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Erdemir Sayan S, Sreekumar R, Bhome R, Mirnezami A, Yagci T, Sayan AE. ERCC1 abundance is an indicator of DNA repair-apoptosis decision upon DNA damage. Cell Death Discov 2024; 10:47. [PMID: 38272916 PMCID: PMC10810800 DOI: 10.1038/s41420-024-01817-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 01/06/2024] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
DNA repair is essential for successful propagation of genetic material and fidelity of transcription. Nucleotide excision repair (NER) is one of the earliest DNA repair mechanisms, functionally conserved from bacteria to human. The fact that number of NER genes vary significantly between prokaryotes and metazoans gives the insight that NER proteins have evolved to acquire additional functions to combat challenges associated with a diploid genome, including being involved in the decision between DNA repair and apoptosis. However, no direct association between apoptosis and NER proteins has been shown to date. In this study, we induced apoptosis with a variety of agents, including oxaliplatin, doxorubicin and TRAIL, and observed changes in the abundance and molecular weight of NER complex proteins. Our results showed that XPA, XPC and ERCC1 protein levels change during DNA damage-induced apoptosis. Among these, ERCC1 decrease was observed as a pre-mitochondria depolarisation event which marks the "point of no return" in apoptosis signalling. ERCC1 decrease was due to proteasomal degradation upon lethal doses of oxaliplatin exposure. When ERCC1 protein was stabilised using proteasome inhibitors, the pro-apoptotic activity of oxaliplatin was attenuated. These results explain why clinical trials using proteasome inhibitors and platinum derivatives showed limited efficacy in carcinoma treatment and also the importance of how deep understanding of DNA repair mechanisms can improve cancer therapy.
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Affiliation(s)
- Sule Erdemir Sayan
- Department of Molecular Biology and Genetics, Gebze Technical University, Kocaeli, 41400, Turkey
| | - Rahul Sreekumar
- Cancer Sciences Unit, University of Southampton, Southampton General Hospital, Somers Cancer Research Building, Southampton, SO16 6YD, UK
| | - Rahul Bhome
- Cancer Sciences Unit, University of Southampton, Southampton General Hospital, Somers Cancer Research Building, Southampton, SO16 6YD, UK
| | - Alex Mirnezami
- Cancer Sciences Unit, University of Southampton, Southampton General Hospital, Somers Cancer Research Building, Southampton, SO16 6YD, UK
| | - Tamer Yagci
- Department of Molecular Biology and Genetics, Gebze Technical University, Kocaeli, 41400, Turkey
| | - A Emre Sayan
- Cancer Sciences Unit, University of Southampton, Southampton General Hospital, Somers Cancer Research Building, Southampton, SO16 6YD, UK.
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2
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Pinto ÉSM, Krause MJ, Dorn M, Feltes BC. The nucleotide excision repair proteins through the lens of molecular dynamics simulations. DNA Repair (Amst) 2023; 127:103510. [PMID: 37148846 DOI: 10.1016/j.dnarep.2023.103510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 04/07/2023] [Accepted: 04/23/2023] [Indexed: 05/08/2023]
Abstract
Mutations that affect the proteins responsible for the nucleotide excision repair (NER) pathway can lead to diseases such as xeroderma pigmentosum, trichothiodystrophy, Cockayne syndrome, and Cerebro-oculo-facio-skeletal syndrome. Hence, understanding their molecular behavior is needed to elucidate these diseases' phenotypes and how the NER pathway is organized and coordinated. Molecular dynamics techniques enable the study of different protein conformations, adaptable to any research question, shedding light on the dynamics of biomolecules. However, as important as they are, molecular dynamics studies focused on DNA repair pathways are still becoming more widespread. Currently, there are no review articles compiling the advancements made in molecular dynamics approaches applied to NER and discussing: (i) how this technique is currently employed in the field of DNA repair, focusing on NER proteins; (ii) which technical setups are being employed, their strengths and limitations; (iii) which insights or information are they providing to understand the NER pathway or NER-associated proteins; (iv) which open questions would be suited for this technique to answer; and (v) where can we go from here. These questions become even more crucial considering the numerous 3D structures published regarding the NER pathway's proteins in recent years. In this work, we tackle each one of these questions, revising and critically discussing the results published in the context of the NER pathway.
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Affiliation(s)
| | - Mathias J Krause
- Institute for Applied and Numerical Mathematics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Márcio Dorn
- Center for Biotechnology, Federal University of Rio Grande do Sul, RS, Brazil; Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil
| | - Bruno César Feltes
- Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
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3
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Reyes HH, Lin YC, Hsu CK, Guevara BEK. A novel XPA splice-site mutation identified in a 4-year-old Filipino girl with xeroderma pigmentosum. Australas J Dermatol 2023; 64:e165-e167. [PMID: 36866916 DOI: 10.1111/ajd.14015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/08/2023] [Accepted: 02/11/2023] [Indexed: 03/04/2023]
Abstract
We herein report a case of a 4-year-old Filipino girl initially seen through online consultation from a general physician. She was born to a 22-year-old primigravid mother, with no birth complications nor a history of consanguinity in the family. During the 1st month of life, she developed hyperpigmented macules over the face, neck, upper back, and limbs, which were exacerbated by sun exposure. At 2 years old, she developed a solitary erythematous papule on the nasal area, which gradually enlarged within one year and developed into an exophytic ulcerating tumor extending to the right supra-alar crease. Xeroderma pigmentosum and squamous cell carcinoma were confirmed by whole-exome sequencing and skin biopsy, respectively.
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Affiliation(s)
- Haider H Reyes
- Department of Dermatology, Southern Philippines Medical Center, Davao City, Philippines
| | - Yu-Chen Lin
- Department of Dermatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chao-Kai Hsu
- Department of Dermatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Bryan Edgar K Guevara
- Department of Dermatology, Southern Philippines Medical Center, Davao City, Philippines.,Brokenshire College School of Medicine, Davao City, Philippines
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4
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Feltes BC. Revisiting the structural features of the xeroderma pigmentosum proteins: Focus on mutations and knowledge gaps. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 789:108416. [PMID: 35690419 DOI: 10.1016/j.mrrev.2022.108416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 06/15/2023]
Abstract
The nucleotide excision repair pathway is a broadly studied DNA repair mechanism because impairments of its key players, the xeroderma pigmentosum proteins (XPA to XPG), are associated with multiple hereditary diseases. Due to the massive number of novel mutations reported for these proteins and new structural data published every year, proper categorization and discussion of relevant observations is needed to organize this extensive inflow of knowledge. This review aims to revisit the structural data of all XP proteins while updating it with the information developed in of the past six years. Discussions and interpretations of mutation outcomes, mechanisms of action, and knowledge gaps regarding their structures are provided, as well as new perspectives based on recent research.
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Affiliation(s)
- Bruno César Feltes
- Department of Theoretical Informatics, Institute of Informatics, Department of Theoretical Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Department of Genetics, Institute of Bioscience, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Department of Biophysics, Institute of Bioscience, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil.
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5
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Lehky TJ, Sackstein P, Tamura D, Quezado M, Wu T, Khan SG, Patronas NJ, Wiggs E, Brewer CC, DiGiovanna JJ, Kraemer KH. Differences in peripheral neuropathy in xeroderma pigmentosum complementation groups A and D as evaluated by nerve conduction studies. BMC Neurol 2021; 21:393. [PMID: 34627174 PMCID: PMC8501575 DOI: 10.1186/s12883-021-02414-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 09/22/2021] [Indexed: 12/14/2022] Open
Abstract
Background Xeroderma pigmentosum (XP) is a rare autosomal recessive genetic disorder with defective DNA nucleotide excision repair and associated with a high frequency of skin cancer. Approximately 25% of patients develop progressive neurological degeneration. Complementation groups XP-A and XP-D are most frequently associated with neurological disorders. Design/methods This is a retrospective review of patients with XP who were evaluated at NIH from 1986 to 2015 and had nerve conduction studies (NCS). In the complementation groups with peripheral neuropathy, further comparisons of the NCS were made with audiological, brain imaging, neuropsychological assessments that were also performed on most of the patients. Limited neuropathology of XP-A and XP-D patients were examined.. Results The 33 patients had NCS: XP-A (9 patients), XP-C (7 patients), XP-D (10 patients), XP-E (1 patient), XP-V (4 patients), and XP-unknown (2 patients). Peripheral neuropathy based on nerve conduction studies was documented only in two complementation groups: 78% (7/9) of XP-A patients had a sensorimotor neuropathy while 50% (5/10) of XP-D patients had a sensory neuropathy only. Analysis of sural sensory nerve amplitude in both complementation groups XP-A and XP-D correlated with sensorineural hearing loss (SNHL), MRI/CT severity, and Full-scale Intelligence Quotient (IQ). Analysis of fibular motor nerve amplitude in complementation XP-A correlated with SNHL and MRI/CT severity. Limited follow-up studies showed gradual loss of NCS responses compared to an earlier and more rapid progression of the hearing loss. Conclusions Despite similar brain imaging and audiological findings patients, XP-A and XP-D complementation groups differ in the type of neuropathy, sensorimotor versus sensory alone. A few cases suggest that sensorineural hearing loss may precede abnormal NCS in XP and therefore serve as valuable clinical indicators of XP patients that will later develop peripheral neuropathy.
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Affiliation(s)
| | - Paul Sackstein
- Laboratory of Cancer Biology and Genetics NCI, NIH, Bethesda, MD, USA.,Medstar Georgetown University Hospital, Washington, DC, USA
| | - Deborah Tamura
- Laboratory of Cancer Biology and Genetics NCI, NIH, Bethesda, MD, USA
| | | | - Tianxia Wu
- Clinical Trials Unit, NINDS, NIH, Bethesda, MD, USA
| | - Sikandar G Khan
- Laboratory of Cancer Biology and Genetics NCI, NIH, Bethesda, MD, USA
| | | | - Edythe Wiggs
- Clinical Trials Unit, NINDS, NIH, Bethesda, MD, USA
| | | | - John J DiGiovanna
- Laboratory of Cancer Biology and Genetics NCI, NIH, Bethesda, MD, USA
| | - Kenneth H Kraemer
- Laboratory of Cancer Biology and Genetics NCI, NIH, Bethesda, MD, USA
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6
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Feltes BC. Every protagonist has a sidekick: Structural aspects of human xeroderma pigmentosum-binding proteins in nucleotide excision repair. Protein Sci 2021; 30:2187-2205. [PMID: 34420242 DOI: 10.1002/pro.4173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 12/30/2022]
Abstract
The seven xeroderma pigmentosum proteins (XPps), XPA-XPG, coordinate the nucleotide excision repair (NER) pathway, promoting the excision of DNA lesions caused by exposition to ionizing radiation, majorly from ultraviolet light. Significant efforts are made to investigate NER since mutations in any of the seven XPps may cause the xeroderma pigmentosum and trichothiodystrophy diseases. However, these proteins collaborate with other pivotal players in all known NER steps to accurately exert their purposes. Therefore, in the old and ever-evolving field of DNA repair, it is imperative to reexamine and describe their structures to understand NER properly. This work provides an up-to-date review of the protein structural aspects of the closest partners that directly interact and influence XPps: RAD23B, CETN2, DDB1, RPA (RPA70, 32, and 14), p8 (GTF2H5), and ERCC1. Structurally and functionally vital domains, regions, and critical residues are reexamined, providing structural lessons and perspectives about these indispensable proteins in the NER and other DNA repair pathways. By gathering all data related to the major human xeroderma pigmentosum-interacting proteins, this review will aid newcomers on the subject and guide structural and functional future studies.
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Affiliation(s)
- Bruno César Feltes
- Department of Theoretical Informatics, Institute of Informatics, Department of Theoretical Informatics, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
- Department of Genetics, Institute of Bioscience, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
- Department of Biophysics, Institute of Bioscience, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
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7
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D'Amico AM, Vasquez KM. The multifaceted roles of DNA repair and replication proteins in aging and obesity. DNA Repair (Amst) 2021; 99:103049. [PMID: 33529944 DOI: 10.1016/j.dnarep.2021.103049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/12/2021] [Accepted: 01/14/2021] [Indexed: 12/14/2022]
Abstract
Efficient mechanisms for genomic maintenance (i.e., DNA repair and DNA replication) are crucial for cell survival. Aging and obesity can lead to the dysregulation of genomic maintenance proteins/pathways and are significant risk factors for the development of cancer, metabolic disorders, and other genetic diseases. Mutations in genes that code for proteins involved in DNA repair and DNA replication can also exacerbate aging- and obesity-related disorders and lead to the development of progeroid diseases. In this review, we will discuss the roles of various DNA repair and replication proteins in aging and obesity as well as investigate the possible mechanisms by which aging and obesity can lead to the dysregulation of these proteins and pathways.
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Affiliation(s)
- Alexandra M D'Amico
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Boulevard, Austin, TX, 78723, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Boulevard, Austin, TX, 78723, USA.
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8
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Feltrin RDS, Segatto ALA, de Souza TA, Schuch AP. Open gaps in the evolution of the eukaryotic nucleotide excision repair. DNA Repair (Amst) 2020; 95:102955. [DOI: 10.1016/j.dnarep.2020.102955] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 08/06/2020] [Accepted: 08/16/2020] [Indexed: 12/24/2022]
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9
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Yan S, Vaziri C. An introduction for the special issue on environmental health and genome integrity. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:660-663. [PMID: 32683747 PMCID: PMC7442621 DOI: 10.1002/em.22400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 05/23/2023]
Abstract
Environmental exposures and genome maintenance mechanisms that respond to environmentally-induced genotoxicity have a profound impact on human health. Eight review articles in this Special Issue (SI) titled "Environmental Health and Genome Integrity" describe emerging new mechanisms by which distinct forms of environmentally-induced DNA damage are remediated, and explain how DNA repair pathway choices impact genome integrity and disease propensity. Here, we provide an introduction to reviews from this SI. Our expanding knowledge of how genotoxic exposures impact the genome will allow us to better predict, prevent and treat environmentally-induced human diseases such as cancer and neurodegenerative disorders.
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Affiliation(s)
- Shan Yan
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina
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10
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Abstract
Nucleotide excision repair (NER) is a highly conserved mechanism to remove helix-distorting DNA lesions. A major substrate for NER is DNA damage caused by environmental genotoxins, most notably ultraviolet radiation. Xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy are three human disorders caused by inherited defects in NER. The symptoms and severity of these diseases vary dramatically, ranging from profound developmental delay to cancer predisposition and accelerated ageing. All three syndromes include developmental abnormalities, indicating an important role for optimal transcription and for NER in protecting against spontaneous DNA damage during embryonic development. Here, we review the current knowledge on genes that function in NER that also affect embryonic development, in particular the development of a fully functional nervous system.
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Affiliation(s)
- Sofia J Araújo
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain.,Institute of Biomedicine, University of Barcelona (IBUB), Barcelona, Spain
| | - Isao Kuraoka
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
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11
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Swope VB, Starner RJ, Rauck C, Abdel-Malek ZA. Endothelin-1 and α-melanocortin have redundant effects on global genome repair in UV-irradiated human melanocytes despite distinct signaling pathways. Pigment Cell Melanoma Res 2019; 33:293-304. [PMID: 31505093 DOI: 10.1111/pcmr.12823] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 08/19/2019] [Accepted: 08/27/2019] [Indexed: 12/26/2022]
Abstract
Human melanocyte homeostasis is sustained by paracrine factors that reduce the genotoxic effects of ultraviolet radiation (UV), the major etiological factor for melanoma. The keratinocyte-derived endothelin-1 (End-1) and α-melanocyte-stimulating hormone (α-MSH) regulate human melanocyte function, proliferation and survival, and enhance repair of UV-induced DNA photoproducts by binding to the Gq - and Gi -protein-coupled endothelin B receptor (EDNRB), and the Gs -protein-coupled melanocortin 1 receptor (MC1R), respectively. We hereby report that End-1 and α-MSH regulate common effectors of the DNA damage response to UV, despite distinct signaling pathways. Both factors activate the two DNA damage sensors ataxia telangiectasia and Rad3-related and ataxia telangiectasia mutated, enhance DNA damage recognition by reducing soluble nuclear and chromatin-bound DNA damage binding protein 2, and increase total and chromatin-bound xeroderma pigmentosum (XP) C. Additionally, α-MSH and End-1 increase total levels and chromatin localization of the damage verification protein XPA, and the levels of γH2AX, which facilitates recruitment of DNA repair proteins to DNA lesions. Activation of EDNRB compensates for MC1R loss of function, thereby reducing the risk of malignant transformation of these vulnerable melanocytes. Therefore, MC1R and EDNRB signaling pathways represent redundant mechanisms that inhibit the genotoxic effects of UV and melanomagenesis.
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Affiliation(s)
- Viki B Swope
- Department of Dermatology, University of Cincinnati, Cincinnati, OH, USA
| | - Renny J Starner
- Department of Dermatology, University of Cincinnati, Cincinnati, OH, USA
| | - Corinne Rauck
- Department of Dermatology, University of Cincinnati, Cincinnati, OH, USA
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12
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Chitale S, Richly H. H4K20me2: Orchestrating the recruitment of DNA repair factors in nucleotide excision repair. Nucleus 2019; 9:212-215. [PMID: 29482435 PMCID: PMC5973261 DOI: 10.1080/19491034.2018.1444327] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The integrity of the genome is maintained by specific DNA repair pathways. The main pathway removing DNA lesions induced by exposure to UV light is nucleotide excision repair (NER). The DNA damage response at chromatin is accompanied by the recruitment of DNA repair factors to the lesion site and the deposition of specific histone marks. The function of these histone marks in NER stays for the most part elusive. We have recently reported that the methyltransferase MMSET catalyzes the dimethylation of histone H4 at lysine 20 (H4K20me2) at the lesion site. The deposition of H4K20me2 at DNA damage sites elicits the recruitment of the NER factor XPA providing evidence for an H4K20me2-dependent DNA repair factor recruitment mechanism during lesion recognition in the global-genomic branch of NER. Here we discuss how H4K20me2 might impact on the chromatin conformation and the DNA damage response.
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Affiliation(s)
- Shalaka Chitale
- a Laboratory of Molecular Epigenetics , Institute of Molecular Biology (IMB) , Mainz , Germany.,b Faculty of Biology , Johannes Gutenberg University , Mainz , Germany
| | - Holger Richly
- a Laboratory of Molecular Epigenetics , Institute of Molecular Biology (IMB) , Mainz , Germany
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13
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Zádori D, Szpisjak L, Németh IB, Reisz Z, Kovacs GG, Szépfalusi N, Németh VL, Maróti Z, Tóth-Molnár E, Oláh J, Vécsei L, Klivényi P, Kalmár T. Predominant neurological phenotype in a Hungarian family with two novel mutations in the XPA gene-case series. Neurol Sci 2019; 41:125-129. [PMID: 31478152 PMCID: PMC6940312 DOI: 10.1007/s10072-019-04044-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 08/13/2019] [Indexed: 11/25/2022]
Abstract
OBJECTIVE The prevalence of xeroderma pigmentosum (XP) is quite low in Europe, which may result in a delay in determining the appropriate diagnosis. Furthermore, some subtypes of XP, including XPA, may manifest themselves with quite severe neurological symptoms in addition to the characteristic dermatological lesions. Accordingly, the aim of the current study is to highlight the predominant neurological aspects of XPA, as well as mild-to-moderate dermatological signs in a Hungarian family with 5 affected siblings. CASE REPORTS The symptoms of the Caucasian male proband started to develop at 13-14 years of age with predominantly cerebellar, hippocampal, and brainstem alterations. His elder sister and three younger brothers all presented similar, but less expressed neurological signs. The diagnostic work-up, including clinical exome sequencing, revealed 2 novel compound heterozygous mutations (p.Gln146_Tyr148delinsHis, p.Arg258TyrfsTer5) in the XPA gene. Surprisingly, only mild-to-moderate dermatological alterations were observed, and less severe characteristic ophthalmological and auditory signs were detected. CONCLUSIONS In summary, we present the first family with genetically confirmed XPA in the Central-Eastern region of Europe, clearly supporting the notion that disturbed function of the C-terminal region of the XPA protein contributes to the development of age-dependent neurologically predominant signs. This case series may help clinicians recognize this rare disorder.
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Affiliation(s)
- Dénes Zádori
- Department of Neurology, Faculty of Medicine, Albert Szent-Györgyi Clinical Center, University of Szeged, Szeged, Hungary
| | - László Szpisjak
- Department of Neurology, Faculty of Medicine, Albert Szent-Györgyi Clinical Center, University of Szeged, Szeged, Hungary
| | - István Balázs Németh
- Department of Dermatology and Allergology, Faculty of Medicine, Albert Szent-Györgyi Clinical Center, University of Szeged, Szeged, Hungary
| | - Zita Reisz
- Department of Pathology, Faculty of Medicine, Albert Szent-Györgyi Clinical Center, University of Szeged, Szeged, Hungary
| | - Gabor G Kovacs
- Institute of Neurology, Medical University of Vienna, Vienna, Austria
| | - Noémi Szépfalusi
- Department of Neurology, Faculty of Medicine, Albert Szent-Györgyi Clinical Center, University of Szeged, Szeged, Hungary
| | - Viola Luca Németh
- Department of Neurology, Faculty of Medicine, Albert Szent-Györgyi Clinical Center, University of Szeged, Szeged, Hungary
| | - Zoltán Maróti
- Genetic Diagnostic Laboratory, Department of Pediatrics and Pediatric Health Center, University of Szeged, Szeged, Korányi fasor 14-15, Szeged, H-6720, Hungary
| | - Edit Tóth-Molnár
- Department of Ophthalmology, Faculty of Medicine, Albert Szent-Györgyi Clinical Center, University of Szeged, Szeged, Hungary
| | - Judit Oláh
- Department of Dermatology and Allergology, Faculty of Medicine, Albert Szent-Györgyi Clinical Center, University of Szeged, Szeged, Hungary
| | - László Vécsei
- Department of Neurology, Faculty of Medicine, Albert Szent-Györgyi Clinical Center, University of Szeged, Szeged, Hungary
- MTA-SZTE Neuroscience Research Group, University of Szeged, Szeged, Hungary
- Interdisciplinary Excellence Center, University of Szeged, Szeged, Hungary
| | - Péter Klivényi
- Department of Neurology, Faculty of Medicine, Albert Szent-Györgyi Clinical Center, University of Szeged, Szeged, Hungary
| | - Tibor Kalmár
- Genetic Diagnostic Laboratory, Department of Pediatrics and Pediatric Health Center, University of Szeged, Szeged, Korányi fasor 14-15, Szeged, H-6720, Hungary.
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14
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Feltes BC, Pedebos C, Bonatto D, Verli H. Dynamics of DDB2-DDB1 complex under different naturally-occurring mutants in Xeroderma Pigmentosum disease. Biochim Biophys Acta Gen Subj 2018; 1862:2579-2589. [DOI: 10.1016/j.bbagen.2018.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 08/02/2018] [Accepted: 08/03/2018] [Indexed: 12/18/2022]
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15
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Pradhan S, Das P, Mattaparthi VSK. Characterizing the Binding Interactions between DNA-Binding Proteins, XPA and XPE: A Molecular Dynamics Approach. ACS OMEGA 2018; 3:15442-15454. [PMID: 31458200 PMCID: PMC6643373 DOI: 10.1021/acsomega.8b01793] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 11/01/2018] [Indexed: 05/23/2023]
Abstract
The scaffold nature of Xeroderma pigmentosum complementation group A (XPA) protein makes it an important member of nucleotide excision repair (NER) that removes bulky DNA lesions with the help of various protein-protein interactions (PPI) and DNA-protein interactions. However, many structural insights of XPA's interaction and the binding patterns with other NER proteins are yet to be understood. Here, we have studied one such crucial PPI of XPA with another NER protein, Xeroderma pigmentosum complementation group A (XPE), by using the previously identified binding site of XPA (residues 185-226) in the Assisted Model Building With Energy Refinement force-field-mediated dynamic system. We studied the relationship between XPA185-226-XPE complex using three different docked models. The major residues observed in all of the models that were responsible for the PPI of this complex were Arg20, Arg47, Asp51, and Leu57 from XPE and the residues Leu191, Gln192, Val193, Trp194, Glu198, Glu202, Glu205, Arg207, Glu209, Gln216, and Phe219 from XPE185-226. During the simulation study, the orientation of XPA was also noted to be changed by almost 180° in models 1 and 3, which remain unchanged in model 2, indicating that XPA interacts with XPE with its N-terminal end facing downward and C-terminal end facing upward. The same was concurrent with the binding of DNA-binding domain region of XPA (aa98-239) with XPE. The N-terminal of XPE was stretched for accommodating XPA. Using the per-residue energy decomposition analysis for the interface residues of all models, the binding affinity between these proteins were found to be dependent on R20, R47, and L57 of XPE and the residues L191, V193, W194, E198, E202, E205, R207, and F219 of XPA. The net binding free energy of the XPA185-226-XPE protein complex was found to be -48.3718 kcal mol-1 for model 1, -49.09 kcal mol-1 for model 2, and -56.51 kcal mol-1 for model 3.
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16
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Feltes BC. Architects meets Repairers: The interplay between homeobox genes and DNA repair. DNA Repair (Amst) 2018; 73:34-48. [PMID: 30448208 DOI: 10.1016/j.dnarep.2018.10.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 10/30/2018] [Indexed: 02/07/2023]
Abstract
Homeobox genes are widely considered the major protagonists of embryonic development and tissue formation. For the past decades, it was established that the deregulation of these genes is intimately related to developmental abnormalities and a broad range of diseases in adults. Since the proper regulation and expression of homeobox genes are necessary for a successful developmental program and tissue function, their relation to DNA repair mechanisms become a necessary discussion. However, important as it is, studies focused on the interplay between homeobox genes and DNA repair are scarce, and there is no critical discussion on the subject. Hence, in this work, I aim to provide the first review of the current knowledge of the interplay between homeobox genes and DNA repair mechanisms, and offer future perspectives on this, yet, young ground for new researches. Critical discussion is conducted, together with a careful assessment of each reviewed topic.
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Affiliation(s)
- Bruno César Feltes
- Institute of Informatics, Department of Theoretical Informatics, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.
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17
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Jarrett SG, Carter KM, Bautista RM, He D, Wang C, D'Orazio JA. Sirtuin 1-mediated deacetylation of XPA DNA repair protein enhances its interaction with ATR protein and promotes cAMP-induced DNA repair of UV damage. J Biol Chem 2018; 293:19025-19037. [PMID: 30327428 DOI: 10.1074/jbc.ra118.003940] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 10/12/2018] [Indexed: 12/31/2022] Open
Abstract
Blunted melanocortin 1 receptor (MC1R) signaling promotes melanocyte genomic instability in part by attenuating cAMP-mediated DNA repair responses, particularly nucleotide excision repair (NER), which recognizes and clears mutagenic photodamage. cAMP-enhanced NER is mediated by interactions between the ataxia telangiectasia-mutated and Rad3-related (ATR) and xeroderma pigmentosum complementation group A (XPA) proteins. We now report a critical role for sirtuin 1 (SIRT1) in regulating ATR-mediated phosphorylation of XPA. SIRT1 deacetylates XPA at residues Lys-63, Lys-67, and Lys-215 to promote interactions with ATR. Mutant XPA containing acetylation mimetics at residues Lys-63, Lys-67, and Lys-215 exhibit blunted UV-dependent ATR-XPA interactions even in the presence of cAMP signals. ATR-mediated phosphorylation of XPA on Ser-196 enhances cAMP-mediated optimization of NER and is promoted by SIRT1-mediated deacetylation of XPA on Lys-63, Lys-67, and Lys-215. Interference with ATR-mediated XPA phosphorylation at Ser-196 by persistent acetylation of XPA at Lys-63, Lys-67, and Lys-215 delays repair of UV-induced DNA damage and attenuates cAMP-enhanced NER. Our study identifies a regulatory ATR-SIRT1-XPA axis in cAMP-mediated regulation melanocyte genomic stability, involving SIRT1-mediated deacetylation (Lys-63, Lys-67, and Lys-215) and ATR-dependent phosphorylation (Ser-196) post-translational modifications of the core NER factor XPA.
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Affiliation(s)
- Stuart G Jarrett
- From the Markey Cancer Center and .,the Departments of Toxicology and Cancer Biology
| | | | | | - Daheng He
- From the Markey Cancer Center and.,Biostatistics and Bioinformatics, and
| | - Chi Wang
- From the Markey Cancer Center and.,Biostatistics and Bioinformatics, and
| | - John A D'Orazio
- From the Markey Cancer Center and .,the Departments of Toxicology and Cancer Biology.,Pediatrics, University of Kentucky College of Medicine, Lexington, Kentucky 40536
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18
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Hasan MM, Kurata H. GPSuc: Global Prediction of Generic and Species-specific Succinylation Sites by aggregating multiple sequence features. PLoS One 2018; 13:e0200283. [PMID: 30312302 PMCID: PMC6193575 DOI: 10.1371/journal.pone.0200283] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/22/2018] [Indexed: 01/09/2023] Open
Abstract
Lysine succinylation is one of the dominant post-translational modification of the protein that contributes to many biological processes including cell cycle, growth and signal transduction pathways. Identification of succinylation sites is an important step for understanding the function of proteins. The complicated sequence patterns of protein succinylation revealed by proteomic studies highlight the necessity of developing effective species-specific in silico strategies for global prediction succinylation sites. Here we have developed the generic and nine species-specific succinylation site classifiers through aggregating multiple complementary features. We optimized the consecutive features using the Wilcoxon-rank feature selection scheme. The final feature vectors were trained by a random forest (RF) classifier. With an integration of RF scores via logistic regression, the resulting predictor termed GPSuc achieved better performance than other existing generic and species-specific succinylation site predictors. To reveal the mechanism of succinylation and assist hypothesis-driven experimental design, our predictor serves as a valuable resource. To provide a promising performance in large-scale datasets, a web application was developed at http://kurata14.bio.kyutech.ac.jp/GPSuc/.
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Affiliation(s)
- Md. Mehedi Hasan
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Kawazu, Iizuka, Fukuoka, Japan
| | - Hiroyuki Kurata
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Kawazu, Iizuka, Fukuoka, Japan
- Biomedi Informatics R&D Center, Kyushu Institute of Technology, Kawazu, Iizuka, Fukuoka, Japan
- * E-mail:
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19
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Pradhan S, Sarma H, Mattaparthi VSK. Investigation of the probable homo-dimer model of the Xeroderma pigmentosum complementation group A (XPA) protein to represent the DNA-binding core. J Biomol Struct Dyn 2018; 37:3322-3336. [PMID: 30205752 DOI: 10.1080/07391102.2018.1517051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The Xeroderma pigmentosum complementation group A (XPA) protein functions as a primary damage verifier and as a scaffold protein in nucleotide excision repair (NER) in all higher organisms. New evidence of XPA's existence as a dimer and the redefinition of its DNA-binding domain (DBD) raises new questions regarding the stability and functional position of XPA in NER. Here, we have investigated XPA's dimeric status with respect to its previously defined DBD (XPA98-219) as well as with its redefined DBD (XPA98-239). We studied the stability of XPA98-210 and XPA98-239 homo-dimer systems using all-atom molecular dynamics simulation, and we have also characterized the protein-protein interactions (PPI) of these two homo-dimeric forms of XPA. After conducting the root mean square deviation (RMSD) analyses, it was observed that the XPA98-239 homo-dimer has better stability than XPA98-210. It was also found that XPA98-239 has a larger number of hydrogen bonds, salt bridges, and hydrophobic interactions than the XPA98-210 homo-dimer. We further found that Lys, Glu, Gln, Asn, and Arg residues shared the major contribution toward the intermolecular interactions in XPA homo-dimers. The binding free energy (BFE) analysis, which used the molecular mechanics Poisson-Boltzmann method (MM-PBSA) and the generalized Born and surface area continuum solvation model (GBSA) for both XPA homo-dimers, also substantiated the positive result in favor of the stability of the XPA98-239 homo-dimer. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sushmita Pradhan
- a Molecular Modelling and Simulation Laboratory, Department of Molecular Biology and Biotechnology , Tezpur University , Tezpur , India
| | - Himakshi Sarma
- a Molecular Modelling and Simulation Laboratory, Department of Molecular Biology and Biotechnology , Tezpur University , Tezpur , India
| | - Venkata Satish Kumar Mattaparthi
- a Molecular Modelling and Simulation Laboratory, Department of Molecular Biology and Biotechnology , Tezpur University , Tezpur , India
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20
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Analysis of the conserved NER helicases (XPB and XPD) and UV-induced DNA damage in Hydra. Biochim Biophys Acta Gen Subj 2018; 1862:2031-2042. [PMID: 29959982 DOI: 10.1016/j.bbagen.2018.06.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 06/04/2018] [Accepted: 06/26/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Nucleotide excision repair (NER) pathway is an evolutionarily conserved mechanism of genome maintenance. It detects and repairs distortions in DNA double helix. Xeroderma Pigmentosum group B (XPB) and group D (XPD) are important helicases in NER and are also critical subunits of TFIIH complex. We have studied XPB and XPD for the first time from the basal metazoan Hydra which exhibits lack of organismal senescence. METHODS In silico analysis of proteins was performed using MEGA 6.0, Clustal Omega, Swiss Model, etc. Gene expression was studied by in situ hybridization and qRT-PCR. Repair of CPDs was studied by DNA blot assay. Interactions between proteins were determined by co- immunoprecipitation. HyXPB and HyXPD were cloned in pET28b, overexpressed and helicase activity of purified proteins was checked. RESULTS In silico analysis revealed presence of seven classical helicase motifs in HyXPB and HyXPD. Both proteins revealed polarity-dependent helicase activity. Hydra repairs most of the thymine dimers induced by UVC (500 J/m2) by 72 h post-UV exposure. HyXPB and HyXPD transcripts, localized all over the body column, remained unaltered post-UV exposure indicating their constitutive expression. In spite of high levels of sequence conservation, XPB and XPD failed to rescue defects in human XPB- and XPD-deficient cell lines. This was due to their inability to get incorporated into the TFIIH multiprotein complex. CONCLUSIONS Present results along with our earlier work on DNA repair proteins in Hydra bring out the utility of Hydra as model system to study evolution of DNA repair mechanisms in metazoans.
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21
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Feng X, Liu J, Gong Y, Gou K, Yang H, Yuan Y, Xing C. DNA repair protein XPA is differentially expressed in colorectal cancer and predicts better prognosis. Cancer Med 2018; 7:2339-2349. [PMID: 29675892 PMCID: PMC6010851 DOI: 10.1002/cam4.1480] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 03/04/2018] [Accepted: 03/13/2018] [Indexed: 12/14/2022] Open
Abstract
As an indispensable factor in DNA damage recognition step of nucleotide excision repair, XPA interacts with a series of proteins to initiate repair process. The expression characteristics of XPA in colorectal cancer (CRC) and its influence on CRC prognosis remain elusive. Tissue specimens of CRC and nontumor adjacent tissues from 283 patients were collected. XPA protein expressions were detected by immunohistochemistry staining. Nonparametric test was used to investigate the difference of XPA expression between CRC and nontumor adjacent tissues, as well as the correlation between XPA expression and clinicopathological parameters of CRC. Univariate and multivariate Cox proportional hazards models were applied to estimate the relationship between XPA expression and CRC prognosis. Meanwhile, we analyzed TCGA data to investigate the relation between XPA mRNA expression and survival of CRC. XPA protein expression was significantly decreased in CRC tissues compared with nontumor adjacent tissues (P = 0.001). Subgroup analysis indicated consistently significant down-regulation of XPA in CRC tissues in age > 60 (P = 0.026), age ≤ 60 (P = 0.008), colon cancer (P = 0.009), and rectal cancer (P = 0.015) patients and males (P = 0.004). For clinicopathological parameters, CRC patients with drinking habits revealed XPA overexpression than nondrinkers (P = 0.032). For prognosis, CRC patients with high XPA protein expression had longer overall survival (OS) (HR = 0.62, 95%CI: 0.39-0.97, P = 0.037). Stratified analysis suggested a better prognosis in relation to high XPA protein expression in patients over 60 years (adjusted HR = 0.48, P = 0.021), with rectal cancer (HR = 0.56, P = 0.037), without distant metastasis (HR = 0.58, P = 0.033), without tumor deposits (HR = 0.40, P = 0.006; adjusted HR = 0.44, P = 0.028), and with tumor diameter over 4 cm (HR = 0.49, P = 0.023). DNA repair protein XPA is significantly decreased in colorectal cancer tissues than in adjacent nontumor tissues. High expression of XPA protein showed significant relationship with better survival of CRC, especially rectal cancer. XPA might be a novel biomarker but might not be an independent factor to predict prognosis of CRC patients.
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Affiliation(s)
- Xue Feng
- Tumor Etiology and Screening Department of Cancer Institute and General SurgeryThe First Hospital of China Medical UniversityShenyang110001China
- Liaoning Provincial Education DepartmentKey Laboratory of Cancer Etiology and PreventionChina Medical UniversityShenyang110001China
| | - Jingwei Liu
- Tumor Etiology and Screening Department of Cancer Institute and General SurgeryThe First Hospital of China Medical UniversityShenyang110001China
- Liaoning Provincial Education DepartmentKey Laboratory of Cancer Etiology and PreventionChina Medical UniversityShenyang110001China
| | - Yuehua Gong
- Tumor Etiology and Screening Department of Cancer Institute and General SurgeryThe First Hospital of China Medical UniversityShenyang110001China
- Liaoning Provincial Education DepartmentKey Laboratory of Cancer Etiology and PreventionChina Medical UniversityShenyang110001China
| | - Kaihua Gou
- Tumor Etiology and Screening Department of Cancer Institute and General SurgeryThe First Hospital of China Medical UniversityShenyang110001China
- Liaoning Provincial Education DepartmentKey Laboratory of Cancer Etiology and PreventionChina Medical UniversityShenyang110001China
| | - Huaiwei Yang
- Tumor Etiology and Screening Department of Cancer Institute and General SurgeryThe First Hospital of China Medical UniversityShenyang110001China
- Liaoning Provincial Education DepartmentKey Laboratory of Cancer Etiology and PreventionChina Medical UniversityShenyang110001China
| | - Yuan Yuan
- Tumor Etiology and Screening Department of Cancer Institute and General SurgeryThe First Hospital of China Medical UniversityShenyang110001China
- Liaoning Provincial Education DepartmentKey Laboratory of Cancer Etiology and PreventionChina Medical UniversityShenyang110001China
| | - Chengzhong Xing
- Tumor Etiology and Screening Department of Cancer Institute and General SurgeryThe First Hospital of China Medical UniversityShenyang110001China
- Liaoning Provincial Education DepartmentKey Laboratory of Cancer Etiology and PreventionChina Medical UniversityShenyang110001China
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22
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Bukowska B, Karwowski BT. Actual state of knowledge in the field of diseases related with defective nucleotide excision repair. Life Sci 2018; 195:6-18. [DOI: 10.1016/j.lfs.2017.12.035] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 12/19/2017] [Accepted: 12/24/2017] [Indexed: 12/11/2022]
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23
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Ben Rekaya M, Naouali C, Messaoud O, Jones M, Bouyacoub Y, Nagara M, Pippucci T, Jmel H, Chargui M, Jerbi M, Alibi M, Dallali H, Bashamboo A, McElreavey K, Romeo G, Barakat A, Zghal M, Yacoub-Youssef H, Abdelhak S. Whole Exome Sequencing allows the identification of two novel groups of Xeroderma pigmentosum in Tunisia, XP-D and XP-E: Impact on molecular diagnosis. J Dermatol Sci 2018; 89:172-180. [DOI: 10.1016/j.jdermsci.2017.10.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 08/02/2017] [Accepted: 10/31/2017] [Indexed: 12/17/2022]
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24
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Chitale S, Richly H. DICER- and MMSET-catalyzed H4K20me2 recruits the nucleotide excision repair factor XPA to DNA damage sites. J Cell Biol 2017; 217:527-540. [PMID: 29233865 PMCID: PMC5800799 DOI: 10.1083/jcb.201704028] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 10/06/2017] [Accepted: 11/08/2017] [Indexed: 12/30/2022] Open
Abstract
The endoribonuclease DICER facilitates chromatin decondensation during lesion recognition following UV exposure. Chitale and Richly show that DICER mediates the recruitment of the methyltransferase MMSET, which catalyzes the dimethylation of histone H4 at lysine 20 and facilitates the recruitment of the nucleotide excision repair factor XPA. Ultraviolet (UV) irradiation triggers the recruitment of DNA repair factors to the lesion sites and the deposition of histone marks as part of the DNA damage response. The major DNA repair pathway removing DNA lesions caused by exposure to UV light is nucleotide excision repair (NER). We have previously demonstrated that the endoribonuclease DICER facilitates chromatin decondensation during lesion recognition in the global-genomic branch of NER. Here, we report that DICER mediates the recruitment of the methyltransferase MMSET to the DNA damage site. We show that MMSET is required for efficient NER and that it catalyzes the dimethylation of histone H4 at lysine 20 (H4K20me2). H4K20me2 at DNA damage sites facilitates the recruitment of the NER factor XPA. Our work thus provides evidence for an H4K20me2-dependent mechanism of XPA recruitment during lesion recognition in the global-genomic branch of NER.
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Affiliation(s)
- Shalaka Chitale
- Laboratory of Molecular Epigenetics, Institute of Molecular Biology, Mainz, Germany.,Faculty of Biology, Johannes Gutenberg University, Mainz, Germany
| | - Holger Richly
- Laboratory of Molecular Epigenetics, Institute of Molecular Biology, Mainz, Germany
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25
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Pradhan S, Mattaparthi VSK. Structural dynamics and interactions of Xeroderma pigmentosum complementation group A (XPA98–210) with damaged DNA. J Biomol Struct Dyn 2017; 36:3341-3353. [DOI: 10.1080/07391102.2017.1388285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Sushmita Pradhan
- Molecular Modelling and Simulation Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784 028, Assam, India
| | - Venkata Satish Kumar Mattaparthi
- Molecular Modelling and Simulation Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784 028, Assam, India
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26
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Zamarrón A, García M, Río MD, Larcher F, Juarranz Á. Effects of photodynamic therapy on dermal fibroblasts from xeroderma pigmentosum and Gorlin-Goltz syndrome patients. Oncotarget 2017; 8:77385-77399. [PMID: 29100394 PMCID: PMC5652786 DOI: 10.18632/oncotarget.20485] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 07/26/2017] [Indexed: 12/22/2022] Open
Abstract
PDT is widely applied for the treatment of non-melanoma skin cancer pre-malignant and malignant lesions (actinic keratosis, basal cell carcinoma and in situ squamous cell carcinoma). In photodynamic therapy (PDT) the interaction of a photosensitizer (PS), light and oxygen leads to the formation of reactive oxygen species (ROS) and thus the selective tumor cells eradication. Xeroderma pigmentosum (XP) and Gorlin-Goltz Syndrome (GS) patients are at high risk of developing skin cancer in sun-exposed areas. Therefore, the use of PDT as a preventive treatment may constitute a very promising therapeutic modality for these syndromes. Given the demonstrated role of cancer associated fibroblasts (CAFs) in tumor progression and the putative CAFs features of some cancer-prone genodermatoses fibroblasts, in this study, we have further characterized the phenotype of XP and GS dermal fibroblasts and evaluated their response to methyl-δ-aminolevulinic acid (MAL)-PDT compared to that of dermal fibroblasts obtained from healthy donors. We show here that XP/GS fibroblasts display clear features of CAFs and present a significantly higher response to PDT, even after being stimulated with UV light, underscoring the value of this therapeutic approach for these rare skin conditions and likely to other forms of skin cancer were CAFs play a major role.
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Affiliation(s)
- Alicia Zamarrón
- Department of Biology, Faculty of Sciences, Autónoma University of Madrid, IRYCIS, Madrid, Spain
| | - Marta García
- Department of Bioengineering, Carlos III University (UC3M), Madrid, Spain
- CIEMAT-Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | - Marcela Del Río
- Department of Bioengineering, Carlos III University (UC3M), Madrid, Spain
- CIEMAT-Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | - Fernando Larcher
- Department of Bioengineering, Carlos III University (UC3M), Madrid, Spain
- CIEMAT-Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | - Ángeles Juarranz
- Department of Biology, Faculty of Sciences, Autónoma University of Madrid, IRYCIS, Madrid, Spain
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27
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Ebert C, Simon N, Schneider S, Carell T. Structural Insights into the Recognition of N
2
-Aryl- and C8-Aryl DNA Lesions by the Repair Protein XPA/Rad14. Chembiochem 2017; 18:1379-1382. [DOI: 10.1002/cbic.201700169] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Indexed: 01/28/2023]
Affiliation(s)
- Charlotte Ebert
- Center for Integrated Protein Science at the Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstrasse 5-13 81377 München Germany
| | - Nina Simon
- Center for Integrated Protein Science at the Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstrasse 5-13 81377 München Germany
| | - Sabine Schneider
- Center for Integrated Protein Science at the Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85748 Garching Germany
| | - Thomas Carell
- Center for Integrated Protein Science at the Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstrasse 5-13 81377 München Germany
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28
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Holcomb N, Goswami M, Han SG, Scott T, D'Orazio J, Orren DK, Gairola CG, Mellon I. Inorganic arsenic inhibits the nucleotide excision repair pathway and reduces the expression of XPC. DNA Repair (Amst) 2017; 52:70-80. [PMID: 28237621 DOI: 10.1016/j.dnarep.2017.02.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 01/11/2017] [Accepted: 02/12/2017] [Indexed: 11/17/2022]
Abstract
Chronic exposure to arsenic, most often through contaminated drinking water, has been linked to several types of cancer in humans, including skin and lung cancer. However, the mechanisms underlying its role in causing cancer are not well understood. There is evidence that exposure to arsenic can enhance the carcinogenicity of UV light in inducing skin cancers and may enhance the carcinogenicity of tobacco smoke in inducing lung cancers. The nucleotide excision repair (NER) pathway removes different types of DNA damage including those produced by UV light and components of tobacco smoke. The aim of the present study was to investigate the effect of sodium arsenite on the NER pathway in human lung fibroblasts (IMR-90 cells) and primary mouse keratinocytes. To measure NER, we employed a slot-blot assay to quantify the introduction and removal of UV light-induced 6-4 photoproducts (6-4 PP) and cyclobutane pyrimidine dimers (CPDs). We find a concentration-dependent inhibition of the removal of 6-4 PPs and CPDs in both cell types treated with arsenite. Treatment of both cell types with arsenite resulted in a significant reduction in the abundance of XPC, a protein that is critical for DNA damage recognition in NER. The abundance of RNA expressed from several key NER genes was also significantly reduced by treatment of IMR-90 cells with arsenite. Finally, treatment of IMR-90 cells with MG-132 abrogated the reduction in XPC protein, suggesting an involvement of the proteasome in the reduction of XPC protein produced by treatment of cells with arsenic. The inhibition of NER by arsenic may reflect one mechanism underlying the role of arsenic exposure in enhancing cigarette smoke-induced lung carcinogenesis and UV light-induced skin cancer, and it may provide some insights into the emergence of arsenic trioxide as a chemotherapeutic agent.
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Affiliation(s)
- Nathaniel Holcomb
- Department of Toxicology and Cancer Biology, The Markey Cancer Center, University of Kentucky, Lexington, KY, United States
| | - Mamta Goswami
- Department of Toxicology and Cancer Biology, The Markey Cancer Center, University of Kentucky, Lexington, KY, United States
| | - Sung Gu Han
- Toxicology Laboratory, Department of Food Science and Biotechnology of Animal Resources, College of Animal Bioscience and Technology, Konkuk University, Seoul 05029, Republic of Korea
| | - Tim Scott
- Department of Toxicology and Cancer Biology, The Markey Cancer Center, University of Kentucky, Lexington, KY, United States
| | - John D'Orazio
- Department of Toxicology and Cancer Biology, The Markey Cancer Center, University of Kentucky, Lexington, KY, United States
| | - David K Orren
- Department of Toxicology and Cancer Biology, The Markey Cancer Center, University of Kentucky, Lexington, KY, United States
| | - C Gary Gairola
- Department of Toxicology and Cancer Biology, The Markey Cancer Center, University of Kentucky, Lexington, KY, United States
| | - Isabel Mellon
- Department of Toxicology and Cancer Biology, The Markey Cancer Center, University of Kentucky, Lexington, KY, United States.
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Dutto I, Cazzalini O, Stivala LA, Prosperi E. An improved method for the detection of nucleotide excision repair factors at local UV DNA damage sites. DNA Repair (Amst) 2017; 51:79-84. [PMID: 28185850 DOI: 10.1016/j.dnarep.2017.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 01/12/2017] [Indexed: 12/19/2022]
Abstract
Among different DNA repair processes that cells use to face with DNA damage, nucleotide excision repair (NER) is particularly important for the removal of a high variety of lesions, including those generated by some antitumor drugs. A number of factors participating in NER, such as the TFIIH complex and the endonuclease XPG are also involved in basal processes, e.g. transcription. For this reason, localization of these factors at DNA damage sites may be difficult. Here we have applied a mild digestion of chromatin with DNase I to improve the in situ extraction necessary to detect chromatin-bound proteins by immunofluorescence. We have compared this method with different extraction protocols and investigated its application on different cell types, and with different antibodies. Our results show that a short DNase I treatment before the immunoreaction, enhances the fluorescence signal of NER proteins, such as XPG, DDB2 and XPC. In addition, our findings indicate that the antibody choice is a critical factor for accurate localization of DNA repair proteins at DNA damage sites. In conclusion, a mild DNA digestion with DNase I improves the immunofluorescence detection of the recruitment of NER factors at local DNA damage sites by enhancing accessibility to the antibodies, independently of the cell type.
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Affiliation(s)
- Ilaria Dutto
- Istituto di Genetica Molecolare del CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Ornella Cazzalini
- Dipartimento di Medicina Molecolare, Unità di Immunologia e Patologia generale, Università di Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Lucia Anna Stivala
- Dipartimento di Medicina Molecolare, Unità di Immunologia e Patologia generale, Università di Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Ennio Prosperi
- Istituto di Genetica Molecolare del CNR, Via Abbiategrasso 207, 27100 Pavia, Italy.
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Musich PR, Li Z, Zou Y. Xeroderma Pigmentosa Group A (XPA), Nucleotide Excision Repair and Regulation by ATR in Response to Ultraviolet Irradiation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 996:41-54. [PMID: 29124689 DOI: 10.1007/978-3-319-56017-5_4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The sensitivity of Xeroderma pigmentosa (XP) patients to sunlight has spurred the discovery and genetic and biochemical analysis of the eight XP gene products (XPA-XPG plus XPV) responsible for this disorder. These studies also have served to elucidate the nucleotide excision repair (NER) process, especially the critical role played by the XPA protein. More recent studies have shown that NER also involves numerous other proteins normally employed in DNA metabolism and cell cycle regulation. Central among these is ataxia telangiectasia and Rad3-related (ATR), a protein kinase involved in intracellular signaling in response to DNA damage, especially DNA damage-induced replicative stresses. This review summarizes recent findings on the interplay between ATR as a DNA damage signaling kinase and as a novel ligand for intrinsic cell death proteins to delay damage-induced apoptosis, and on ATR's regulation of XPA and the NER process for repair of UV-induced DNA adducts. ATR's regulatory role in the cytosolic-to-nuclear translocation of XPA will be discussed. In addition, recent findings elucidating a non-NER role for XPA in DNA metabolism and genome stabilization at ds-ssDNA junctions, as exemplified in prematurely aging progeroid cells, also will be reviewed.
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Affiliation(s)
- Phillip R Musich
- Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
| | - Zhengke Li
- Department of Cancer Genetics and Epigenetics, City of Hope Comprehensive Cancer Center, 1500 E Duarte Rd, Duarte, CA, 91007, USA
| | - Yue Zou
- Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA.
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Transcriptional and Posttranslational Regulation of Nucleotide Excision Repair: The Guardian of the Genome against Ultraviolet Radiation. Int J Mol Sci 2016; 17:ijms17111840. [PMID: 27827925 PMCID: PMC5133840 DOI: 10.3390/ijms17111840] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 10/31/2016] [Accepted: 11/01/2016] [Indexed: 11/24/2022] Open
Abstract
Ultraviolet (UV) radiation from sunlight represents a constant threat to genome stability by generating modified DNA bases such as cyclobutane pyrimidine dimers (CPD) and pyrimidine-pyrimidone (6-4) photoproducts (6-4PP). If unrepaired, these lesions can have deleterious effects, including skin cancer. Mammalian cells are able to neutralize UV-induced photolesions through nucleotide excision repair (NER). The NER pathway has multiple components including seven xeroderma pigmentosum (XP) proteins (XPA to XPG) and numerous auxiliary factors, including ataxia telangiectasia and Rad3-related (ATR) protein kinase and RCC1 like domain (RLD) and homologous to the E6-AP carboxyl terminus (HECT) domain containing E3 ubiquitin protein ligase 2 (HERC2). In this review we highlight recent data on the transcriptional and posttranslational regulation of NER activity.
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Metal binding mediated conformational change of XPA protein:a potential cytotoxic mechanism of nickel in the nucleotide excision repair. J Mol Model 2016; 22:156. [PMID: 27307058 DOI: 10.1007/s00894-016-3017-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/26/2016] [Indexed: 12/13/2022]
Abstract
Nucleotide excision repair (NER) is a pivotal life process for repairing DNA nucleotide mismatch caused by chemicals, metal ions, radiation, and other factors. As the initiation step of NER, the xeroderma pigmentosum complementation group A protein (XPA) recognizes damaged DNA molecules, and recruits the replication protein A (RPA), another important player in the NER process. The stability of the Zn(2+)-chelated Zn-finger domain of XPA center core portion (i.e., XPA98-210) is the foundation of its biological functionality, while the displacement of the Zn(2+) by toxic metal ions (such as Ni(2+), a known human carcinogen and allergen) may impair the effectiveness of NER and hence elevate the chance of carcinogenesis. In this study, we first calculated the force field parameters for the bonded model in the metal center of the XPA98-210 system, showing that the calculated results, including charges, bonds, angles etc., are congruent with previously reported results measured by spectrometry experiments and quantum chemistry computation. Then, comparative molecular dynamics simulations using these parameters revealed the changes in the conformation and motion mode of XPA98-210 Zn-finger after the substitution of Zn(2+) by Ni(2+). The results showed that Ni(2+) dramatically disrupted the relative positions of the four Cys residues in the Zn-finger structure, forcing them to collapse from a tetrahedron into an almost planar structure. Finally, we acquired the binding mode of XPA98-210 with its ligands RPA70N and DNA based on molecular docking and structural alignment. We found that XPA98-210's Zn-finger domain primarily binds to a V-shaped cleft in RPA70N, while the cationic band in its C-terminal subdomain participates in the recognition of damaged DNA. In addition, this article sheds light on the multi-component interaction pattern among XPA, DNA, and other NER-related proteins (i.e., RPA70N, RPA70A, RPA70B, RPA70C, RPA32, and RPA14) based on previously reported structural biology information. Thus, we derived a putative cytotoxic mechanism associated with the nickel ion, where the Ni(2+) disrupts the conformation of the XPA Zn-finger, directly weakening its interaction with RPA70N, and thus lowering the effectiveness of the NER process. In sum, this work not only provides a theoretical insight into the multi-protein interactions involved in the NER process and potential cytotoxic mechanism associated with Ni(2+) binding in XPA, but may also facilitate rational anti-cancer drug design based on the NER mechanism.
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Sugitani N, Sivley RM, Perry KE, Capra JA, Chazin WJ. XPA: A key scaffold for human nucleotide excision repair. DNA Repair (Amst) 2016; 44:123-135. [PMID: 27247238 DOI: 10.1016/j.dnarep.2016.05.018] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nucleotide excision repair (NER) is essential for removing many types of DNA lesions from the genome, yet the mechanisms of NER in humans remain poorly understood. This review summarizes our current understanding of the structure, biochemistry, interaction partners, mechanisms, and disease-associated mutations of one of the critical NER proteins, XPA.
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Affiliation(s)
- Norie Sugitani
- Departments of Biochemistry, Biological Sciences, Biomedical Informatics, Chemistry, and Computer Science, and Vanderbilt Genetics Institute and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232-7917, United States
| | - Robert M Sivley
- Departments of Biochemistry, Biological Sciences, Biomedical Informatics, Chemistry, and Computer Science, and Vanderbilt Genetics Institute and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232-7917, United States
| | - Kelly E Perry
- Departments of Biochemistry, Biological Sciences, Biomedical Informatics, Chemistry, and Computer Science, and Vanderbilt Genetics Institute and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232-7917, United States
| | - John A Capra
- Departments of Biochemistry, Biological Sciences, Biomedical Informatics, Chemistry, and Computer Science, and Vanderbilt Genetics Institute and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232-7917, United States
| | - Walter J Chazin
- Departments of Biochemistry, Biological Sciences, Biomedical Informatics, Chemistry, and Computer Science, and Vanderbilt Genetics Institute and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232-7917, United States.
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Ahmed M, Dorling L, Kerns S, Fachal L, Elliott R, Partliament M, Rosenstein BS, Vega A, Gómez-Caamaño A, Barnett G, Dearnaley DP, Hall E, Sydes M, Burnet N, Pharoah PDP, Eeles R, West CML. Common genetic variation associated with increased susceptibility to prostate cancer does not increase risk of radiotherapy toxicity. Br J Cancer 2016; 114:1165-74. [PMID: 27070714 PMCID: PMC4865979 DOI: 10.1038/bjc.2016.94] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/04/2016] [Accepted: 03/08/2016] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Numerous germline single-nucleotide polymorphisms increase susceptibility to prostate cancer, some lying near genes involved in cellular radiation response. This study investigated whether prostate cancer patients with a high genetic risk have increased toxicity following radiotherapy. METHODS The study included 1560 prostate cancer patients from four radiotherapy cohorts: RAPPER (n=533), RADIOGEN (n=597), GenePARE (n=290) and CCI (n=150). Data from genome-wide association studies were imputed with the 1000 Genomes reference panel. Individuals were genetically similar with a European ancestry based on principal component analysis. Genetic risks were quantified using polygenic risk scores. Regression models tested associations between risk scores and 2-year toxicity (overall, urinary frequency, decreased stream, rectal bleeding). Results were combined across studies using standard inverse-variance fixed effects meta-analysis methods. RESULTS A total of 75 variants were genotyped/imputed successfully. Neither non-weighted nor weighted polygenic risk scores were associated with late radiation toxicity in individual studies (P>0.11) or after meta-analysis (P>0.24). No individual variant was associated with 2-year toxicity. CONCLUSION Patients with a high polygenic susceptibility for prostate cancer have no increased risk for developing late radiotherapy toxicity. These findings suggest that patients with a genetic predisposition for prostate cancer, inferred by common variants, can be safely treated using current standard radiotherapy regimens.
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Affiliation(s)
- Mahbubl Ahmed
- The Institute of Cancer Research, Royal Marsden NHS Foundation Trust, 123 Old Brompton Road, London SW7 3RP, UK
| | - Leila Dorling
- Centre for Cancer Genetic Epidemiology, Strangeways Research Laboratory, Worts Causeway, Cambridge CB1 8RN, UK
| | - Sarah Kerns
- Department of Radiation Oncology, University of Rochester Medical Centre, Saunders Research Building, 265 Crittenden Boulevard, Rochester, NY 14620, USA
| | - Laura Fachal
- Centre for Cancer Genetic Epidemiology, Strangeways Research Laboratory, Worts Causeway, Cambridge CB1 8RN, UK
- Genomic Medicine Group, CIBERER, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - Rebecca Elliott
- Institute of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie Hospital NHS Foundation Trust, Manchester M20 4BX, UK
| | | | - Barry S Rosenstein
- Department of Radiation Oncology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, IDIS, CIBERER, Santiago de Compostela 15706, Spain
| | - Antonio Gómez-Caamaño
- Department of Radiation Oncology, USC University Hospital Complex, SERGAS, Santiago de Compostela, Spain
| | - Gill Barnett
- Centre for Cancer Genetic Epidemiology, Strangeways Research Laboratory, Worts Causeway, Cambridge CB1 8RN, UK
| | - David P Dearnaley
- The Institute of Cancer Research, Royal Marsden NHS Foundation Trust, 123 Old Brompton Road, London SW7 3RP, UK
| | - Emma Hall
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London SM2 5NG, UK
| | - Matt Sydes
- Clinical Trials Unit (CTU), Medical Research Council, London WC2B 6NH, UK
| | - Neil Burnet
- Department of Oncology, Addenbrookes Hospital, Hills Road, Cambridge CB2 0QQ UK
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Strangeways Research Laboratory, Worts Causeway, Cambridge CB1 8RN, UK
| | - Ros Eeles
- The Institute of Cancer Research, Royal Marsden NHS Foundation Trust, 123 Old Brompton Road, London SW7 3RP, UK
| | - Catharine M L West
- Institute of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie Hospital NHS Foundation Trust, Manchester M20 4BX, UK
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Abstract
Nucleotide excision repair (NER) is a highly versatile and efficient DNA repair process, which is responsible for the removal of a large number of structurally diverse DNA lesions. Its extreme broad substrate specificity ranges from DNA damages formed upon exposure to ultraviolet radiation to numerous bulky DNA adducts induced by mutagenic environmental chemicals and cytotoxic drugs used in chemotherapy. Defective NER leads to serious diseases, such as xeroderma pigmentosum (XP). Eight XP complementation groups are known of which seven (XPA-XPG) are caused by mutations in genes involved in the NER process. The eighth gene, XPV, codes for the DNA polymerase ɳ, which replicates through DNA lesions in a process called translesion synthesis (TLS). Over the past decade, detailed structural information of these DNA repair proteins involved in eukaryotic NER and TLS have emerged. These structures allow us now to understand the molecular mechanism of the NER and TLS processes in quite some detail and we have begun to understand the broad substrate specificity of NER. In this review, we aim to highlight recent advances in the process of damage recognition and repair as well as damage tolerance by the XP proteins.
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36
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Barros ACD, Takeda AAS, Dreyer TR, Velazquez-Campoy A, Kobe B, Fontes MRM. Structural and Calorimetric Studies Demonstrate that Xeroderma Pigmentosum Type G (XPG) Can Be Imported to the Nucleus by a Classical Nuclear Import Pathway via a Monopartite NLS Sequence. J Mol Biol 2016; 428:2120-31. [PMID: 26812207 DOI: 10.1016/j.jmb.2016.01.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 01/08/2016] [Accepted: 01/14/2016] [Indexed: 11/16/2022]
Abstract
Xeroderma pigmentosum type G (XPG) proteins are involved in DNA lesion recognition and promotion of nucleotide excision repair. Specific mutations in these proteins may lead to Cockayne syndrome, in which the patients may display severe developmental retardation and neurological abnormalities. No structural information is available for their spacer region or the C-terminal domain, which are important, respectively, for specific nucleotide excision repair activity and substrate specificity, as well as nuclear translocation. Immunofluorescence studies suggested two specific regions of the XPG C-terminus as potential bipartite nuclear localization sequences, which would be responsible for its translocation to the nucleus by the classical nuclear import pathway mediated by the importin-α (Impα). Thus, in order to test these hypotheses and gain insight into the structural basis for the nuclear import process for the XPG protein, we solved the crystal structures of complexes formed by the Impα and peptides corresponding to both putative nuclear localization signal (NLS) sequences (XPG1 and XPG2) and performed isothermal titration calorimetry assays to determine their binding affinities. Structural experiments confirm the binding of both NLS peptides to Impα but, unexpectedly, they bind to the receptor as monopartite NLSs. The isothermal titration calorimetry assays demonstrated that XPG1 and XPG2 peptides bind to two separate binding sites, but with high affinity to the major NLS-binding site of the Impα, resembling classical monopartite SV40 TAg NLS. The results lead to insights about what distinguishes monopartite and bipartite NLSs, as well as the differential roles of XPG1 and XPG2 NLSs in the nuclear localization of XPG.
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Affiliation(s)
- Andrea C de Barros
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, 18618-970 Brazil
| | - Agnes A S Takeda
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, 18618-970 Brazil
| | - Thiago R Dreyer
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, 18618-970 Brazil
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems, Joint-Unit Institute of Physical Chemistry "Rocasolano"-Consejo Superior de Investigaciones Científicas-Institute of Biocomputation and Physics of Complex Systems, University of Zaragoza, Zaragoza, 50018, Spain; Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, Zaragoza, 50018, Spain; Fundacion Agencia Aragonesa para la Investigación y el Desarrollo, Government of Aragon, Zaragoza, 50018, Spain
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Marcos R M Fontes
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, 18618-970 Brazil.
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Arnal A, Tissot T, Ujvari B, Nunney L, Solary E, Laplane L, Bonhomme F, Vittecoq M, Tasiemski A, Renaud F, Pujol P, Roche B, Thomas F. The guardians of inherited oncogenic vulnerabilities. Evolution 2015; 70:1-6. [DOI: 10.1111/evo.12809] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 10/21/2015] [Accepted: 10/24/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Audrey Arnal
- CREEC, MIVEGEC; UMR IRD/CNRS/UM 5290; 911 Avenue Agropolis, BP 64501 34394, Montpellier Cedex 5 France
| | - Tazzio Tissot
- CREEC, MIVEGEC; UMR IRD/CNRS/UM 5290; 911 Avenue Agropolis, BP 64501 34394, Montpellier Cedex 5 France
| | - Beata Ujvari
- Centre for Integrative Ecology, School of Life and Environmental Sciences; Deakin University; Waurn Ponds Australia
| | - Leonard Nunney
- Department of Biology; University of California; Riverside California
- Center for Evolution and Cancer; University of California San Francisco; San Francisco California
| | - Eric Solary
- INSERM U1009; Université Paris-Sud; Gustave Roussy Villejuif France
| | - Lucie Laplane
- INSERM U1009; Université Paris-Sud; Gustave Roussy Villejuif France
| | - François Bonhomme
- ISEM Institut des sciences de l’évolution, Université Montpellier 2; CNRS; Montpellier Cedex France
| | - Marion Vittecoq
- CREEC, MIVEGEC; UMR IRD/CNRS/UM 5290; 911 Avenue Agropolis, BP 64501 34394, Montpellier Cedex 5 France
- Centre de Recherche de la Tour du Valat; le Sambuc; 13200 Arles France
| | - Aurélie Tasiemski
- University of Lille, CNRS; UMR 8198 - Evo-Eco-Paleo, 59000 Lille; France
| | - François Renaud
- CREEC, MIVEGEC; UMR IRD/CNRS/UM 5290; 911 Avenue Agropolis, BP 64501 34394, Montpellier Cedex 5 France
| | - Pascal Pujol
- Service de génétique médicale et chromosomique, Unité d'oncogénétique, CHRU de Montpellier; Hôpital Arnaud de Villeneuve; 371 Avenue du Doyen Gaston Giraud 34295 Montpellier France
| | - Benjamin Roche
- CREEC, MIVEGEC; UMR IRD/CNRS/UM 5290; 911 Avenue Agropolis, BP 64501 34394, Montpellier Cedex 5 France
- International Center for Mathematical and Computational Modeling of Complex Systems (UMI IRD/UPMC UMMISCO); 32 Avenue Henri Varagnat; 93143 Bondy Cedex France
| | - Frédéric Thomas
- CREEC, MIVEGEC; UMR IRD/CNRS/UM 5290; 911 Avenue Agropolis, BP 64501 34394, Montpellier Cedex 5 France
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