be different from gene to gene, and from region to region of a gene. However, Rad16 is solely responsible for repairing the nontranscribed strand of actively transcribed genes.
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Affiliation(s)
- Shisheng Li
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA.
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Ribar B, Prakash L, Prakash S. ELA1 and CUL3 are required along with ELC1 for RNA polymerase II polyubiquitylation and degradation in DNA-damaged yeast cells. Mol Cell Biol 2007; 27:3211-6. [PMID: 17296727 PMCID: PMC1899920 DOI: 10.1128/mcb.00091-07] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Treatment of yeast and human cells with DNA-damaging agents elicits lysine 48-linked polyubiquitylation of Rpb1, the largest subunit of RNA polymerase II (Pol II), which targets Pol II for proteasomal degradation. However, the ubiquitin ligase (E3) responsible for Pol II polyubiquitylation has not been identified in humans or the yeast Saccharomyces cerevisiae. Here we show that elongin A (Ela1) and cullin 3 (Cul3) are required for Pol II polyubiquitylation and degradation in yeast cells, and on the basis of these and other observations, we propose that an E3 comprised of elongin C (Elc1), Ela1, Cul3, and the RING finger protein Roc1 (Rbx1) mediates this process in yeast cells. This study provides, in addition to the identification of the E3 required for Pol II polyubiquitylation and degradation in yeast cells, the first evidence for a specific function in yeast for a member of the elongin C/BC-box protein/cullin family of ligases. Also, these observations raise the distinct possibility that the elongin C-containing ubiquitin ligase, the von Hippel-Lindau tumor suppressor complex, promotes Pol II polyubiquitylation and degradation in human cells.
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Affiliation(s)
- Balazs Ribar
- University of Texas Medical Branch at Galveston, 301 University Blvd., Galveston, TX 77555-1061, USA
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Reed SH, Gillette TG. Nucleotide excision repair and the ubiquitin proteasome pathway—Do all roads lead to Rome? DNA Repair (Amst) 2007; 6:149-56. [PMID: 17150417 DOI: 10.1016/j.dnarep.2006.10.026] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2006] [Accepted: 10/10/2006] [Indexed: 01/25/2023]
Abstract
It is clear that components of the proteasome and the ubiquitin proteasome pathway play a direct mechanistic role in the regulation of a variety of DNA repair processes. Intriguingly, a wealth of evidence suggests that this is also the case during the regulation of gene transcription. Here we review our current understanding of how the ubiquitin proteasome pathway influences nucleotide excision repair, and discuss how studies that investigate the role of this pathway in the regulation of gene transcription might also contribute to our mechanistic understanding of its role in DNA repair.
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Affiliation(s)
- Simon H Reed
- The Department of Pathology, Cardiff University, School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom.
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Osley MA, Tsukuda T, Nickoloff JA. ATP-dependent chromatin remodeling factors and DNA damage repair. Mutat Res 2007; 618:65-80. [PMID: 17291544 PMCID: PMC1904433 DOI: 10.1016/j.mrfmmm.2006.07.011] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2006] [Accepted: 07/31/2006] [Indexed: 02/08/2023]
Abstract
The organization of eukaryotic DNA into chromatin poses a barrier to all processes that require access of enzymes and regulatory factors to their sites of action. While the majority of studies in this area have concentrated on the role of chromatin in the regulation of transcription, there has been a recent emphasis on the relationship of chromatin to DNA damage repair. In this review, we focus on the role of chromatin in nucleotide excision repair (NER) and double-strand break (DSB) repair. NER and DSB repair use very different enzymatic machineries, and these two modes of DNA damage repair are also differentially affected by chromatin. Only a small number of nucleosomes are likely to be involved in NER, while a more extensive region of chromatin is involved in DSB repair. However, a key feature of both NER and DSB repair pathways is the participation of ATP-dependent chromatin remodeling factors at various points in the repair process. We discuss recent data that have identified roles for SWI/SNF-related chromatin remodeling factors in the two repair pathways.
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Affiliation(s)
- Mary Ann Osley
- Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA.
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Lehoczký P, McHugh PJ, Chovanec M. DNA interstrand cross-link repair in Saccharomyces cerevisiae. FEMS Microbiol Rev 2006; 31:109-33. [PMID: 17096663 DOI: 10.1111/j.1574-6976.2006.00046.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
DNA interstrand cross-links (ICL) present a formidable challenge to the cellular DNA repair apparatus. For Escherichia coli, a pathway which combines nucleotide excision repair (NER) and homologous recombination repair (HRR) to eliminate ICL has been characterized in detail, both genetically and biochemically. Mechanisms of ICL repair in eukaryotes have proved more difficult to define, primarily as a result of the fact that several pathways appear compete for ICL repair intermediates, and also because these competing activities are regulated in the cell cycle. The budding yeast Saccharomyces cerevisiae has proven a powerful tool for dissecting ICL repair. Important roles for NER, HRR and postreplication/translesion synthesis pathways have all been identified. Here we review, with reference to similarities and differences in higher eukaryotes, what has been discovered to date concerning ICL repair in this simple eukaryote.
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Affiliation(s)
- Peter Lehoczký
- Department of Molecular Genetics, Cancer Research Institute, Bratislava, Slovak Republic
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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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Ribar B, Prakash L, Prakash S. Requirement of ELC1 for RNA polymerase II polyubiquitylation and degradation in response to DNA damage in Saccharomyces cerevisiae. Mol Cell Biol 2006; 26:3999-4005. [PMID: 16705154 PMCID: PMC1489084 DOI: 10.1128/mcb.00293-06] [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] [Indexed: 11/20/2022] Open
Abstract
Treatment of Saccharomyces cerevisiae and human cells with DNA-damaging agents such as UV light or 4-nitroquinoline-1-oxide induces polyubiquitylation of the largest RNA polymerase II (Pol II) subunit, Rpb1, which results in rapid Pol II degradation by the proteasome. Here we identify a novel role for the yeast Elc1 protein in mediating Pol II polyubiquitylation and degradation in DNA-damaged yeast cells and propose the involvement of a ubiquitin ligase, of which Elc1 is a component, in this process. In addition, we present genetic evidence for a possible involvement of Elc1 in Rad7-Rad16-dependent nucleotide excision repair (NER) of lesions from the nontranscribed regions of the genome and suggest a role for Elc1 in increasing the proficiency of repair of nontranscribed DNA, where as a component of the Rad7-Rad16-Elc1 ubiquitin ligase, it would promote the efficient turnover of the NER ensemble from the lesion site in a Rad23-19S proteasomal complex-dependent reaction.
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Affiliation(s)
- Balazs Ribar
- Sealy Center for Molecular Science, University of Texas Medical Branch at Galveston, Galveston, TX 77555-1061, USA
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42
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Flaus A, Martin DMA, Barton GJ, Owen-Hughes T. Identification of multiple distinct Snf2 subfamilies with conserved structural motifs. Nucleic Acids Res 2006; 34:2887-905. [PMID: 16738128 PMCID: PMC1474054 DOI: 10.1093/nar/gkl295] [Citation(s) in RCA: 511] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2006] [Revised: 03/18/2006] [Accepted: 04/05/2006] [Indexed: 12/14/2022] Open
Abstract
The Snf2 family of helicase-related proteins includes the catalytic subunits of ATP-dependent chromatin remodelling complexes found in all eukaryotes. These act to regulate the structure and dynamic properties of chromatin and so influence a broad range of nuclear processes. We have exploited progress in genome sequencing to assemble a comprehensive catalogue of over 1300 Snf2 family members. Multiple sequence alignment of the helicase-related regions enables 24 distinct subfamilies to be identified, a considerable expansion over earlier surveys. Where information is known, there is a good correlation between biological or biochemical function and these assignments, suggesting Snf2 family motor domains are tuned for specific tasks. Scanning of complete genomes reveals all eukaryotes contain members of multiple subfamilies, whereas they are less common and not ubiquitous in eubacteria or archaea. The large sample of Snf2 proteins enables additional distinguishing conserved sequence blocks within the helicase-like motor to be identified. The establishment of a phylogeny for Snf2 proteins provides an opportunity to make informed assignments of function, and the identification of conserved motifs provides a framework for understanding the mechanisms by which these proteins function.
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Affiliation(s)
- Andrew Flaus
- Division of Gene Regulation and Expression, University of DundeeDundee DD1 5EH, Scotland, UK
- Bioinformatics and Computational Biology Research Group, School of Life Sciences, University of DundeeDundee DD1 5EH, Scotland, UK
| | - David M. A. Martin
- Bioinformatics and Computational Biology Research Group, School of Life Sciences, University of DundeeDundee DD1 5EH, Scotland, UK
| | - Geoffrey J. Barton
- Bioinformatics and Computational Biology Research Group, School of Life Sciences, University of DundeeDundee DD1 5EH, Scotland, UK
| | - Tom Owen-Hughes
- To whom correspondence should be addressed. Tel: +44 0 1382 385796; Fax: +44 0 1382 388702;
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den Dulk B, Sun SM, de Ruijter M, Brandsma JA, Brouwer J. Rad33, a new factor involved in nucleotide excision repair in Saccharomyces cerevisiae. DNA Repair (Amst) 2006; 5:683-92. [PMID: 16595192 DOI: 10.1016/j.dnarep.2006.02.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2005] [Revised: 02/04/2006] [Accepted: 02/07/2006] [Indexed: 11/25/2022]
Abstract
In Saccharomyces cerevisiae the Rad4-Rad23 complex is involved in initial damage recognition and responsible for recruiting the other NER proteins to the site of the lesion. The Rad4-Rad23 complex is essential for both NER subpathways, Transcription Coupled Repair (TCR) and Global Genome Repair (GGR). Previously, we reported on the role of the Rad4 homologue YDR314C in NER. YDR314C is essential for preferential repair of the transcribed strand in RNA pol I transcribed rDNA. In large scale interaction studies it was shown that YDR314C physically interacts with a small protein encoded by the ORF YML011C. In the present study we show that YML011C is involved in NER and we propose to designate the YML011C ORF RAD33. Cells deleted for RAD33 display intermediate UV sensitivity that is epistatic with NER. Strand specific repair analysis shows that GGR in RNA pol II transcribed regions is completely defective in rad33 mutants whereas TCR is still active, albeit much less efficient. In RNA pol I transcribed rDNA both GGR and TCR are fully dependent on Rad33. We show that in both rad23 and rad33 cells Rad4 and YDR314C protein levels are significantly reduced. The homology of YDR314C to Rad4, together with the similar relation of both proteins to Rad33 prompted us to propose RAD34 as name for the YDR314C gene. Although the rad23rad33 double mutant is considerably more UV sensitive than a rad23 or rad33 single mutant, deletion of RAD33 in a rad23 background does not lead to a further reduction of Rad4 or Rad34 protein levels. This suggests that the role of Rad33 is not solely the stabilization of Rad4 and Rad34 but that Rad33 has an additional role in NER.
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Affiliation(s)
- Ben den Dulk
- MGC Department of Molecular Genetics, Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
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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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45
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Chen S, Davies AA, Sagan D, Ulrich HD. The RING finger ATPase Rad5p of Saccharomyces cerevisiae contributes to DNA double-strand break repair in a ubiquitin-independent manner. Nucleic Acids Res 2005; 33:5878-86. [PMID: 16224103 PMCID: PMC1258175 DOI: 10.1093/nar/gki902] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Tolerance to replication-blocking DNA lesions is achieved by means of ubiquitylation of PCNA, the processivity clamp for replicative DNA polymerases, by components of the RAD6 pathway. In the yeast Saccharomyces cerevisiae the ubiquitin ligase (E3) responsible for polyubiquitylation of the clamp is the RING finger protein Rad5p. Interestingly, the RING finger, responsible for the protein's E3 activity, is embedded in a conserved DNA-dependent ATPase domain common to helicases and chromatin remodeling factors of the SWI/SNF family. Here, we demonstrate that the Rad5p ATPase domain provides the basis for a function of the protein in DNA double-strand break repair via a RAD52- and Ku-independent pathway mediated by the Mre11/Rad50/Xrs2 protein complex. This activity is distinct and separable from the contribution of the RING domain to ubiquitin conjugation to PCNA. Moreover, we show that the Rad5 protein physically associates with the single-stranded DNA regions at a processed double-strand break in vivo. Our observations suggest that Rad5p is a multifunctional protein that—by means of independent enzymatic activities inherent in its RING and ATPase domains—plays a modulating role in the coordination of repair events and replication fork progression in response to various different types of DNA lesions.
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Affiliation(s)
- Shuhua Chen
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-StrasseD-35043 Marburg, Germany
- Cancer Research UK, London Research Institute, Clare Hall LaboratoriesBlanche Lane, South Mimms, Herts EN6 3LD, UK
| | - Adelina A. Davies
- Cancer Research UK, London Research Institute, Clare Hall LaboratoriesBlanche Lane, South Mimms, Herts EN6 3LD, UK
| | - Daniel Sagan
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-StrasseD-35043 Marburg, Germany
| | - Helle D. Ulrich
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-StrasseD-35043 Marburg, Germany
- Cancer Research UK, London Research Institute, Clare Hall LaboratoriesBlanche Lane, South Mimms, Herts EN6 3LD, UK
- To whom correspondence should be addressed. Tel: +44 1707 62 5821; Fax: +44 1707 62 5550;
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46
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Wang QE, Zhu Q, Wani G, El-Mahdy MA, Li J, Wani AA. DNA repair factor XPC is modified by SUMO-1 and ubiquitin following UV irradiation. Nucleic Acids Res 2005; 33:4023-34. [PMID: 16030353 PMCID: PMC1178000 DOI: 10.1093/nar/gki684] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Nucleotide excision repair (NER) is the major DNA repair process that removes diverse DNA lesions including UV-induced photoproducts. There are more than 20 proteins involved in NER. Among them, XPC is thought to be one of the first proteins to recognize DNA damage during global genomic repair (GGR), a sub-pathway of NER. In order to study the mechanism through which XPC participates in GGR, we investigated the possible modifications of XPC protein upon UV irradiation in mammalian cells. Western blot analysis of cell lysates from UV-irradiated normal human fibroblast, prepared by direct boiling in an SDS lysis buffer, showed several anti-XPC antibody-reactive bands with molecular weight higher than the original XPC protein. The reciprocal immunoprecipitation and siRNA transfection analysis demonstrated that XPC protein is modified by SUMO-1 and ubiquitin. By using several NER-deficient cell lines, we found that DDB2 and XPA are required for UV-induced XPC modifications. Interestingly, both the inactivation of ubiquitylation and the treatment of proteasome inhibitors quantitatively inhibited the UV-induced XPC modifications. Furthermore, XPC protein is degraded significantly following UV irradiation in XP-A cells in which sumoylation of XPC does not occur. Taken together, we conclude that XPC protein is modified by SUMO-1 and ubiquitin following UV irradiation and these modifications require the functions of DDB2 and XPA, as well as the ubiquitin-proteasome system. Our results also suggest that at least one function of UV-induced XPC sumoylation is related to the stabilization of XPC protein.
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Affiliation(s)
- Qi-En Wang
- Department of Radiology, The Ohio State University103 Wiseman Hall, 400 W. 12th Avenue, Columbus, OH 43210, USA
| | - Qianzheng Zhu
- Department of Radiology, The Ohio State University103 Wiseman Hall, 400 W. 12th Avenue, Columbus, OH 43210, USA
| | - Gulzar Wani
- Department of Radiology, The Ohio State University103 Wiseman Hall, 400 W. 12th Avenue, Columbus, OH 43210, USA
| | - Mohamed A. El-Mahdy
- Department of Radiology, The Ohio State University103 Wiseman Hall, 400 W. 12th Avenue, Columbus, OH 43210, USA
| | - Jinyou Li
- Department of Radiology, The Ohio State University103 Wiseman Hall, 400 W. 12th Avenue, Columbus, OH 43210, USA
| | - Altaf A. Wani
- Department of Radiology, The Ohio State University103 Wiseman Hall, 400 W. 12th Avenue, Columbus, OH 43210, USA
- Department of Molecular and Cellular Biochemistry, The Ohio State University103 Wiseman Hall, 400 W. 12th Avenue, Columbus, OH 43210, USA
- James Cancer Hospital and Solove Research Institute, The Ohio State University103 Wiseman Hall, 400 W. 12th Avenue, Columbus, OH 43210, USA
- To whom correspondence should be addressed. Tel: +1 614 293 0865; Fax: +1 614 293 0802;
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Reed SH. Nucleotide excision repair in chromatin: The shape of things to come. DNA Repair (Amst) 2005; 4:909-18. [PMID: 15905137 DOI: 10.1016/j.dnarep.2005.04.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2005] [Indexed: 11/26/2022]
Abstract
Much of our mechanistic understanding of nucleotide excision repair (NER) has been derived from biochemical studies that have analysed the reaction as it occurs on DNA substrates that are not representative of DNA as it exists in the living cell. These studies have been extremely useful in deciphering the core mechanism of the NER reaction, but efforts to understand how NER operates in chromatin have been hampered in part because assembling DNA into nucleosomes, the first level of chromatin compaction, is inhibitory to NER in vitro. However, recent research using biochemical, genetic and cell-based studies is now providing us with the first insights into the molecular mechanism of NER as it occurs in the cellular context. A number of recent studies have provided glimpses of a chromatin--NER connection. Here I review this literature and evaluate how it might aid our understanding, and shape our future research into NER.
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Affiliation(s)
- Simon H Reed
- Department of Pathology, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.
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Ortolan TG, Chen L, Tongaonkar P, Madura K. Rad23 stabilizes Rad4 from degradation by the Ub/proteasome pathway. Nucleic Acids Res 2004; 32:6490-500. [PMID: 15601997 PMCID: PMC545455 DOI: 10.1093/nar/gkh987] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Rad23 protein interacts with the nucleotide excision-repair (NER) factor Rad4, and the dimer can bind damaged DNA. Rad23 also binds ubiquitinated proteins and promotes their degradation by the proteasome. Rad23/proteasome interaction is required for efficient NER, although the specific role of the Ub/proteasome system in DNA repair is unclear. We report that the availability of Rad4 contributes significantly to the cellular tolerance to UV light. Mutations in the proteasome, and in genes encoding the ubiquitin-conjugating enzymes Ubc4 and Ubc5, stabilized Rad4 and increased tolerance to UV light. A short amino acid sequence, previously identified in human Rad23, mediates the interaction between Rad23 and Rad4. We determined that this motif was required for stabilizing Rad4, and could function independently of the intact protein. A ubiquitin-like (UbL) domain in Rad23 binds the proteasome, and is required for conferring full resistance to DNA damage. However, Rad23/proteasome interaction appears unrelated to Rad23-mediated stabilization of Rad4. Specifically, simultaneous expression of a Rad23 mutant that could not bind the proteasome, with a mutant that could not interact with Rad4, fully suppressed the UV sensitivity of rad23Delta, demonstrating that Rad23 performs two independent, but concurrent roles in NER.
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Affiliation(s)
- Tatiana G Ortolan
- Department of Biochemistry, Robert Wood Johnson Medical School, 683 Hoes Lane, Piscataway, NJ 08854, USA
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