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Smerdon MJ, Wyrick JJ, Delaney S. A half century of exploring DNA excision repair in chromatin. J Biol Chem 2023; 299:105118. [PMID: 37527775 PMCID: PMC10498010 DOI: 10.1016/j.jbc.2023.105118] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 08/03/2023] Open
Abstract
DNA in eukaryotic cells is packaged into the compact and dynamic structure of chromatin. This packaging is a double-edged sword for DNA repair and genomic stability. Chromatin restricts the access of repair proteins to DNA lesions embedded in nucleosomes and higher order chromatin structures. However, chromatin also serves as a signaling platform in which post-translational modifications of histones and other chromatin-bound proteins promote lesion recognition and repair. Similarly, chromatin modulates the formation of DNA damage, promoting or suppressing lesion formation depending on the chromatin context. Therefore, the modulation of DNA damage and its repair in chromatin is crucial to our understanding of the fate of potentially mutagenic and carcinogenic lesions in DNA. Here, we survey many of the landmark findings on DNA damage and repair in chromatin over the last 50 years (i.e., since the beginning of this field), focusing on excision repair, the first repair mechanism studied in the chromatin landscape. For example, we highlight how the impact of chromatin on these processes explains the distinct patterns of somatic mutations observed in cancer genomes.
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Affiliation(s)
- Michael J Smerdon
- Biochemistry and Biophysics, School of Molecular Biosciences, Washington State University, Pullman, Washington, USA.
| | - John J Wyrick
- Genetics and Cell Biology, School of Molecular Biosciences, Washington State University, Pullman, Washington, USA
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, Rhode Island, USA
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2
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Zhang YL, Peng H, Ying SH, Feng MG. Efficient Photoreactivation of Solar UV-Injured Metarhizium robertsii by Rad1 and Rad10 Linked to DNA Photorepair-Required Proteins. Photochem Photobiol 2022. [PMID: 36441642 DOI: 10.1111/php.13752] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/26/2022] [Indexed: 11/29/2022]
Abstract
Nucleotide excision repair (NER) of ultraviolet (UV)-induced DNA lesions known as cyclobutane pyrimidine dimer (CPD) and (6-4)-pyrimidine-pyrimidone (6-4PP) photoproducts depends on the activities of multiple anti-UV radiation (RAD) proteins in budding yeast. However, NER remains poorly known in filamentous fungi, whose DNA lesions are photorepaired by one or two photolyases, namely CPD-specific Phr1 and/or 6-4PP-specific Phr2. Previously, the white collar proteins WC1 and WC2 were proven to regulate expressions of phr2 and phr1 and photorepair 6-4PP and CDP DNA lesions, respectively, in Metarhizium robertsii, a filamentous entomopathogenic-phytoendophytic fungus. We report here high activities of orthologous Rad1 and Rad10 in 5-h photoreactivation of UVB-injured or UVB-inactivated conidia but a severely compromised capability of their reactivating those conidia via 24-h dark incubation in M. robertsii. The null mutants of rad1 and rad10 were much more compromised in conidial UVB resistance and photoreactivation capability than the previous null mutants of phr1, phr2, wc1 and wc2. Multiple protein-protein (Rad1-Rad10, Rad1-WC2, Rad10-Phr1, WC1-Phr1/2 and WC2-Phr1/2) interactions detected suggest direct/indirect links of Rad1 and Rad10 to Phr1/2 and WC1/2 and an importance of the links for their photoreactivation activities. Conclusively, Rad1 and Rad10 photoreactivate UVB-impaired M. robertsii through their interactions with the DNA photorepair-required proteins.
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Affiliation(s)
- Yi-Lu Zhang
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Han Peng
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Sheng-Hua Ying
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ming-Guang Feng
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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3
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Yu L, Xu SY, Tong SM, Ying SH, Feng MG. Optional strategies for low-risk and non-risk applications of fungal pesticides to avoid solar ultraviolet damage. PEST MANAGEMENT SCIENCE 2022; 78:4660-4667. [PMID: 35864789 DOI: 10.1002/ps.7086] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/12/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Solar ultraviolet (UV) irradiation is harmful to formulated conidia as active ingredients of fungal pesticides and hence restrains their field application in sunny days of summer, a season requiring frequent pest controls. This conflict makes it necessary to explore optimal strategies for the application of fungal pesticides to suppress pest populations but avoid solar UV damage during summer. RESULTS The conidia of Beauveria bassiana, a wide-spectrum fungal pesticide, were tolerable to UVB (major solar UV wavelengths) damage of ≤0.5 J cm-2 . The damage of this upper limit caused a loss of conidial viability and infectivity if not photoreactivated by light exposure after irradiation. Intriguingly, the light exposure resulted in a high photoreactivation rate of UVB-inactivated conidia and an insignificant or marginal difference in insecticidal activity between normal conidia and those photoreactivated. Modeling analysis of solar UVB intensity recorded hourly over the daylight of five sunny summer days from 5:00 am to 7:00 pm at 30° 17'57'' N and 120°5'7'' E revealed a variation of daily accumulated UVB dose from 2.07 to 2.78 J cm-2 , which was far beyond the upper limit. A more tolerable dose of ~0.2 J cm-2 appeared between 3:00 pm and 5:00 pm, and no harmful dose accumulated between 5:00 pm and 7:00 pm. CONCLUSION Fungal UVB tolerance, fungal photoreactivation capability and the daily accumulation pattern of solar UV irradiation are based to propose an optional strategy for low-risk or non-risk application of fungal pesticides after 3:00 or 5:00 pm during summer. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Lei Yu
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Si-Yuan Xu
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Sen-Miao Tong
- College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, China
| | - Sheng-Hua Ying
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ming-Guang Feng
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
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4
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Yu L, Xu SY, Luo XC, Ying SH, Feng MG. Rad1 and Rad10 Tied to Photolyase Regulators Protect Insecticidal Fungal Cells from Solar UV Damage by Photoreactivation. J Fungi (Basel) 2022; 8:1124. [PMID: 36354891 PMCID: PMC9692854 DOI: 10.3390/jof8111124] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/18/2022] [Accepted: 10/21/2022] [Indexed: 09/02/2023] Open
Abstract
Beauveria bassiana serves as a main source of global fungal insecticides, which are based on the active ingredient of formulated conidia vulnerable to solar ultraviolet (UV) irradiation and restrained for all-weather application in green agriculture. The anti-UV proteins Rad1 and Rad10 are required for the nucleotide excision repair (NER) of UV-injured DNA in model yeast, but their anti-UV roles remain rarely exploredin filamentous fungi. Here, Rad1 and Rad10 orthologues that accumulated more in the nuclei than the cytoplasm of B. bassiana proved capable of reactivating UVB-impaired or UVB-inactivated conidia efficiently by 5h light exposure but incapable of doing so by 24 h dark incubation (NER) if the accumulated UVB irradiation was lethal. Each orthologue was found interacting with the other and two white collar proteins (WC1 and WC2), which proved to be regulators of two photolyases (Phr1 and Phr2) and individually more efficient in the photorepair of UVB-induced DNA lesions than either photolyase alone. The fungal photoreactivation activity was more or far more compromised when the protein-protein interactions were abolished in the absence of Rad1 or Rad10 than when either Phr1 or Phr2 lost function. The detected protein-protein interactions suggest direct links of either Rad1 or Rad10 to two photolyase regulators. In B. bassiana, therefore, Rad1 and Rad10 tied to the photolyase regulators have high activities in the photoprotection of formulated conidia from solar UV damage but insufficient NER activities in the field, where night (dark) time is too short, and no other roles in the fungal lifecycle in vitro and in vivo.
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Affiliation(s)
| | | | | | | | - Ming-Guang Feng
- Institute of Microbiology, Collegeof Life Sciences, Zhejiang University, Hangzhou 310058, China
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Tong SM, Feng MG. Molecular basis and regulatory mechanisms underlying fungal insecticides' resistance to solar ultraviolet irradiation. PEST MANAGEMENT SCIENCE 2022; 78:30-42. [PMID: 34397162 DOI: 10.1002/ps.6600] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
Resistance to solar ultraviolet (UV) irradiation is crucial for field-persistent control efficacies of fungal formulations against arthropod pests, because their active ingredients are formulated conidia very sensitive to solar UV wavelengths. This review seeks to summarize advances in studies aiming to quantify, understand and improve conidial UV resistance. One focus of studies has been on the many sets of genes that have been revealed in the postgenomic era to contribute to or mediate UV resistance in the insect pathogens serving as main sources of fungal insecticides. Such genetic studies have unveiled the broad basis of UV-resistant molecules including cytosolic solutes, cell wall components, various antioxidant enzymes, and numerous effectors and signaling proteins, that function in developmental, biosynthetic and stress-responsive pathways. Another focus has been on the molecular basis and regulatory mechanisms underlying photorepair of UV-induced DNA lesions and photoreactivation of UV-impaired conidia. Studies have shed light upon a photoprotective mechanism depending on not only one or two photorepair-required photolyases, but also two white collar proteins and other partners that play similar or more important roles in photorepair via interactions with photolyases. Research hotspots are suggested to explore a regulatory network of fungal photoprotection and to improve the development and application strategies of UV-resistant fungal insecticides. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Sen-Miao Tong
- College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, China
| | - Ming-Guang Feng
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
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Peng H, Guo CT, Tong SM, Ying SH, Feng MG. Two white collar proteins protect fungal cells from solar UV damage by their interactions with two photolyases in Metarhizium robertsii. Environ Microbiol 2021; 23:4925-4938. [PMID: 33438355 DOI: 10.1111/1462-2920.15398] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 01/09/2021] [Accepted: 01/09/2021] [Indexed: 12/14/2022]
Abstract
The photolyases PHR1 and PHR2 enable photorepair of fungal DNA lesions in the forms of UV-induced cyclobutane pyrimidine dimer (CPD) and (6-4)-pyrimidine-pyrimidone (6-4PP) photoproducts, but their regulation remains mechanistically elusive. Here, we report that the white collar proteins WC1 and WC2 mutually interacting to form a light-responsive transcription factor regulate photolyase expression required for fungal UV resistance in the insect-pathogenic fungus Metharhizum robertsii. Conidial UVB resistance decreased by 54% in Δwc1 and 67% in Δwc2. Five-hour exposure of UVB-inactivated conidia to visible light resulted in photoreactivation rates of 30% and 9% for the Δwc1 and Δwc2 mutants, contrasting to 79%-82% for wild-type and complemented strains. Importantly, abolished transcription of phr1 in Δwc-2 and of phr2 in Δwc1 resulted in incapable photorepair of CDP and 6-4PP DNA lesions in UVB-impaired Δwc2 and Δwc1 cells respectively. Yeast two-hybrid assays revealed interactions of either WC protein with both PHR1 and PHR2. Therefore, the essential roles for WC1 and WC2 in both photorepair of UVB-induced DNA lesions and photoreactivation of UVB-inactivated conidia rely upon their interactions with, and hence transcriptional activation of, PHR1 and PHR2. These findings uncover a novel WC-cored pathway that mediates filamentous fungal response and adaptation to solar UV irradiation.
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Affiliation(s)
- Han Peng
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Chong-Tao Guo
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Sen-Miao Tong
- College of Agricultural and Food Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Sheng-Hua Ying
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Ming-Guang Feng
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
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7
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Li L, Li B, Xie C, Zhang T, Borassi C, Estevez JM, Li X, Liu X. Arabidopsis RAD23B regulates pollen development by mediating degradation of KRP1. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4010-4019. [PMID: 32242227 DOI: 10.1093/jxb/eraa167] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 04/02/2020] [Indexed: 06/11/2023]
Abstract
The ubiquitin (Ub)/26S proteasome system (UPS) plays a key role in plant growth, development, and survival by directing the turnover of numerous regulatory proteins. In the UPS, the ubiquitin-like (UBL) and ubiquitin-associated (UBA) domains function as hubs for ubiquitin-mediated protein degradation. Radiation sensitive 23 (RAD23), which has been identified as a UBL/UBA protein, contributes to the progression of the cell cycle, stress responses, ER proteolysis, and DNA repair. Here, we report that pollen development is arrested at the microspore stage in a rad23b null mutant. We demonstrate that RAD23B can directly interact with KIP-related protein 1 (KRP1) through its UBL-UBA domains. In addition, plants overexpressing KRP1 have defects in pollen development, which is a phenotype similar to the rad23b mutant. RAD23B promotes the degradation of KRP1 in vivo, which is accumulated following treatment with the proteasome inhibitor MG132. Our results indicate that RAD23B plays an important in pollen development by controlling the turnover of the key cell cycle protein, KRP1.
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Affiliation(s)
- Lan Li
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation Hunan University, Changsha, P. R. China
| | - Bin Li
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation Hunan University, Changsha, P. R. China
| | - Chong Xie
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation Hunan University, Changsha, P. R. China
| | - Teng Zhang
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation Hunan University, Changsha, P. R. China
| | - Cecilia Borassi
- Fundación Instituto Leloir and IIBBA-CONICET, Av. Patricias Argentinas 435, Buenos Aires CP, Argentina
| | - José M Estevez
- Fundación Instituto Leloir and IIBBA-CONICET, Av. Patricias Argentinas 435, Buenos Aires CP, Argentina
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile and Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Xiushan Li
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation Hunan University, Changsha, P. R. China
| | - Xuanming Liu
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation Hunan University, Changsha, P. R. China
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8
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Photoprotective Role of Photolyase-Interacting RAD23 and Its Pleiotropic Effect on the Insect-Pathogenic Fungus Beauveria bassiana. Appl Environ Microbiol 2020; 86:AEM.00287-20. [PMID: 32245759 DOI: 10.1128/aem.00287-20] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/22/2020] [Indexed: 02/07/2023] Open
Abstract
RAD23 can repair yeast DNA lesions through nucleotide excision repair (NER), a mechanism that is dependent on proteasome activity and ubiquitin chains but different from photolyase-depending photorepair of UV-induced DNA damages. However, this accessory NER protein remains functionally unknown in filamentous fungi. In this study, orthologous RAD23 in Beauveria bassiana, an insect-pathogenic fungus that is a main source of fungal insecticides, was found to interact with the photolyase PHR2, enabling repair of DNA lesions by degradation of UVB-induced cytotoxic (6-4)-pyrimidine-pyrimidine photoproducts under visible light, and it hence plays an essential role in the photoreactivation of UVB-inactivated conidia but no role in reactivation of such conidia through NER in dark conditions. Fluorescence-labeled RAD23 was shown to normally localize in the cytoplasm, to migrate to vacuoles in the absence of carbon, nitrogen, or both, and to enter nuclei under various stresses, which include UVB, a harmful wavelength of sunlight. Deletion of the rad23 gene resulted in an 84% decrease in conidial UVB resistance, a 95% reduction in photoreactivation rate of UVB-inactivated conidia, and a drastic repression of phr2 A yeast two-hybrid assay revealed a positive RAD23-PHR2 interaction. Overexpression of phr2 in the Δrad23 mutant largely mitigated the severe defect of the Δrad23 mutant in photoreactivation. Also, the deletion mutant was severely compromised in radial growth, conidiation, conidial quality, virulence, multiple stress tolerance, and transcriptional expression of many phenotype-related genes. These findings unveil not only the pleiotropic effects of RAD23 in B. bassiana but also a novel RAD23-PHR2 interaction that is essential for the photoprotection of filamentous fungal cells from UVB damage.IMPORTANCE RAD23 is able to repair yeast DNA lesions through nucleotide excision in full darkness, a mechanism distinct from photolyase-dependent photorepair of UV-induced DNA damage but functionally unknown in filamentous fungi. Our study unveils that the RAD23 ortholog in a filamentous fungal insect pathogen varies in subcellular localization according to external cues, interacts with a photolyase required for photorepair of cytotoxic (6-4)-pyrimidine-pyrimidine photoproducts in UV-induced DNA lesions, and plays an essential role in conidial UVB resistance and reactivation of UVB-inactivated conidia under visible light rather than in the dark, as required for nucleotide excision repair. Loss-of-function mutations of RAD23 exert pleiotropic effects on radial growth, aerial conidiation, multiple stress responses, virulence, virulence-related cellular events, and phenotype-related gene expression. These findings highlight a novel mechanism underlying the photoreactivation of UVB-impaired fungal cells by RAD23 interacting with the photolyase, as well as its essentiality for filamentous fungal life.
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9
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Liu R, Cheng WJ, Ye F, Zhang YD, Zhong QP, Dong HF, Tang HB, Jiang H. Comparative Transcriptome Analyses of Schistosoma japonicum Derived From SCID Mice and BALB/c Mice: Clues to the Abnormality in Parasite Growth and Development. Front Microbiol 2020; 11:274. [PMID: 32218772 PMCID: PMC7078119 DOI: 10.3389/fmicb.2020.00274] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 02/06/2020] [Indexed: 12/13/2022] Open
Abstract
Schistosomiasis, caused by the parasitic flatworms called schistosomes, remains one of the most prevailing parasitic diseases in the world. The prodigious oviposition of female worms after maturity is the main driver of pathology due to infection, yet our understanding about the regulation of development and reproduction of schistosomes is limited. Here, we comparatively profiled the transcriptome of Schistosoma japonicum recovered from SCID and BALB/c mice, which were collected 35 days post-infection, when prominent morphological abnormalities could be observed in schistosomes from SCID mice, by performing RNA-seq analysis. Of the 11,183 identified genes, 62 differentially expressed genes (DEGs) with 39 upregulated and 23 downregulated messenger RNAs (mRNAs) were found in male worms from SCID mice (S_M) vs. male worms from BALB/c mice (B_M), and 240 DEGs with 152 upregulated and 88 downregulated mRNAs were found in female worms from SCID mice (S_F) vs. female worms from BALB/c mice (B_F). We also tested nine DEGs with a relatively higher expression abundance in the gonads of the worms (ovary, vitellaria, or testis), suggesting their potential biological significance in the development and reproduction of the parasites. Gene ontology (GO) enrichment analysis revealed that GO terms such as “microtubule-based process,” “multicellular organismal development,” and “Rho protein signal transduction” were significantly enriched in the DEGs in S_F vs. B_F, whereas GO terms such as “oxidation–reduction process,” “response to stress,” and “response to DNA damage stimulus” were significantly enriched in the DEGs in S_M vs. B_M. These results revealed that the differential expression of some important genes might contribute to the morphological abnormalities of worms in SCID mice. Furthermore, we selected one DEG, the mitochondrial prohibitin complex protein 1 (Phb1), to perform double-stranded RNA (dsRNA)-mediated RNA interference (RNAi) in vivo targeting the worms in BALB/c mice, and we found that it was essential for the growth and reproductive development of both male and female S. japonicum worms. Taken together, these results provided a wealth of information on the differential gene expression profiles of schistosomes from SCID mice when compared with those from BALB/c mice, which were potentially involved in regulating the growth and development of schistosomes. These findings contributed to an understanding of parasite biology and provided a rich resource for the exploitation of antischistosomal intervention targets.
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Affiliation(s)
- Rong Liu
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Wen-Jun Cheng
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Feng Ye
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Yao-Dan Zhang
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Qin-Ping Zhong
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Hui-Fen Dong
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Hong-Bin Tang
- Laboratory Animal Center, School of Medicine, Wuhan University, Wuhan, China
| | - Hong Jiang
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
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10
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Butler RM, McKenzie RC, Jones CL, Flanagan CE, Woollard WJ, Demontis M, Ferreira S, Tosi I, John S, Whittaker SJ, Mitchell TJ. Contribution of STAT3 and RAD23B in Primary Sézary Cells to Histone Deacetylase Inhibitor FK228 Resistance. J Invest Dermatol 2019; 139:1975-1984.e2. [PMID: 30910759 DOI: 10.1016/j.jid.2019.03.1130] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 02/23/2019] [Accepted: 03/06/2019] [Indexed: 01/12/2023]
Abstract
FK228 (romidepsin) and suberoylanilide hydroxamic acid (vorinostat) are histone deacetylase inhibitors (HDACi) approved by the US Food and Drug Administration for cutaneous T-cell lymphoma (CTCL), including the leukemic subtype Sézary syndrome. This study investigates RAD23B and STAT3 gene perturbations in a large cohort of primary Sézary cells and the effect of FK228 treatment on tyrosine phosphorylation of STAT3 (pYSTAT3) and RAD23B expression. We report RAD23B copy number variation in 10% (12/119, P ≤ 0.01) of SS patients, associated with reduced mRNA expression (P = 0.04). RAD23B knockdown in a CTCL cell line led to a reduction in FK228-induced apoptosis. Histone deacetylase inhibitor treatment significantly reduced pYSTAT3 in primary Sézary cells and was partially mediated by RAD23B. A distinct pattern of RAD23B-pYSTAT3 co-expression in primary Sézary cells was detected. Critically, Sézary cells harboring the common STAT3 Y640F variant were less sensitive to FK228-induced apoptosis and exogenous expression of STAT3 Y640F, and D661Y conferred partial resistance to STAT3 transcriptional inhibition by FK228 (P ≤ 0.0024). These findings suggest that RAD23B and STAT3 gene perturbations could reduce sensitivity to histone deacetylase inhibitors in SS patients.
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Affiliation(s)
- Rosie M Butler
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, London, UK
| | - Robert C McKenzie
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, London, UK
| | - Christine L Jones
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, London, UK
| | - Charlotte E Flanagan
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, London, UK
| | - Wesley J Woollard
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, London, UK
| | - Maria Demontis
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, London, UK
| | - Silvia Ferreira
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, London, UK
| | - Isabella Tosi
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, London, UK
| | - Susan John
- Department of Immunology, Infection and Inflammatory Disease, King's College London, Guy's Hospital, London, UK
| | - Sean J Whittaker
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, London, UK
| | - Tracey J Mitchell
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, London, UK.
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11
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Chen X, Randles L, Shi K, Tarasov SG, Aihara H, Walters KJ. Structures of Rpn1 T1:Rad23 and hRpn13:hPLIC2 Reveal Distinct Binding Mechanisms between Substrate Receptors and Shuttle Factors of the Proteasome. Structure 2016; 24:1257-1270. [PMID: 27396824 DOI: 10.1016/j.str.2016.05.018] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/10/2016] [Accepted: 05/25/2016] [Indexed: 12/14/2022]
Abstract
Three receptors (Rpn1/S2/PSMD2, Rpn10/S5a, Rpn13/Adrm1) in the proteasome bind substrates by interacting with conjugated ubiquitin chains and/or shuttle factors (Rad23/HR23, Dsk2/PLIC/ubiquilin, Ddi1) that carry ubiquitinated substrates to proteasomes. We solved the structure of two such receptors with their preferred shuttle factor, namely hRpn13(Pru):hPLIC2(UBL) and scRpn1 T1:scRad23(UBL). We find that ubiquitin folds in Rad23 and Dsk2 are fine-tuned by residue substitutions to achieve high affinity for Rpn1 and Rpn13, respectively. A single substitution in hPLIC2 yields enhanced interactions with the Rpn13 ubiquitin contact surface and sterically blocks hRpn13 binding to its preferred ubiquitin chain type, K48-linked chains. Rpn1 T1 binds two ubiquitins in tandem and we find that Rad23 binds exclusively to the higher-affinity Helix28/Helix30 site. Rad23 contacts at Helix28/Helix30 are optimized compared to ubiquitin by multiple conservative amino acid substitutions. Thus, shuttle factors deliver substrates to proteasomes through fine-tuned ubiquitin-like surfaces.
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Affiliation(s)
- Xiang Chen
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Leah Randles
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Ke Shi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sergey G Tarasov
- Biophysics Resource, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Kylie J Walters
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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12
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Zhou Z, Humphryes N, van Eijk P, Waters R, Yu S, Kraehenbuehl R, Hartsuiker E, Reed SH. UV induced ubiquitination of the yeast Rad4-Rad23 complex promotes survival by regulating cellular dNTP pools. Nucleic Acids Res 2015; 43:7360-70. [PMID: 26150418 PMCID: PMC4551923 DOI: 10.1093/nar/gkv680] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 06/22/2015] [Indexed: 11/13/2022] Open
Abstract
Regulating gene expression programmes is a central facet of the DNA damage response. The Dun1 kinase protein controls expression of many DNA damage induced genes, including the ribonucleotide reductase genes, which regulate cellular dNTP pools. Using a combination of gene expression profiling and chromatin immunoprecipitation, we demonstrate that in the absence of DNA damage the yeast Rad4–Rad23 nucleotide excision repair complex binds to the promoters of certain DNA damage response genes including DUN1, inhibiting their expression. UV radiation promotes the loss of occupancy of the Rad4–Rad23 complex from the regulatory regions of these genes, enabling their induction and thereby controlling the production of dNTPs. We demonstrate that this regulatory mechanism, which is dependent on the ubiquitination of Rad4 by the GG-NER E3 ligase, promotes UV survival in yeast cells. These results support an unanticipated regulatory mechanism that integrates ubiquitination of NER DNA repair factors with the regulation of the transcriptional response controlling dNTP production and cellular survival after UV damage.
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Affiliation(s)
- Zheng Zhou
- Institute of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK College of Biology, Hunan University, Changsha 410082, China
| | - Neil Humphryes
- Institute of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK New York University Department of Biology,1009 Silver Center, 100 Washington Square East, NY, USA
| | - Patrick van Eijk
- Institute of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Raymond Waters
- Institute of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Shirong Yu
- Institute of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK Cambridge Epigenetix, Jonas Webb Building, Babraham Campus, Cambridge, CB22 3AT, UK
| | - Rolf Kraehenbuehl
- North West Cancer Research Institute, Bangor University, Brambell Building, Bangor, LL57 2UW, UK
| | - Edgar Hartsuiker
- North West Cancer Research Institute, Bangor University, Brambell Building, Bangor, LL57 2UW, UK
| | - Simon H Reed
- Institute of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
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13
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Lans H, Vermeulen W. Nucleotide Excision Repair in Caenorhabditis elegans. Mol Biol Int 2011; 2011:542795. [PMID: 22091407 PMCID: PMC3195855 DOI: 10.4061/2011/542795] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 06/18/2011] [Indexed: 01/23/2023] Open
Abstract
Nucleotide excision repair (NER) plays an essential role in many organisms across life domains to preserve and faithfully transmit DNA to the next generation. In humans, NER is essential to prevent DNA damage-induced mutation accumulation and cell death leading to cancer and aging. NER is a versatile DNA repair pathway that repairs many types of DNA damage which distort the DNA helix, such as those induced by solar UV light. A detailed molecular model of the NER pathway has emerged from in vitro and live cell experiments, particularly using model systems such as bacteria, yeast, and mammalian cell cultures. In recent years, the versatility of the nematode C. elegans to study DNA damage response (DDR) mechanisms including NER has become increasingly clear. In particular, C. elegans seems to be a convenient tool to study NER during the UV response in vivo, to analyze this process in the context of a developing and multicellular organism, and to perform genetic screening. Here, we will discuss current knowledge gained from the use of C. elegans to study NER and the response to UV-induced DNA damage.
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Affiliation(s)
- Hannes Lans
- Department of Genetics, Medical Genetics Center, Erasmus MC, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Genetics, Medical Genetics Center, Erasmus MC, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
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14
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Mao P, Smerdon MJ. Yeast deubiquitinase Ubp3 interacts with the 26 S proteasome to facilitate Rad4 degradation. J Biol Chem 2010; 285:37542-50. [PMID: 20876584 DOI: 10.1074/jbc.m110.170175] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Deubiquitinating enzymes (DUBs) function in a variety of cellular processes by removing ubiquitin moieties from substrates, but their role in DNA repair has not been elucidated. Yeast Rad4-Rad23 heterodimer is responsible for recognizing DNA damage in nucleotide excision repair (NER). Rad4 binds to UV damage directly while Rad23 stabilizes Rad4 from proteasomal degradation. Here, we show that disruption of yeast deubiquitinase UBP3 leads to enhanced UV resistance, increased repair of UV damage and Rad4 levels in rad23Δ cells, and elevated Rad4 stability. A catalytically inactive Ubp3 (Ubp3-C469A), however, is unable to affect NER or Rad4. Consistent with its role in down-regulating Rad4, Ubp3 physically interacts with Rad4 and the proteasome, both in vivo and in vitro, suggesting that Ubp3 associates with the proteasome to facilitate Rad4 degradation and thus suppresses NER.
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Affiliation(s)
- Peng Mao
- Biochemistry and Biophysics, School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-7520, USA
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15
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Involvement of global genome repair, transcription coupled repair, and chromatin remodeling in UV DNA damage response changes during development. PLoS Genet 2010; 6:e1000941. [PMID: 20463888 PMCID: PMC2865526 DOI: 10.1371/journal.pgen.1000941] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2009] [Accepted: 04/06/2010] [Indexed: 01/22/2023] Open
Abstract
Nucleotide Excision Repair (NER), which removes a variety of helix-distorting lesions from DNA, is initiated by two distinct DNA damage-sensing mechanisms. Transcription Coupled Repair (TCR) removes damage from the active strand of transcribed genes and depends on the SWI/SNF family protein CSB. Global Genome Repair (GGR) removes damage present elsewhere in the genome and depends on damage recognition by the XPC/RAD23/Centrin2 complex. Currently, it is not well understood to what extent both pathways contribute to genome maintenance and cell survival in a developing organism exposed to UV light. Here, we show that eukaryotic NER, initiated by two distinct subpathways, is well conserved in the nematode Caenorhabditis elegans. In C. elegans, involvement of TCR and GGR in the UV-induced DNA damage response changes during development. In germ cells and early embryos, we find that GGR is the major pathway contributing to normal development and survival after UV irradiation, whereas in later developmental stages TCR is predominantly engaged. Furthermore, we identify four ISWI/Cohesin and four SWI/SNF family chromatin remodeling factors that are implicated in the UV damage response in a developmental stage dependent manner. These in vivo studies strongly suggest that involvement of different repair pathways and chromatin remodeling proteins in UV-induced DNA repair depends on developmental stage of cells.
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16
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Farmer LM, Book AJ, Lee KH, Lin YL, Fu H, Vierstra RD. The RAD23 family provides an essential connection between the 26S proteasome and ubiquitylated proteins in Arabidopsis. THE PLANT CELL 2010; 22:124-42. [PMID: 20086187 PMCID: PMC2828702 DOI: 10.1105/tpc.109.072660] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Revised: 12/07/2009] [Accepted: 12/22/2009] [Indexed: 05/20/2023]
Abstract
The ubiquitin (Ub)/26S proteasome system (UPS) directs the turnover of numerous regulatory proteins, thereby exerting control over many aspects of plant growth, development, and survival. The UPS is directed in part by a group of Ub-like/Ub-associated (UBL/UBA) proteins that help shuttle ubiquitylated proteins to the 26S proteasome for breakdown. Here, we describe the collection of UBL/UBA proteins in Arabidopsis thaliana, including four isoforms that comprise the RADIATION SENSITIVE23 (RAD23) family. The nuclear-enriched RAD23 proteins bind Ub conjugates, especially those linked internally through Lys-48, via their UBA domains, and associate with the 26S proteasome Ub receptor RPN10 via their N-terminal UBL domains. Whereas homozygous mutants individually affecting the four RAD23 genes are without phenotypic consequences (rad23a, rad23c, and rad23d) or induce mild phyllotaxy and sterility defects (rad23b), higher-order mutant combinations generate severely dwarfed plants, with the quadruple mutant displaying reproductive lethality. Both the synergistic effects of a rad23b-1 rpn10-1 combination and the response of rad23b plants to mitomycin C suggest that RAD23b regulates cell division. Taken together, RAD23 proteins appear to play an essential role in the cell cycle, morphology, and fertility of plants through their delivery of UPS substrates to the 26S proteasome.
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Affiliation(s)
- Lisa M. Farmer
- Department of Genetics, University of Wisconsin, Madison, WI 53706
| | - Adam J. Book
- Department of Genetics, University of Wisconsin, Madison, WI 53706
| | - Kwang-Hee Lee
- Department of Genetics, University of Wisconsin, Madison, WI 53706
| | - Ya-Ling Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
| | - Hongyong Fu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
| | - Richard D. Vierstra
- Department of Genetics, University of Wisconsin, Madison, WI 53706
- Address correspondence to
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17
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Al-Moghrabi NM, Al-Sharif IS, Aboussekhra A. The RAD9-dependent gene trans-activation is required for excision repair of active genes but not for repair of non-transcribed DNA. Mutat Res 2009; 663:60-8. [PMID: 19428371 DOI: 10.1016/j.mrfmmm.2009.01.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Revised: 01/20/2009] [Accepted: 01/26/2009] [Indexed: 10/21/2022]
Abstract
The Saccharomyces cerevisiae RAD9 and RAD24 are two cell cycle checkpoint genes required for UV-dependent up-regulation of a battery of genes involved in different metabolic pathways. RAD9 is also implicated in nucleotide excision repair (NER); however, its precise role is still unclear. For the present study, we made use of the high-resolution primer extension technique to show that the RAD9-deleted cells are deficient in the repair of both strands of the URA3 gene. Interestingly, this defect was suppressed by over-expressing the RAD24 gene, suggesting that the role of RAD9 in NER is indirect probably through the UV-dependent trans-activation of some NER factors. Accordingly, we present evidence that the inhibition of UV-related de novo protein synthesis by cycloheximide has no effect on the rad9Delta mutant while it suppresses the correcting effect of RAD24 over-expression. Importantly, we have also shown that RAD9 has no role in repair of transcriptionally inactive DNA sequences (URA3 promoter and transcriptionally silent GAL10 gene). Furthermore, de novo protein synthesis was not required for NER in the absence of transcription-coupled NER. This implies that RAD9-dependent gene up-regulation is required for NER only when this process is coupled to transcription.
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Affiliation(s)
- Nisreen M Al-Moghrabi
- King Faisal Specialist Hospital & Research Center, Department of Biological and Medical Research, Riyadh, Saudi Arabia
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18
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Zhou Y, Kou H, Wang Z. Tfb5 interacts with Tfb2 and facilitates nucleotide excision repair in yeast. Nucleic Acids Res 2007; 35:861-71. [PMID: 17215295 PMCID: PMC1807977 DOI: 10.1093/nar/gkl1085] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
TFIIH is indispensable for nucleotide excision repair (NER) and RNA polymerase II transcription. Its tenth subunit was recently discovered in yeast as Tfb5. Unlike other TFIIH subunits, Tfb5 is not essential for cell survival. We have analyzed the role of Tfb5 in NER. NER was deficient in the tfb5 deletion mutant cell extracts, and was specifically complemented by purified Tfb5 protein. In contrast to the extreme ultraviolet (UV) sensitivity of rad14 mutant cells that lack any NER activity, tfb5 deletion mutant cells were moderately sensitive to UV radiation, resembling that of the tfb1-101 mutant cells in which TFIIH activity is compromised but not eliminated. Thus, Tfb5 protein directly participates in NER and is an accessory NER protein that stimulates the repair to the proficient level. Lacking a DNA binding activity, Tfb5 was found to interact with the core TFIIH subunit Tfb2, but not with other NER proteins. The Tfb5–Tfb2 interaction was correlated with the cellular NER function of Tfb5, supporting the functional importance of this interaction. Our results led to a model in which Tfb5 acts as an architectural stabilizer conferring structural rigidity to the core TFIIH such that the complex is maintained in its functional architecture.
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Affiliation(s)
| | | | - Zhigang Wang
- To whom correspondence should be addressed. Tel: +1 859 323 5784; Fax: +1 859 323 1059;
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19
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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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20
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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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21
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Conconi A, Paquette M, Fahy D, Bespalov VA, Smerdon MJ. Repair-independent chromatin assembly onto active ribosomal genes in yeast after UV irradiation. Mol Cell Biol 2005; 25:9773-83. [PMID: 16260595 PMCID: PMC1280247 DOI: 10.1128/mcb.25.22.9773-9783.2005] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chromatin rearrangements occur during repair of cyclobutane pyrimidine dimers (CPDs) by nucleotide excision repair (NER). Thereafter, the original structure must be restored to retain normal genomic functions. How NER proceeds through nonnucleosomal chromatin and how open chromatin is reestablished after repair are unknown. We analyzed NER in ribosomal genes (rDNA), which are present in multiple copies but only a fraction are actively transcribed and nonnucleosomal. We show that removal of CPDs is fast in the active rDNA and that chromatin reorganization occurs during NER. Furthermore, chromatin assembles on nonnucleosomal rDNA during the early events of NER but in the absence of DNA repair. The resumption of transcription after removal of CPDs correlates with the reappearance of nonnucleosomal chromatin. To date, only the passage of replication machinery was thought to package ribosomal genes in nucleosomes. In this report, we show that early events after formation of UV photoproducts in DNA also promote chromatin assembly.
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Affiliation(s)
- Antonio Conconi
- Département de Microbiologie et d'Infectiologie, Faculté de Médecine, Poste 7446, Université de Sherbrooke, 3001 12th Ave. Nord, Sherbrooke, QC J1H 5N4, Canada.
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22
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Zuo Z, Mahajan PB. Recombinant expression of maize nucleotide excision repair protein Rad23 in Escherichia coli. Protein Expr Purif 2005; 41:287-97. [PMID: 15866714 DOI: 10.1016/j.pep.2005.02.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2004] [Revised: 02/02/2005] [Indexed: 11/20/2022]
Abstract
Nucleotide excision is a highly conserved DNA repair pathway for correcting DNA lesions that cause distortion of the double helical structure. The protein heterodimer XPC-Rad23 is involved in recognition of and binding to such lesions. We have isolated full-length cDNAs encoding two different members of the maize Rad23 family. The deduced amino acid sequences of both maize orthologues show a high degree of homology to plant and animal Rad23 proteins. The cDNA encoding maize Rad23A was cloned as an in-frame C-terminal fusion of glutathione S-transferase. This chimera was expressed in Escherichia coli as a soluble protein and purified to homogeneity using glutathione-agarose followed by MonoQ column chromatography. Purified recombinant maize Rad23 protein was used to generate polyclonal antibodies that cross-react with a approximately 48-kDa protein in extracts from plant as well as mammalian cells. The purified recombinant protein and antibodies would be useful reagents to study the biochemistry of nucleotide excision repair in plants.
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Affiliation(s)
- Zhuang Zuo
- Gene Discovery and Modification Laboratory, Department of Transformation Research, Pioneer Hi-Bred International, Inc. (A DuPont Company), Johnston, IA 50131, USA
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23
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Okuda Y, Nishi R, Ng JMY, Vermeulen W, van der Horst GTJ, Mori T, Hoeijmakers JHJ, Hanaoka F, Sugasawa K. Relative levels of the two mammalian Rad23 homologs determine composition and stability of the xeroderma pigmentosum group C protein complex. DNA Repair (Amst) 2005; 3:1285-95. [PMID: 15336624 DOI: 10.1016/j.dnarep.2004.06.010] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2004] [Accepted: 03/18/2004] [Indexed: 11/17/2022]
Abstract
Mammalian cells express two Rad23 homologs, HR23A and HR23B, which have been implicated in regulation of proteolysis via the ubiquitin/proteasome pathway. Recently, the proteins have been shown to stabilize xeroderma pigmentosum group C (XPC) protein that is involved in DNA damage recognition for nucleotide excision repair (NER). Because the vast majority of XPC forms a complex with HR23B rather than HR23A, we investigated possible differences between the two Rad23 homologs in terms of their effects on the XPC protein. In wild-type mouse embryonic fibroblasts (MEFs), endogenous XPC was found to be relatively stable, while its steady-state level and stability appeared significantly reduced by targeted disruption of the mHR23B gene, but not by that of mHR23A. Loss of both mHR23 genes caused a strong further reduction of the XPC protein level. Quantification of the two mHR23 proteins revealed that in normal cells mHR23B is actually approximately 10 times more abundant than mHR23A. In addition, overexpression of mHR23A in the mHR23A/B double knock out cells restored not only the steady-state level and stability of the XPC protein, but also cellular NER activity to near wild-type levels. These results indicate that the two Rad23 homologs are largely functionally equivalent in NER, and that the difference in expression levels explains for a major part the difference in complex formation with as well as stabilization effects on XPC.
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Affiliation(s)
- Yuki Okuda
- Cellular Physiology Laboratory, RIKEN Discovery Research Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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24
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Xie Z, Liu S, Zhang Y, Wang Z. Roles of Rad23 protein in yeast nucleotide excision repair. Nucleic Acids Res 2004; 32:5981-90. [PMID: 15545636 PMCID: PMC534619 DOI: 10.1093/nar/gkh934] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Nucleotide excision repair (NER) removes many different types of DNA lesions. Most NER proteins are indispensable for repair. In contrast, the yeast Rad23 represents a class of accessory NER proteins, without which NER activity is reduced but not eliminated. In mammals, the complex of HR23B (Rad23 homolog) and XPC (yeast Rad4 homolog) has been suggested to function in the damage recognition step of NER. However, the precise function of Rad23 or HR23B in NER remains unknown. Recently, it was suggested that the primary function of RAD23 protein in NER is its stabilization of XPC protein. Here, we tested the significance of Rad23-mediated Rad4 stabilization in NER, and analyzed the repair and biochemical activities of purified yeast Rad23 protein. Cellular Rad4 was indeed stabilized by Rad23 in the absence of DNA damage. Persistent overexpression of Rad4 in rad23 mutant cells, however, largely failed to complement the ultraviolet sensitivity of the mutant. Consistently, deficient NER in rad23 mutant cell extracts could not be complemented by purified Rad4 protein in vitro. In contrast, partial complementation was observed with purified Rad23 protein. Specific complementation to the level of wild-type repair was achieved by adding purified Rad23 together with small amounts of Rad4 protein to rad23 mutant cell extracts. Purified Rad23 protein was unable to bind to DNA, but stimulated the binding activity of purified Rad4 protein to N-acetyl-2-aminofluorene-damaged DNA. These results support two roles of Rad23 protein in NER: (i) its direct participation in the repair biochemistry, possibly due to its stimulatory activity on Rad4-mediated damage binding/recognition; and (ii) its stabilization of cellular Rad4 protein.
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Affiliation(s)
- Zhongwen Xie
- Graduate Center for Toxicology, University of Kentucky, Lexington, KY 40536, USA
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25
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Al-Moghrabi NM, Al-Sharif IS, Aboussekhra A. UV-induced de novo protein synthesis enhances nucleotide excision repair efficiency in a transcription-dependent manner in S. cerevisiae. DNA Repair (Amst) 2004; 2:1185-97. [PMID: 14599741 DOI: 10.1016/j.dnarep.2003.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
DNA damage results in the up-regulation of several genes involved in different cellular physiological processes, such as the nucleotide excision repair (NER) mechanism that copes with a broad range of DNA alterations, including the carcinogenic ultraviolet (UV) light-induced pyrimidine dimers (PDs). There are two NER sub-pathways: transcription coupled repair (TCR) that is specific for the transcribed strands (TS) of active genes and global genomic repair (GGR) that repairs non-transcribed DNA sequences (NTD) and the non-transcribed strands (NTS) of expressed genes. To elucidate the role of UV-dependent de novo protein synthesis in nucleotide excision repair in the budding yeast, we investigated the effect of the protein synthesis inhibitor, cycloheximide, on the removal of PDs. Log phase as well as G(1)-synchronized cells were treated with the drug shortly before UV irradiation and immediately thereafter, and the repair of damaged DNA was assessed with the high resolution primer extension technique. The results show that in both cellular conditions, the inhibition of UV-dependent de novo protein synthesis by cycloheximide impairs the excision repair of the transcriptionally active GAL10 and URA3 genes, with a greater effect on the non-transcribed strands. This indicates that UV-mediated de novo protein synthesis is required for efficient nucleotide excision repair, but not for the preferential repair of the TSs. On the other hand, cycloheximide did not affect the repair of either strand of the repressed GAL10 gene or the non-transcribed promoter region of the URA3 gene, showing that UV-induced de novo protein synthesis is not required for PD removal from transcriptionally inactive DNA sequences. Together, these data show that despite the fact that NTD and NTSs are normally repaired by the GGR sub-pathway, their requirement for UV-dependent de novo protein synthesis is different, which may suggest a difference in the processing of UV lesions in these non-transcribed sequences of the genome.
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Affiliation(s)
- Nisreen M Al-Moghrabi
- Department of Biological and Medical Research, King Faisal Specialist Hospital and Research Center, MBC #03, PO Box 3354, Riyadh 11211, Saudi Arabia
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26
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Marti TM, Kunz C, Fleck O. Repair of damaged and mismatched DNA by the XPC homologues Rhp41 and Rhp42 of fission yeast. Genetics 2003; 164:457-67. [PMID: 12807767 PMCID: PMC1462589 DOI: 10.1093/genetics/164.2.457] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Rhp41 and Rhp42 of Schizosaccharomyces pombe are homologues of human XPC, which is involved in nucleotide excision repair (NER) of damaged DNA. Inactivation of rhp41 caused moderate sensitivity to ultraviolet (UV) radiation. In addition, an increase of mitotic mutation rates was observed in the rhp41 mutant, which was dependent on active translesion polymerase Z. UV sensitivity and mutation rates were not different between rhp42 and wild type, but compared to rhp41 were further increased in rhp41 rhp42 cells. Transcription of the fbp1 gene (induced in vegetative cells) and of the SPBC1289.14 gene (induced during meiosis) was strongly blocked by UV-induced damages in the rhp41 mutant, but not, or only slightly, reduced in rhp42 background. NER-dependent short-patch repair of mismatches formed during meiosis was slightly affected in rhp41, moderately affected in rhp42, and absent in rhp41 rhp42. Epistasis analysis with rhp7 and rhp26 indicates that Rhp41 and Rhp42 are both involved in the global genome and transcription-coupled repair subpathways of NER. Rhp41 plays a major role in damage repair and Rhp42 in mismatch repair.
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Affiliation(s)
- Thomas M Marti
- Institute of Cell Biology, University of Bern, Switzerland
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27
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Lommel L, Ortolan T, Chen L, Madura K, Sweder KS. Proteolysis of a nucleotide excision repair protein by the 26 S proteasome. Curr Genet 2002; 42:9-20. [PMID: 12420141 DOI: 10.1007/s00294-002-0332-9] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2002] [Revised: 08/28/2002] [Accepted: 08/29/2002] [Indexed: 12/01/2022]
Abstract
The 26 S proteasome degrades a broad spectrum of proteins and interacts with several nucleotide excision repair (NER) proteins, including the complex of Rad4 and Rad23 that binds preferentially to UV-damaged DNA. The rate of NER is increased in yeast strains with mutations in genes encoding subunits of the 26 S proteasome, indicating that it could negatively regulate a repair process. The specific function of the 26 S proteasome in DNA repair is unclear. It might degrade DNA repair proteins after repair is completed or act as a molecular chaperone to promote the assembly or disassembly of the repair complex. In this study, we show that Rad4 is ubiquitylated and that Rad23 can control this process. We also find that ubiquitylated Rad4 is degraded by the 26 S proteasome. However, the interaction of Rad23 with Rad4 is not only to control degradation of Rad4, but also to assist in assembling the NER incision complex at UV-induced cyclobutane pyrimidine dimers. We speculate that, following the completion of DNA repair, specific repair proteins might be degraded by the proteasome to regulate repair.
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Affiliation(s)
- Lori Lommel
- Susan Lehman Cullman Laboratory for Cancer Research, Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 164 Frelinghuysen Road, Piscataway 08854-8020, USA
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28
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van Brabant AJ, Stan R, Ellis NA. DNA helicases, genomic instability, and human genetic disease. Annu Rev Genomics Hum Genet 2002; 1:409-59. [PMID: 11701636 DOI: 10.1146/annurev.genom.1.1.409] [Citation(s) in RCA: 203] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DNA helicases are a highly conserved group of enzymes that unwind DNA. They function in all processes in which access to single-stranded DNA is required, including DNA replication, DNA repair and recombination, and transcription of RNA. Defects in helicases functioning in one or more of these processes can result in characteristic human genetic disorders in which genomic instability and predisposition to cancer are common features. So far, different helicase genes have been found mutated in six such disorders. Mutations in XPB and XPD can result in xeroderma pigmentosum, Cockayne syndrome, or trichothiodystrophy. Mutations in the RecQ-like genes BLM, WRN, and RECQL4 can result in Bloom syndrome, Werner syndrome, and Rothmund-Thomson syndrome, respectively. Because XPB and XPD function in both nucleotide excision repair and transcription initiation, the cellular phenotypes associated with a deficiency of each one of them include failure to repair mutagenic DNA lesions and defects in the recovery of RNA transcription after UV irradiation. The functions of the RecQ-like genes are unknown; however, a growing body of evidence points to a function in restarting DNA replication after the replication fork has become stalled. The genomic instability associated with mutations in the RecQ-like genes includes spontaneous chromosome instability and elevated mutation rates. Mouse models for nearly all of these entities have been developed, and these should help explain the widely different clinical features that are associated with helicase mutations.
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Affiliation(s)
- A J van Brabant
- Department of Human Genetics, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA
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29
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Ng JMY, Vrieling H, Sugasawa K, Ooms MP, Grootegoed JA, Vreeburg JTM, Visser P, Beems RB, Gorgels TGMF, Hanaoka F, Hoeijmakers JHJ, van der Horst GTJ. Developmental defects and male sterility in mice lacking the ubiquitin-like DNA repair gene mHR23B. Mol Cell Biol 2002; 22:1233-45. [PMID: 11809813 PMCID: PMC134644 DOI: 10.1128/mcb.22.4.1233-1245.2002] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
mHR23B encodes one of the two mammalian homologs of Saccharomyces cerevisiae RAD23, a ubiquitin-like fusion protein involved in nucleotide excision repair (NER). Part of mHR23B is complexed with the XPC protein, and this heterodimer functions as the main damage detector and initiator of global genome NER. While XPC defects exist in humans and mice, mutations for mHR23A and mHR23B are not known. Here, we present a mouse model for mHR23B. Unlike XPC-deficient cells, mHR23B(-/-) mouse embryonic fibroblasts are not UV sensitive and retain the repair characteristics of wild-type cells. In agreement with the results of in vitro repair studies, this indicates that mHR23A can functionally replace mHR23B in NER. Unexpectedly, mHR23B(-/-) mice show impaired embryonic development and a high rate (90%) of intrauterine or neonatal death. Surviving animals display a variety of abnormalities, including retarded growth, facial dysmorphology, and male sterility. Such abnormalities are not observed in XPC and other NER-deficient mouse mutants and point to a separate function of mHR23B in development. This function may involve regulation of protein stability via the ubiquitin/proteasome pathway and is not or only in part compensated for by mHR23A.
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Affiliation(s)
- Jessica M Y Ng
- MGC-Department of Cell Biology and Genetics, Centre for Biomedical Genetics, Erasmus University Rotterdam, Rotterdam, The Netherlands
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30
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Sweder K, Madura K. Regulation of repair by the 26S proteasome. J Biomed Biotechnol 2002; 2:94-105. [PMID: 12488589 PMCID: PMC153791 DOI: 10.1155/s1110724302205033] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2002] [Accepted: 05/10/2002] [Indexed: 11/17/2022] Open
Abstract
Cellular processes such as transcription and DNA repair may be regulated through diverse mechanisms, including RNA synthesis, protein synthesis, posttranslational modification and protein degradation. The 26S proteasome, which is responsible for degrading a broad spectrum of proteins, has been shown to interact with several nucleotide excision repair proteins, including xeroderma pigmentosum B protein (XPB), Rad4, and Rad23. Rad4 and Rad23 form a complex that binds preferentially to UV-damaged DNA. The 26S proteasome may regulate repair by degrading DNA repair proteins after repair is completed or, alternatively, the proteasome may act as a molecular chaperone to promote disassembly of the repair complex. In either case, the interaction between the proteasome and nucleotide excision repair depends on proteins like Rad23 that bind ubiquitin-conjugated proteins and the proteasome. While the iteration between Rad4 and Rad23 is well established, it will be interesting to determine what other proteins are regulated in a Rad23-dependent manner.
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Affiliation(s)
- K. Sweder
- Susan Lehman Cullman Laboratory for Cancer Research, Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 164 Frelinghuysen Road, Piscataway, NJ 08854-8020, USA
| | - K. Madura
- Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, 675 Hoes Lane, Piscataway, NJ 08854-5635, USA
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31
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Gillette TG, Huang W, Russell SJ, Reed SH, Johnston SA, Friedberg EC. The 19S complex of the proteasome regulates nucleotide excision repair in yeast. Genes Dev 2001; 15:1528-39. [PMID: 11410533 PMCID: PMC312714 DOI: 10.1101/gad.869601] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Previous studies suggest that the amino-terminal ubiquitin-like (ubl) domain of Rad23 protein can recruit the proteasome for a stimulatory role during nucleotide excision repair in the yeast Saccharomyces cerevisiae. In this report, we show that the 19S regulatory complex of the yeast proteasome can affect nucleotide excision repair independently of Rad23 protein. Strains with mutations in 19S regulatory subunits (but not 20S subunits) of the proteasome promote partial recovery of nucleotide excision repair in vivo in rad23 deletion mutants, but not in other nucleotide excision repair-defective strains tested. In addition, a strain that expresses a temperature-degradable ATPase subunit of the 19S regulatory complex manifests a dramatically increased rate of nucleotide excision repair in vivo. These data indicate that the 19S regulatory complex of the 26S proteasome can negatively regulate the rate of nucleotide excision repair in yeast and suggest that Rad23 protein not only recruits the 19S regulatory complex, but also can mediate functional interactions between the 19S regulatory complex and the nucleotide excision repair machinery. The 19S regulatory complex of the yeast proteasome functions in nucleotide excision repair independent of proteolysis.
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Affiliation(s)
- T G Gillette
- Laboratory of Molecular Pathology, Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9072, USA
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32
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Clarke DJ, Mondesert G, Segal M, Bertolaet BL, Jensen S, Wolff M, Henze M, Reed SI. Dosage suppressors of pds1 implicate ubiquitin-associated domains in checkpoint control. Mol Cell Biol 2001; 21:1997-2007. [PMID: 11238935 PMCID: PMC86795 DOI: 10.1128/mcb.21.6.1997-2007.2001] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In budding yeast, anaphase initiation is controlled by ubiquitin-dependent degradation of Pds1p. Analysis of pds1 mutants implicated Pds1p in the DNA damage, spindle assembly, and S-phase checkpoints. Though some components of these pathways are known, others remain to be identified. Moreover, the essential function of Pds1p, independent of its role in checkpoint control, has not been elucidated. To identify loci that genetically interact with PDS1, we screened for dosage suppressors of a temperature-sensitive pds1 allele, pds1-128, defective for checkpoint control at the permissive temperature and essential for viability at 37 degrees C. Genetic and functional interactions of two suppressors are described. RAD23 and DDI1 suppress the temperature and hydroxyurea, but not radiation or nocodazole, sensitivity of pds1-128. rad23 and ddi1 mutants are partially defective in S-phase checkpoint control but are proficient in DNA damage and spindle assembly checkpoints. Therefore, Rad23p and Ddi1p participate in a subset of Pds1p-dependent cell cycle controls. Both Rad23p and Ddi1p contain ubiquitin-associated (UBA) domains which are required for dosage suppression of pds1-128. UBA domains are found in several proteins involved in ubiquitin-dependent proteolysis, though no function has been assigned to them. Deletion of the UBA domains of Rad23p and Ddi1p renders cells defective in S-phase checkpoint control, implicating UBA domains in checkpoint signaling. Since Pds1p destruction, and thus checkpoint regulation of mitosis, depends on ubiquitin-dependent proteolysis, we propose that the UBA domains functionally interact with the ubiquitin system to control Pds1p degradation in response to checkpoint activation.
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Affiliation(s)
- D J Clarke
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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33
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Lommel L, Chen L, Madura K, Sweder K. The 26S proteasome negatively regulates the level of overall genomic nucleotide excision repair. Nucleic Acids Res 2000; 28:4839-45. [PMID: 11121474 PMCID: PMC115242 DOI: 10.1093/nar/28.24.4839] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Regulation of protein expression can be achieved through destruction of proteins by the 26S: proteasome. Cellular processes that are regulated by proteolysis include cell cycle progression, stress responses and differentiation. Several nucleotide excision repair proteins in yeast and humans, such as Rad23, Rad4 and XPB, have been shown to co-purify with Cim3 and Cim5, AAA ATPases of the 19S: proteasome regulatory subunit. However, it has not been determined if nucleotide excision repair is regulated through protein destruction. We measured nucleotide excision repair in yeast mutants that are defective in proteasome function and found that the repair of the transcribed and non-transcribed strands of an RNA polymerase II-transcribed reporter gene was increased in the absence of proteasome function. Additionally, overexpression of the Rad4 repair protein, which is bound to the repair/proteolytic factor Rad23, conferred higher rates of nucleotide excision repair. Based on our data we suggest that a protein (or proteins) involved in nucleotide excision repair or in regulation of repair is degraded by the 26S proteasome. We propose that decreased proteasome function enables increased DNA repair, due to the transient accumulation of a specific repair factor, perhaps Rad4.
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Affiliation(s)
- L Lommel
- Laboratory for Cancer Research, College of Pharmacy, Rutgers, The State University of New Jersey, 164 Frelinghuysen Road, Piscataway, NJ 08854-8020, USA
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34
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Conconi A, Jager-Vottero P, Zhang X, Beard BC, Smerdon MJ. Mitotic viability and metabolic competence in UV-irradiated yeast cells. Mutat Res 2000; 459:55-64. [PMID: 10677683 DOI: 10.1016/s0921-8777(99)00057-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Colony formation is the classic method for measuring survival of yeast cells. This method measures mitotic viability and can underestimate the fraction of cells capable of carrying out other DNA processing events. Here, we report an alternative method, based on cell metabolism, to determine the fraction of surviving cells after ultraviolet (UV) irradiation. The reduction of 2,3,5-triphenyl tetrazolium chloride (or TTC) to formazan in mitochondria was compared with cell colony formation and DNA repair capacity in wt cells and two repair-deficient strains (rad1Delta and rad7Delta). Both TTC reduction and cell colony formation gave a linear response with different ratios of mitotically viable cells and heat-inactivated cells. However, monitoring the formation of formazan in non-dividing yeast cells that are partially (rad7Delta) or totally (wt) proficient at DNA repair is a more accurate measure of cell survival after UV irradiation. Before repair of UV photoproducts (cis-syn cyclobutane pyrimidine dimers or CPDs) is complete, these two assays give very different results, implying that many damaged cells are metabolically competent but cannot replicate. For example, only 25% of the rad7Delta cells are mitotically viable after a UV dose of 12 J/m(2)75% of these cells are metabolically competent and remove over 55% of the CPDs from their genomic DNA. Moreover, repair of CPDs in wt cells dramatically decreases after the first few hours of liquid holding (L.H.; incubation in water) and correlates with a substantial decrease in cell metabolism over the same time period. In contrast, cell colony formation may be the more accurate indicator of cell survival after UV irradiation of rad1Delta cells (i.e., cells with little DNA repair activity). These results indicate that the metabolic competence of UV-irradiated, non-dividing yeast cells is a much better indicator of cell survival than mitotic viability in partially (or totally) repair proficient yeast cultures.
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Affiliation(s)
- A Conconi
- Department of Biochemistry and Biophysics, Washington State University, Pullman, WA 99164-4660, USA
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35
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Lombaerts M, Goeloe JI, den Dulk H, Brandsma JA, Brouwer J. Identification and characterization of the rhp23(+) DNA repair gene in Schizosaccharomyces pombe. Biochem Biophys Res Commun 2000; 268:210-5. [PMID: 10652237 DOI: 10.1006/bbrc.2000.2100] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have identified rhp23(+), the ortholog of the Saccharomyces cerevisiae RAD23 and human HHR23A and HHR23B genes, in Schizosaccharomyces pombe and examined its role in cell survival and DNA repair. In S. pombe two repair mechanisms are operative on UV-induced photoproducts, i.e., UV damage repair (UVDR) and nucleotide excision repair (NER). Here we show that Rhp23 is solely involved in NER and study its role in DNA repair in the absence of the UVDR pathway. S. pombe rhp23-deficient cells are sensitive toward UV irradiation, although not as sensitive as complete NER-deficient cells. Furthermore we demonstrate that the residual survival observed in rhp23-deficient cells is NER dependent. Despite this NER-dependent survival, uvde rhp23 double mutants are unable to repair cyclobutane pyrimidine dimers. The inability to remove these photolesions from both DNA strands clearly demonstrates that rhp23(+) is involved in transcription coupled repair as well as global genome repair.
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Affiliation(s)
- M Lombaerts
- Medical Genetics Centre South-West Netherlands, Leiden University, Leiden, 2300 RA, The Netherlands
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36
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Iwanejko L, Smith KN, Loeillet S, Nicolas A, Fabre F. Disruption and functional analysis of six ORFs on chromosome XV: YOL117w, YOL115w ( TRF4), YOL114c, YOL112w ( MSB4), YOL111c and YOL072w. Yeast 1999; 15:1529-39. [PMID: 10514570 DOI: 10.1002/(sici)1097-0061(199910)15:14<1529::aid-yea457>3.0.co;2-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
We have carried out the systematic disruption of six ORFs on chromosome XV, of Saccharomyces cerevisiae using the long flanking homology technique to replace each with the KanMX cassette; we have also constructed plasmids containing replacement cassettes and cognate clones for each ORF. Disruption of three of the ORFs-YOL117w, YOL114c, and YOL112w (also known as MSB4)-does not result in any noteworthy phenotype with respect to temperature or nutritional requirements, but yol112w mutants with an additional disruption of YNL293w, which encodes a protein similar to Yol112w, exhibit a slow growth phenotype. The protein specified by YOL114c shares similarity with the human DS-1 protein. Disruption of YOL115w confers slow growth, cold sensitivity and poor sporulation; this ORF has been described elsewhere as TRF4, which encodes a topoisomerase I-related protein. Cells with disruptions of YOL111c, whose product is weakly similar to the human ubiquitin-like protein GdX, are slightly impaired in mating. Mutants disrupted for YOL072w, the predicted product of which is unrelated to any protein of known function, grow slowly, are cold-sensitive and sporulate with reduced efficiency.
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Affiliation(s)
- L Iwanejko
- Institut Curie, Section de Recherche, CNRS UMR 144, 26 Rue d'Ulm, 75248 Paris Cedex 05, France
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37
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Abstract
The main pathway by which mammalian cells remove DNA damage caused by UV light and some other mutagens is nucleotide excision repair (NER). The best characterised components of the human NER process are those proteins defective in the inherited disorder xeroderma pigmentosum (XP). The proteins known to be involved in the first steps of the NER reaction (damage recognition and incision-excision) are heterotrimeric RPA, XPA, the 6 to 9 subunit TFIIH, XPC-hHR23B, XPG, and ERCC1-XPF. Many interactions between these proteins have been found in recent years using different methods both in mammalian cells and for the homologous proteins in yeast. There are virtually no quantitative measurements of the relative strengths of these interactions. Higher order associations between these proteins in solution and even the existence of a complete "repairosome" complex have been reported, which would have implications both for the mechanism of repair and for the interplay between NER and other cellular processes. Nevertheless, evidence for a completely pre-assembled functional repairosome in solution is inconclusive and the order of action of repair factors on damaged DNA is uncertain.
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Affiliation(s)
- S J Araújo
- Imperial Cancer Research Fund, Clare Hall Laboratories, South Mimms, Hertfordshire, UK
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38
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Russell SJ, Reed SH, Huang W, Friedberg EC, Johnston SA. The 19S regulatory complex of the proteasome functions independently of proteolysis in nucleotide excision repair. Mol Cell 1999; 3:687-95. [PMID: 10394357 DOI: 10.1016/s1097-2765(01)80001-0] [Citation(s) in RCA: 164] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The 26S proteasome degrades proteins targeted by the ubiquitin pathway, a function thought to explain its role in cellular processes. The proteasome interacts with the ubiquitin-like N terminus of Rad23, a nucleotide excision repair (NER) protein, in Saccharomyces cerevisiae. Deletion of the ubiquitin-like domain causes UV radiation sensitivity. Here, we show that the ubiquitin-like domain of Rad23 is required for optimal activity of an in vitro NER system. Inhibition of proteasomal ATPases diminishes NER activity in vitro and increases UV sensitivity in vivo. Surprisingly, blockage of protein degradation by the proteasome has no effect on the efficiency of NER. This establishes that the regulatory complex of the proteasome has a function independent of protein degradation.
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Affiliation(s)
- S J Russell
- Department of Medicine and Biochemistry, University of Texas Southwestern Medical Center, Dallas 75235, USA
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39
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Smerdon MJ, Conconi A. Modulation of DNA damage and DNA repair in chromatin. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1999; 62:227-55. [PMID: 9932456 DOI: 10.1016/s0079-6603(08)60509-7] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA is packaged in the highly compact and dynamic structure of chromatin in eukaryotic cells. It is generally accepted that DNA processing events in the nucleus, such as transcription, replication, recombination, and repair, are restricted by this packaging. For some processes (e.g., transcription), the chromatin fiber is "preset" in a more open structure to allow access of proteins to specific regions of DNA within this structural hierarchy. These regions contain modified nucleosomes that accommodate a less compact state of chromatin and allow access to specific regions of DNA. DNA repair proteins, however, must access DNA lesions in all structural domains of chromatin after sudden insult to the genome. Damaged DNA must be recognized, removed, and replaced by repair enzymes at all levels of chromatin packaging. Therefore, the modulation of DNA damage and its repair in chromatin is crucial to our understanding of the fate of potential mutagenic and carcinogenic lesions in DNA. In this review, we discuss the modulation of DNA damage and DNA repair by chromatin structure, and the modulation of chromatin structure by these events.
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Affiliation(s)
- M J Smerdon
- Department of Biochemistry and Biophysics, Washington State University, Pullman 99164, USA
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40
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Abstract
Damage to DNA occurs in all living things, and the toxicity and/or mutagenicity of the damage products are reduced through the activities of one or more DNA repair pathways. The mechanisms of DNA repair are best understood in microorganisms and mammals, but the field has recently expanded to include both plants and lower animals. These recent advances in our understanding of the molecular and classical genetics of DNA repair in higher plants include such aspects as the repair of UV-induced pyrimidine dimers, the correction of mismatched bases, and the rejoining of double strand breaks.
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Affiliation(s)
- AB Britt
- Section of Plant Biology, University of California, Davis, CA 95616, USA
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41
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Guzder SN, Sung P, Prakash L, Prakash S. Affinity of yeast nucleotide excision repair factor 2, consisting of the Rad4 and Rad23 proteins, for ultraviolet damaged DNA. J Biol Chem 1998; 273:31541-6. [PMID: 9813069 DOI: 10.1074/jbc.273.47.31541] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Saccharomyces cerevisiae Rad4 and Rad23 proteins are required for the nucleotide excision repair of UV light-damaged DNA. Previous studies have indicated that these two DNA repair proteins are associated in a tight complex, which we refer to as nucleotide excision repair factor 2 (NEF2). In a reconstituted nucleotide excision repair reaction, incision of UV-damaged DNA is dependent on NEF2, indicating a role of NEF2 in an early step of the repair process. NEF2 does not, however, possess an enzymatic activity, and its function in the damage-specific incision reaction has not yet been defined. Here we use a DNA mobility shift assay to demonstrate that NEF2 binds specifically to UV-damaged DNA. Elimination of cyclobutane pyrimidine dimers from the UV-damaged DNA by enzymatic photoreactivation has little effect on the affinity of NEF2 for the DNA, suggesting that NEF2 recognizes the 6-(1, 2)-dihydro-2-oxo-4-pyrimidinyl)-5-methyl-2,4-(1H,3H)-pyrimidinedione photoproducts in the damaged DNA. These results highlight the intricacy of the DNA damage-demarcation reaction during nucleotide excision repair in eukaryotes.
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Affiliation(s)
- S N Guzder
- Sealy Center for Molecular Science, University of Texas Medical Branch, Galveston, Texas 77555-1061, USA
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42
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Gragerov A, Kino T, Ilyina-Gragerova G, Chrousos GP, Pavlakis GN. HHR23A, the human homologue of the yeast repair protein RAD23, interacts specifically with Vpr protein and prevents cell cycle arrest but not the transcriptional effects of Vpr. Virology 1998; 245:323-30. [PMID: 9636371 DOI: 10.1006/viro.1998.9138] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Yeast two-hybrid selection of proteins interacting with human immunodeficiency virus type 1 Vpr identified HHR23A, a human homologue of the yeast DNA repair protein RAD23, as a specific interactor. A small 57-amino-acid C-terminal portion of HHR23A was sufficient for Vpr interaction. When introduced into human cells by transfection, full-length HHR23A or its C-terminal fragments were able to alleviate Vpr-induced cell cycle arrest, suggesting that HHR23A may participate in the pathway leading to G2 arrest by Vpr. We have also examined the effects of HHR23 on the recently identified transcription coactivator function of Vpr. The two Vpr functions are independent, since we have identified mutants lacking either the cell cycle arrest or the coactivator function. Our analysis showed that excess of HHR23A does not affect the coactivator function of Vpr, while it affects the cell cycle arresting function. Therefore, a simple sequestering model for Vpr in the presence of excess HHR23A is not supported. We propose that the interaction of HHR23A with Vpr may affect specifically pathways leading to cell cycle regulation.
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Affiliation(s)
- A Gragerov
- ABL-Basic Research Program, NCI-Frederick Cancer Research and Development Center, Maryland 21702-1201, USA
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43
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Abstract
Numerous studies have demonstrated a requirement in plants for repair of DNA damage arising from either intrinsic or extrinsic sources. Investigations also have revealed a capacity for repair of certain types of DNA damage, and conversely, identified mutants apparently defective in such repair. This article provides a concise overview of nuclear DNA repair mechanisms in higher plants, particularly those processes concerned with the repair of UV-induced lesions, and includes surveys of UV-sensitive mutants and genes implicated in DNA repair.
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Affiliation(s)
- E J Vonarx
- School of Biological and Chemical Sciences, Deakin University, Geelong, Victoria 3217, Australia
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Sturm A, Lienhard S. Two isoforms of plant RAD23 complement a UV-sensitive rad23 mutant in yeast. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 1998; 13:815-821. [PMID: 9681019 DOI: 10.1046/j.1365-313x.1998.00075.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
DNA repair by nucleotide excision (NER) has been demonstrated in plant cells at the biochemical level but until now none of the molecular components of the plant NER complex has been identified. In this paper, the cloning and characterization of two isoforms of RAD23 from carrot (Daucus carota L.) are reported. It has been suggested that RAD23 in yeast is an assembly factor of the NER complex required for transcription-coupled repair as well as efficient overall genome repair. A functional assay demonstrated that both plant homologues complement the UV-sensitive phenotype of a rad23 deletion mutant of yeast. This result suggests that homologous polypeptides may catalyse NER in plants and yeast and, possibly, by a similar mechanism.
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Affiliation(s)
- A Sturm
- Friedrich Miescher Institute, Basel, Switzerland.
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Schauber C, Chen L, Tongaonkar P, Vega I, Lambertson D, Potts W, Madura K. Rad23 links DNA repair to the ubiquitin/proteasome pathway. Nature 1998; 391:715-8. [PMID: 9490418 DOI: 10.1038/35661] [Citation(s) in RCA: 363] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Rad23 is an evolutionarily conserved protein that is important for nucleotide excision repair. A regulatory role has been proposed for Rad23 because rad23 mutants are sensitive to ultraviolet light but are still capable of incising damaged DNA. Here we show that Rad23 interacts with the 26S proteasome through an amino-terminal ubiquitin-like domain (UbL[R23]). The carboxy terminus of Rad23 binds to the Rad4 DNA repair protein and creates a link between the DNA repair and proteasome pathways. The ultraviolet sensitivity caused by deletion of the UbL(R23) domain may therefore arise from its inability to interact with the proteasome. The fusion proteins glutathione S-transferase (GST)-Rad23 and Rad4-haemagglutinin (HA), and the proteasome subunits Cim3 and Cim5, cofractionate through consecutive chromatography steps. The ubiquitin-like domain of human Rad23 (UbL[HRB]) also interacts with the human proteasome. These results demonstrate that ubiquitin-like domains (UbLs) represent a new class of proteasome-interacting motifs.
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Affiliation(s)
- C Schauber
- Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway 08854, USA
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46
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Nucleotide Excision Repair in Yeast: Recent Progress and Implications. DNA Repair (Amst) 1998. [DOI: 10.1007/978-3-642-48770-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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47
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Withers-Ward ES, Jowett JB, Stewart SA, Xie YM, Garfinkel A, Shibagaki Y, Chow SA, Shah N, Hanaoka F, Sawitz DG, Armstrong RW, Souza LM, Chen IS. Human immunodeficiency virus type 1 Vpr interacts with HHR23A, a cellular protein implicated in nucleotide excision DNA repair. J Virol 1997; 71:9732-42. [PMID: 9371639 PMCID: PMC230283 DOI: 10.1128/jvi.71.12.9732-9742.1997] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) vpr gene is an evolutionarily conserved gene among the primate lentiviruses HIV-1, HIV-2, and simian immunodeficiency viruses. One of the unique functions attributed to the vpr gene product is the arrest of cells in the G2 phase of the cell cycle. Here we demonstrate that Vpr interacts physically with HHR23A, one member of an evolutionarily conserved gene family involved in nucleotide excision repair. Interaction of Vpr with HHR23A was initially identified through a yeast two-hybrid screen and was confirmed by the demonstration of direct binding between bacterially expressed recombinant and transiently expressed or chemically synthesized protein products. Visualization of HHR23A and Vpr by indirect immunofluorescence and confocal microscopy indicates that the two proteins colocalize at or about the nuclear membrane. We also map the Vpr-binding domain in HHR23A to a C-terminal 45-amino-acid region of the protein previously shown to have homology to members of the ubiquitination pathway. Overexpression of HHR23A and a truncated derivative which includes the Vpr-binding domain results in a partial alleviation of the G2 arrest induced by Vpr, suggesting that the interaction between Vpr and HHR23A is critical for cell cycle arrest induced by Vpr. These results provide further support for the hypothesis that Vpr interferes with the normal function of a protein or proteins involved in the DNA repair process and, thus, in the transmission of signals that allow cells to transit from the G2 to the M phase of the cell cycle.
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Affiliation(s)
- E S Withers-Ward
- Department of Microbiology and Immunology, UCLA School of Medicine, Los Angeles, California 90095-1678, USA
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Masutani C, Araki M, Sugasawa K, van der Spek PJ, Yamada A, Uchida A, Maekawa T, Bootsma D, Hoeijmakers JH, Hanaoka F. Identification and characterization of XPC-binding domain of hHR23B. Mol Cell Biol 1997; 17:6915-23. [PMID: 9372923 PMCID: PMC232548 DOI: 10.1128/mcb.17.12.6915] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
hHR23B was originally isolated as a component of a protein complex that specifically complements nucleotide excision repair (NER) defects of xeroderma pigmentosum group C cell extracts in vitro and was identified as one of two human homologs of the Saccharomyces cerevisiae NER gene product Rad23. Recombinant hHR23B has previously been shown to significantly stimulate the NER activity of recombinant human XPC protein (rhXPC). In this study we identify and functionally characterize the XPC-binding domain of hHR23B protein. We prepared various internal as well as terminal deletion products of hHR23B protein in a His-tagged form and examined their binding with rhXPC by using nickel-chelating Sepharose. We demonstrate that a domain covering 56 amino acids of hHR23B is required for binding to rhXPC as well as for stimulation of in vitro NER reactions. Interestingly, a small polypeptide corresponding to the XPC-binding domain is sufficient to exert stimulation of XPC NER activity. Comparison with known crystal structures and analysis with secondary structure programs provided strong indications that the binding domain has a predominantly amphipathic alpha-helical character, consistent with evidence that the affinity with XPC is based on hydrophobic interactions. Our work shows that binding to XPC alone is required and sufficient for the role of hHR23B in in vitro NER but does not rule out the possibility that the protein has additional functions in vivo.
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Affiliation(s)
- C Masutani
- Institute for Molecular and Cellular Biology, Osaka University, Suita, Japan
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49
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Reagan MS, Friedberg EC. Recovery of RNA polymerase II synthesis following DNA damage in mutants of Saccharomyces cerevisiae defective in nucleotide excision repair. Nucleic Acids Res 1997; 25:4257-63. [PMID: 9336455 PMCID: PMC147034 DOI: 10.1093/nar/25.21.4257] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We have measured the kinetics of the recovery of mRNA synthesis in the inducible GAL10 and RNR3 genes after exposure of yeast cells to ultraviolet (UV) radiation. Such recovery is abolished in mutant strains defective in nucleotide excision repair (NER) of DNA, including a rad23 mutant. Mutants defective in the RAD7 or RAD16 genes, which are required for the repair of the non-transcribed strand but not the transcribed strand of transcriptionally active genes, show slightly faster recovery of RNA synthesis than wild-type strains. A strain deleted of the RAD26 gene, which is known to be required for strand-specific NER in yeast, manifested delayed recovery of mRNA synthesis, whereas a rad28 mutant, which does not show defective strand-specific repair, showed normal kinetics of recovery. Measurement of the recovery of expression of selected individual yeast genes by Northern analysis following exposure of cells to UV radiation apparently correlates directly with the capacity of cells for strand-specific NER.
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Affiliation(s)
- M S Reagan
- Laboratory of Molecular Pathology, Department of Pathology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75235, USA
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50
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Wang Z, Wei S, Reed SH, Wu X, Svejstrup JQ, Feaver WJ, Kornberg RD, Friedberg EC. The RAD7, RAD16, and RAD23 genes of Saccharomyces cerevisiae: requirement for transcription-independent nucleotide excision repair in vitro and interactions between the gene products. Mol Cell Biol 1997; 17:635-43. [PMID: 9001217 PMCID: PMC231789 DOI: 10.1128/mcb.17.2.635] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Nucleotide excision repair (NER) is a biochemical process required for the repair of many different types of DNA lesions. In the yeast Saccharomyces cerevisiae, the RAD7, RAD16, and RAD23 genes have been specifically implicated in NER of certain transcriptionally repressed loci and in the nontranscribed strand of transcriptionally active genes. We have used a cell-free system to study the roles of the Rad7, Rad16, and Rad23 proteins in NER. Transcription-independent NER of a plasmid substrate was defective in rad7, rad16, and rad23 mutant extracts. Complementation studies with a previously purified NER protein complex (nucleotide excision repairosome) indicate that Rad23 is a component of the repairosome, whereas Rad7 and Rad16 proteins were not found in this complex. Complementation studies with rad4, rad7, rad16, and rad23 mutant extracts suggest physical interactions among these proteins. This conclusion was confirmed by experiments using the yeast two-hybrid assay, which demonstrated the following pairwise interactions: Rad4 with Rad23, Rad4 with Rad7, and Rad7 with Rad16. Additionally, interaction between the Rad7 and Rad16 proteins was demonstrated in vitro. Our results show that Rad7, Rad16, and Rad23 are required for transcription-independent NER in vitro. This process may involve a unique protein complex which is distinct from the repairosome and which contains at least the Rad4, Rad7, and Rad16 proteins.
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Affiliation(s)
- Z Wang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas 75235, USA
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