1
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Lotsof ER, Krajewski AE, Anderson-Steele B, Rogers J, Zhang L, Yeo J, Conlon SG, Manlove AH, Lee JK, David SS. NEIL1 Recoding due to RNA Editing Impacts Lesion-Specific Recognition and Excision. J Am Chem Soc 2022; 144:14578-14589. [PMID: 35917336 DOI: 10.1021/jacs.2c03625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A-to-I RNA editing is widespread in human cells but is uncommon in the coding regions of proteins outside the nervous system. An unusual target for recoding by the adenosine deaminase ADAR1 is the pre-mRNA of the base excision DNA repair enzyme NEIL1 that results in the conversion of a lysine (K) to arginine (R) within the lesion recognition loop and alters substrate specificity. Differences in base removal by unedited (UE, K242) vs edited (Ed, R242) NEIL1 were evaluated using a series of oxidatively modified DNA bases to provide insight into the chemical and structural features of the lesion base that impact isoform-specific repair. We find that UE NEIL1 exhibits higher activity than Ed NEIL1 toward the removal of oxidized pyrimidines, such as thymine glycol, uracil glycol, 5-hydroxyuracil, and 5-hydroxymethyluracil. Gas-phase calculations indicate that the relative rates in excision track with the more stable lactim tautomer and the proton affinity of N3 of the base lesion. These trends support the contribution of tautomerization and N3 protonation in NEIL1 excision catalysis of these pyrimidine base lesions. Structurally similar but distinct substrate lesions, 5-hydroxycytosine and guanidinohydantoin, are more efficiently removed by the Ed NEIL1 isoform, consistent with the inherent differences in tautomerization, proton affinities, and lability. We also observed biphasic kinetic profiles and lack of complete base removal with specific combinations of the lesion and NEIL1 isoform, suggestive of multiple lesion binding modes. The complexity of NEIL1 isoform activity implies multiple roles for NEIL1 in safeguarding accurate repair and as an epigenetic regulator.
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Affiliation(s)
- Elizabeth R Lotsof
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Allison E Krajewski
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08854, United States
| | - Brittany Anderson-Steele
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - JohnPatrick Rogers
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Lanxin Zhang
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08854, United States
| | - Jongchan Yeo
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Savannah G Conlon
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Amelia H Manlove
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Jeehiun K Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08854, United States
| | - Sheila S David
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
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2
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Tran A, Zheng S, White DS, Curry AM, Cen Y. Retracted Article: Divergent synthesis of 5-substituted pyrimidine 2'-deoxynucleosides and their incorporation into oligodeoxynucleotides for the survey of uracil DNA glycosylases. Chem Sci 2020; 11:11818-11826. [PMID: 34123208 PMCID: PMC8162711 DOI: 10.1039/d0sc04161k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/07/2020] [Indexed: 11/21/2022] Open
Abstract
Recent studies have indicated that 5-methylcytosine (5mC) residues in DNA can be oxidized and potentially deaminated to the corresponding thymine analogs. Some of these oxidative DNA damages have been implicated as new epigenetic markers that could have profound influences on chromatin function as well as disease pathology. In response to oxidative damage, the cells have a complex network of repair systems that recognize, remove and rebuild the lesions. However, how the modified nucleobases are detected and repaired remains elusive, largely due to the limited availability of synthetic oligodeoxynucleotides (ODNs) containing these novel DNA modifications. A concise and divergent synthetic strategy to 5mC derivatives has been developed. These derivatives were further elaborated to the corresponding phosphoramidites to enable the site-specific incorporation of modified nucleobases into ODNs using standard solid-phase DNA synthesis. The synthetic methodology, along with the panel of ODNs, is of great value to investigate the biological functions of epigenetically important nucleobases, and to elucidate the diversity in chemical lesion repair.
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Affiliation(s)
- Ai Tran
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences Colchester VT 05446 USA
| | - Song Zheng
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences Colchester VT 05446 USA
| | - Dawanna S White
- Department of Medicinal Chemistry, Virginia Commonwealth University Richmond VA 23219 USA +1-804-828-7405
| | - Alyson M Curry
- Department of Medicinal Chemistry, Virginia Commonwealth University Richmond VA 23219 USA +1-804-828-7405
| | - Yana Cen
- Department of Medicinal Chemistry, Virginia Commonwealth University Richmond VA 23219 USA +1-804-828-7405
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University Richmond VA 23219 USA
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3
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Sharma N, Pasala MS, Prakash A. Mitochondrial DNA: Epigenetics and environment. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2019; 60:668-682. [PMID: 31335990 PMCID: PMC6941438 DOI: 10.1002/em.22319] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/08/2019] [Accepted: 07/11/2019] [Indexed: 05/22/2023]
Abstract
Maintenance of the mitochondrial genome is essential for proper cellular function. For this purpose, mitochondrial DNA (mtDNA) needs to be faithfully replicated, transcribed, translated, and repaired in the face of constant onslaught from endogenous and environmental agents. Although only 13 polypeptides are encoded within mtDNA, the mitochondrial proteome comprises over 1500 proteins that are encoded by nuclear genes and translocated to the mitochondria for the purpose of maintaining mitochondrial function. Regulation of mtDNA and mitochondrial proteins by epigenetic changes and post-translational modifications facilitate crosstalk between the nucleus and the mitochondria and ultimately lead to the maintenance of cellular health and homeostasis. DNA methyl transferases have been identified in the mitochondria implicating that methylation occurs within this organelle; however, the extent to which mtDNA is methylated has been debated for many years. Mechanisms of demethylation within this organelle have also been postulated, but the exact mechanisms and their outcomes is still an active area of research. Mitochondrial dysfunction in the form of altered gene expression and ATP production, resulting from epigenetic changes, can lead to various conditions including aging-related neurodegenerative disorders, altered metabolism, changes in circadian rhythm, and cancer. Here, we provide an overview of the epigenetic regulation of mtDNA via methylation, long and short noncoding RNAs, and post-translational modifications of nucleoid proteins (as mitochondria lack histones). We also highlight the influence of xenobiotics such as airborne environmental pollutants, contamination from heavy metals, and therapeutic drugs on mtDNA methylation. Environ. Mol. Mutagen., 60:668-682, 2019. © 2019 Wiley Periodicals, Inc.
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4
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Papaluca A, Wagner JR, Saragovi HU, Ramotar D. UNG-1 and APN-1 are the major enzymes to efficiently repair 5-hydroxymethyluracil DNA lesions in C. elegans. Sci Rep 2018; 8:6860. [PMID: 29717169 PMCID: PMC5931555 DOI: 10.1038/s41598-018-25124-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/13/2018] [Indexed: 11/16/2022] Open
Abstract
In Caenorhabditis elegans, two DNA glycosylases, UNG-1 and NTH-1, and two AP endonucleases, APN-1 and EXO-3, have been characterized from the base-excision repair (BER) pathway that repairs oxidatively modified DNA bases. UNG-1 removes uracil, while NTH-1 can remove 5-hydroxymethyluracil (5-hmU), an oxidation product of thymine, as well as other lesions. Both APN-1 and EXO-3 can incise AP sites and remove 3′-blocking lesions at DNA single strand breaks, and only APN-1 possesses 3′- to 5′-exonulease and nucleotide incision repair activities. We used C. elegans mutants to study the role of the BER pathway in processing 5-hmU. We observe that ung-1 mutants exhibited a decrease in brood size and lifespan, and an elevated level of germ cell apoptosis when challenged with 5-hmU. These phenotypes were exacerbated by RNAi downregulation of apn-1 in the ung-1 mutant. The nth-1 or exo-3 mutants displayed wild type phenotypes towards 5-hmU. We show that partially purified UNG-1 can act on 5-hmU lesion in vitro. We propose that UNG-1 removes 5-hmU incorporated into the genome and the resulting AP site is cleaved by APN-1 or EXO-3. In the absence of UNG-1, the 5-hmU is removed by NTH-1 creating a genotoxic 3′-blocking lesion that requires the action of APN-1.
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Affiliation(s)
- Arturo Papaluca
- Maisonneuve-Rosemont Hospital, Research Center, Université de Montréal, Department of Medicine, 5415 Boul. de l'Assomption, Montréal, Québec, H1T2M4, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Department of Pharmacology and Therapeutics, McGill University, Department of Pharmacology and Therapeutics, 3755 Chemin de la Côte Sainte-Catherine, Québec, Montréal, H3T1E2, Canada
| | - J Richard Wagner
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12 Avenue Nord, Sherbrooke, Québec, J1H5N4, Canada
| | - H Uri Saragovi
- Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Department of Pharmacology and Therapeutics, McGill University, Department of Pharmacology and Therapeutics, 3755 Chemin de la Côte Sainte-Catherine, Québec, Montréal, H3T1E2, Canada
| | - Dindial Ramotar
- Maisonneuve-Rosemont Hospital, Research Center, Université de Montréal, Department of Medicine, 5415 Boul. de l'Assomption, Montréal, Québec, H1T2M4, Canada.
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5
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Slyvka A, Mierzejewska K, Bochtler M. Nei-like 1 (NEIL1) excises 5-carboxylcytosine directly and stimulates TDG-mediated 5-formyl and 5-carboxylcytosine excision. Sci Rep 2017; 7:9001. [PMID: 28827588 PMCID: PMC5566547 DOI: 10.1038/s41598-017-07458-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 06/26/2017] [Indexed: 01/01/2023] Open
Abstract
Thymine DNA glycosylase (TDG) and Nei-like 1 (NEIL1) have both been implicated in the base excision repair step of active DNA demethylation. The robust glycosylase activity of TDG on DNA substrates containing 5-formylcytosine (5fC) or 5-carboxylcytosine (5caC) is universally accepted, but the mode of action of NEIL1 is still debated. Based on genetic experiments, it has been suggested that NEIL1 acts redundantly with TDG and excises 5fC and 5caC directly. However, this result has been disputed, and it was suggested instead that NEIL1 is recruited by the monofunctional TDG for the 2′-deoxyribose excision step. Using purified human NEIL1 and its catalytically impaired P2T and E3Q variants as controls, we detect NEIL1 activity on 5caC, but not a 5fC containing dsDNA substrate. We confirm direct NEIL1 TDG binding and NEIL1 mediated 2′-deoxyribose excision downstream of TDG glycosylase activity. NEIL1 acts not only downstream of TDG, but also enhances TDG activity on 5fC or 5caC containing DNA. NEIL1 mediated enhancement of the TDG glycosylase activity is substrate specific and does not occur for dsDNA with a T/G mismatch.
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Affiliation(s)
- Anton Slyvka
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland
| | - Karolina Mierzejewska
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland
| | - Matthias Bochtler
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland. .,Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Pawinskiego 5a, 02-106, Warsaw, Poland.
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6
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Alsøe L, Sarno A, Carracedo S, Domanska D, Dingler F, Lirussi L, SenGupta T, Tekin NB, Jobert L, Alexandrov LB, Galashevskaya A, Rada C, Sandve GK, Rognes T, Krokan HE, Nilsen H. Uracil Accumulation and Mutagenesis Dominated by Cytosine Deamination in CpG Dinucleotides in Mice Lacking UNG and SMUG1. Sci Rep 2017; 7:7199. [PMID: 28775312 PMCID: PMC5543110 DOI: 10.1038/s41598-017-07314-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 06/23/2017] [Indexed: 12/30/2022] Open
Abstract
Both a DNA lesion and an intermediate for antibody maturation, uracil is primarily processed by base excision repair (BER), either initiated by uracil-DNA glycosylase (UNG) or by single-strand selective monofunctional uracil DNA glycosylase (SMUG1). The relative in vivo contributions of each glycosylase remain elusive. To assess the impact of SMUG1 deficiency, we measured uracil and 5-hydroxymethyluracil, another SMUG1 substrate, in Smug1−/− mice. We found that 5-hydroxymethyluracil accumulated in Smug1−/− tissues and correlated with 5-hydroxymethylcytosine levels. The highest increase was found in brain, which contained about 26-fold higher genomic 5-hydroxymethyluracil levels than the wild type. Smug1−/− mice did not accumulate uracil in their genome and Ung−/− mice showed slightly elevated uracil levels. Contrastingly, Ung−/−Smug1−/− mice showed a synergistic increase in uracil levels with up to 25-fold higher uracil levels than wild type. Whole genome sequencing of UNG/SMUG1-deficient tumours revealed that combined UNG and SMUG1 deficiency leads to the accumulation of mutations, primarily C to T transitions within CpG sequences. This unexpected sequence bias suggests that CpG dinucleotides are intrinsically more mutation prone. In conclusion, we showed that SMUG1 efficiently prevent genomic uracil accumulation, even in the presence of UNG, and identified mutational signatures associated with combined UNG and SMUG1 deficiency.
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Affiliation(s)
- Lene Alsøe
- Department of Clinical Molecular Biology, Ahus Campus, University of Oslo, Oslo, Norway.,Akershus University Hospital, Lørenskog, Norway
| | - Antonio Sarno
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,The Liaison Committee for Education, Research and Innovation in Central Norway, Trondheim, Norway
| | - Sergio Carracedo
- Department of Clinical Molecular Biology, Ahus Campus, University of Oslo, Oslo, Norway.,Akershus University Hospital, Lørenskog, Norway
| | - Diana Domanska
- Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316, Oslo, Norway
| | | | - Lisa Lirussi
- Department of Clinical Molecular Biology, Ahus Campus, University of Oslo, Oslo, Norway.,Akershus University Hospital, Lørenskog, Norway
| | - Tanima SenGupta
- Department of Clinical Molecular Biology, Ahus Campus, University of Oslo, Oslo, Norway.,Akershus University Hospital, Lørenskog, Norway
| | - Nuriye Basdag Tekin
- Department of Clinical Molecular Biology, Ahus Campus, University of Oslo, Oslo, Norway.,Akershus University Hospital, Lørenskog, Norway
| | - Laure Jobert
- Department of Clinical Molecular Biology, Ahus Campus, University of Oslo, Oslo, Norway.,Akershus University Hospital, Lørenskog, Norway.,LifeTechnologies AS, Ullernschauseen 52, 0379, Oslo, Norway
| | - Ludmil B Alexandrov
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.,Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.,University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, 87102, USA
| | - Anastasia Galashevskaya
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | | | - Geir Kjetil Sandve
- Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316, Oslo, Norway
| | - Torbjørn Rognes
- Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316, Oslo, Norway.,Department of Microbiology, Oslo University Hospital, Rikshospitalet, PO Box 4950 Nydalen, NO-0424, Oslo, Norway
| | - Hans E Krokan
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Hilde Nilsen
- Department of Clinical Molecular Biology, Ahus Campus, University of Oslo, Oslo, Norway. .,Akershus University Hospital, Lørenskog, Norway.
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7
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8
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Bauer NC, Corbett AH, Doetsch PW. The current state of eukaryotic DNA base damage and repair. Nucleic Acids Res 2015; 43:10083-101. [PMID: 26519467 PMCID: PMC4666366 DOI: 10.1093/nar/gkv1136] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/16/2015] [Indexed: 12/15/2022] Open
Abstract
DNA damage is a natural hazard of life. The most common DNA lesions are base, sugar, and single-strand break damage resulting from oxidation, alkylation, deamination, and spontaneous hydrolysis. If left unrepaired, such lesions can become fixed in the genome as permanent mutations. Thus, evolution has led to the creation of several highly conserved, partially redundant pathways to repair or mitigate the effects of DNA base damage. The biochemical mechanisms of these pathways have been well characterized and the impact of this work was recently highlighted by the selection of Tomas Lindahl, Aziz Sancar and Paul Modrich as the recipients of the 2015 Nobel Prize in Chemistry for their seminal work in defining DNA repair pathways. However, how these repair pathways are regulated and interconnected is still being elucidated. This review focuses on the classical base excision repair and strand incision pathways in eukaryotes, considering both Saccharomyces cerevisiae and humans, and extends to some important questions and challenges facing the field of DNA base damage repair.
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Affiliation(s)
- Nicholas C Bauer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Paul W Doetsch
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
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9
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Shinmura K, Kato H, Kawanishi Y, Goto M, Tao H, Inoue Y, Nakamura S, Sugimura H. NEIL1 p.Gln282Stop variant is predominantly localized in the cytoplasm and exhibits reduced activity in suppressing mutations. Gene 2015; 571:33-42. [PMID: 26095805 DOI: 10.1016/j.gene.2015.06.043] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 04/21/2015] [Accepted: 06/16/2015] [Indexed: 01/04/2023]
Abstract
Human NEIL1 protein is a DNA glycosylase known to be involved in the repair of oxidized DNA lesions. A c.C844T germline variant of the NEIL1 gene has recently been identified in the Japanese population, however, the p.Q282Stop-type protein produced from this variant gene has not yet been characterized. In this study to determine whether the NEIL1 c.C844T variant might be a defective allele, we investigated the subcellular localization of the p.Q282Stop-type protein and its ability to suppress the development of mutations in mammalian cells. In contrast to the nuclear localization of wild-type (WT) NEIL1, the p.Q282Stop-type protein tagged with GFP or FLAG was localized predominantly in the cytoplasm of human H1299 cells. Mutant forms of the putative nuclear localization signal (NLS, amino acid sequences 359 to 378) of NEIL1-GFP resulted in predominant cytoplasmic localization of the mutants, suggesting that the abnormal localization of p.Q282Stop-type NEIL1 may also be caused by a loss of the putative NLS in the protein. Next, V79 mammalian cell lines inducibly expressing WT NEIL1 or p.Q282Stop-type NEIL1 were established using the piggyBac transposon vector system, and the mutation frequency was compared between the cell lines by HPRT assay. The frequency of mutations induced by glucose oxidase, an oxidative stress inducer, was higher in the p.Q282Stop-type NEIL1-transposed cells than that in the WT NEIL1-transposed cells. Finally, the Cancer Genome Atlas (TCGA) data showed an increased number of somatic mutations in primary carcinomas containing a truncating NEIL1 mutation. These results suggest that p.Q282Stop-type NEIL1 is predominantly localized in the cytoplasm, possibly due to a loss of the NLS, and possesses a reduced ability to suppress the onset of mutations, both findings suggesting that NEIL1 c.C844T is a defective allele.
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Affiliation(s)
- Kazuya Shinmura
- Department of Tumor Pathology, Hamamatsu University School of Medicine, Hamamatsu, Japan.
| | - Hisami Kato
- Department of Tumor Pathology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yuichi Kawanishi
- Research Equipment Center, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Masanori Goto
- Division of Carcinogenesis and Prevention, National Cancer Center Research Institute, Tokyo, Japan
| | - Hong Tao
- Department of Tumor Pathology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yusuke Inoue
- Department of Tumor Pathology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Satoki Nakamura
- Department of Tumor Pathology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Haruhiko Sugimura
- Department of Tumor Pathology, Hamamatsu University School of Medicine, Hamamatsu, Japan
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10
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Sharbeen G, McCarroll J, Goldstein D, Phillips PA. Exploiting base excision repair to improve therapeutic approaches for pancreatic cancer. Front Nutr 2015; 2:10. [PMID: 25988138 PMCID: PMC4428371 DOI: 10.3389/fnut.2015.00010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 03/10/2015] [Indexed: 12/13/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDA) is a highly chemoresistant and metastatic disease with a dismal 5-year survival rate of 6%. More effective therapeutic targets and approaches are urgently needed to tackle this devastating disease. The base excision repair (BER) pathway has been identified as a predictor of therapeutic response, prognostic factor, and therapeutic target in a variety of cancers. This review will discuss our current understanding of BER in PDA and its potential to improve PDA treatment.
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Affiliation(s)
- George Sharbeen
- Pancreatic Cancer Translational Research Group, Lowy Cancer Research Centre, Prince of Wales Clinical School, UNSW Australia , Sydney, NSW , Australia
| | - Joshua McCarroll
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Australia , Sydney, NSW , Australia
| | - David Goldstein
- Pancreatic Cancer Translational Research Group, Lowy Cancer Research Centre, Prince of Wales Clinical School, UNSW Australia , Sydney, NSW , Australia
| | - Phoebe A Phillips
- Pancreatic Cancer Translational Research Group, Lowy Cancer Research Centre, Prince of Wales Clinical School, UNSW Australia , Sydney, NSW , Australia
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11
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Pfaffeneder T, Spada F, Wagner M, Brandmayr C, Laube SK, Eisen D, Truss M, Steinbacher J, Hackner B, Kotljarova O, Schuermann D, Michalakis S, Kosmatchev O, Schiesser S, Steigenberger B, Raddaoui N, Kashiwazaki G, Müller U, Spruijt CG, Vermeulen M, Leonhardt H, Schär P, Müller M, Carell T. Tet oxidizes thymine to 5-hydroxymethyluracil in mouse embryonic stem cell DNA. Nat Chem Biol 2014; 10:574-81. [PMID: 24838012 DOI: 10.1038/nchembio.1532] [Citation(s) in RCA: 219] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 04/17/2014] [Indexed: 12/25/2022]
Abstract
Ten eleven translocation (Tet) enzymes oxidize the epigenetically important DNA base 5-methylcytosine (mC) stepwise to 5-hydroxymethylcytosine (hmC), 5-formylcytosine and 5-carboxycytosine. It is currently unknown whether Tet-induced oxidation is limited to cytosine-derived nucleobases or whether other nucleobases are oxidized as well. We synthesized isotopologs of all major oxidized pyrimidine and purine bases and performed quantitative MS to show that Tet-induced oxidation is not limited to mC but that thymine is also a substrate that gives 5-hydroxymethyluracil (hmU) in mouse embryonic stem cells (mESCs). Using MS-based isotope tracing, we show that deamination of hmC does not contribute to the steady-state levels of hmU in mESCs. Protein pull-down experiments in combination with peptide tracing identifies hmU as a base that influences binding of chromatin remodeling proteins and transcription factors, suggesting that hmU has a specific function in stem cells besides triggering DNA repair.
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Affiliation(s)
- Toni Pfaffeneder
- 1] Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany. [2]
| | - Fabio Spada
- 1] Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany. [2]
| | - Mirko Wagner
- 1] Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany. [2]
| | - Caterina Brandmayr
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Silvia K Laube
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - David Eisen
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Matthias Truss
- Charité Universitätsklinikum, Otto-Heubner-Centrum für Kinder und Jugendmedizin, Klinik für Allgemeine Pädiatrie, Labor für Pädiatrische Molekularbiologie, Berlin, Germany
| | - Jessica Steinbacher
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Benjamin Hackner
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Olga Kotljarova
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - David Schuermann
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Stylianos Michalakis
- Center for Integrated Protein Science at the Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-Universität München, München, Germany
| | - Olesea Kosmatchev
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Stefan Schiesser
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Barbara Steigenberger
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Nada Raddaoui
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Gengo Kashiwazaki
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Udo Müller
- Center for Integrated Protein Science at the Department of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Cornelia G Spruijt
- Department of Molecular Cancer Research, Cancer Genomics Netherlands, Utrecht, The Netherlands
| | - Michiel Vermeulen
- 1] Department of Molecular Cancer Research, Cancer Genomics Netherlands, Utrecht, The Netherlands. [2]
| | - Heinrich Leonhardt
- Center for Integrated Protein Science at the Department of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Primo Schär
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Markus Müller
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Thomas Carell
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
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12
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Ho CK, Siu-wai C, Siu PM, Benzie IF. Genoprotection and genotoxicity of green tea (Camellia sinensis): Are they two sides of the same redox coin? Redox Rep 2014; 18:150-4. [PMID: 23849339 DOI: 10.1179/1351000213y.0000000051] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
OBJECTIVES Regular intake of green tea associates with lower DNA damage and increased resistance of DNA to oxidant challenge. However, in vitro pro-oxidant effects of green tea have been reported. Both effects could be mediated by hydrogen peroxide (H2O2) which is generated by autoxidation of tea catechins. In large amounts, H2O2 is genotoxic, but low concentrations could activate the redox-sensitive antioxidant response element (ARE) via the Keap-1/Nrf2 redox switch, inducing genoprotective adaptations. Our objective was to test this hypothesis. METHODS Peripheral lymphocytes from healthy volunteers were incubated for 30 minutes at 37°C in freshly prepared tea solutions (0.005, 0.01, 0.05%w/v (7, 14, 71 µmol/l total catechins) in phosphate buffered saline (PBS), with PBS as control) in the presence and absence of catalase (CAT). H2O2 in tea was measured colorimetrically. Oxidation-induced DNA lesions were measured by the Fpg-assisted comet assay. RESULTS H2O2 concentrations in 0.005, 0.01, and 0.05% green tea after 30 minutes at 37°C were, respectively, ∼3, ∼7, and ∼52 µmol/l. Cells incubated in 0.005 and 0.01% tea showed less (P < 0.001) DNA damage compared to control cells. Cells treated with 0.05% green tea showed ∼50% (P < 0.001) more DNA damage. The presence of CAT prevented this damage, but did not remove the genoprotective effects of low-dose tea. No significant changes in expression of ARE-associated genes (HMOX1, NRF2, KEAP1, BACH1, and hOGG1) were seen in cells treated with tea or tea + CAT. CONCLUSION Genoprotection by low-dose green tea could be due to direct antioxidant protection by green tea polyphenols, or to H2O2-independent signalling pathways.
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Affiliation(s)
- Cyrus K Ho
- The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
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13
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Kidane D, Chae WJ, Czochor J, Eckert KA, Glazer PM, Bothwell ALM, Sweasy JB. Interplay between DNA repair and inflammation, and the link to cancer. Crit Rev Biochem Mol Biol 2014; 49:116-39. [PMID: 24410153 DOI: 10.3109/10409238.2013.875514] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
DNA damage and repair are linked to cancer. DNA damage that is induced endogenously or from exogenous sources has the potential to result in mutations and genomic instability if not properly repaired, eventually leading to cancer. Inflammation is also linked to cancer. Reactive oxygen and nitrogen species (RONs) produced by inflammatory cells at sites of infection can induce DNA damage. RONs can also amplify inflammatory responses, leading to increased DNA damage. Here, we focus on the links between DNA damage, repair, and inflammation, as they relate to cancer. We examine the interplay between chronic inflammation, DNA damage and repair and review recent findings in this rapidly emerging field, including the links between DNA damage and the innate immune system, and the roles of inflammation in altering the microbiome, which subsequently leads to the induction of DNA damage in the colon. Mouse models of defective DNA repair and inflammatory control are extensively reviewed, including treatment of mouse models with pathogens, which leads to DNA damage. The roles of microRNAs in regulating inflammation and DNA repair are discussed. Importantly, DNA repair and inflammation are linked in many important ways, and in some cases balance each other to maintain homeostasis. The failure to repair DNA damage or to control inflammatory responses has the potential to lead to cancer.
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Affiliation(s)
- Dawit Kidane
- Departments of Therapeutic Radiology and Genetics
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14
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Brooks SC, Adhikary S, Rubinson EH, Eichman BF. Recent advances in the structural mechanisms of DNA glycosylases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:247-71. [PMID: 23076011 DOI: 10.1016/j.bbapap.2012.10.005] [Citation(s) in RCA: 128] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 09/24/2012] [Accepted: 10/05/2012] [Indexed: 02/06/2023]
Abstract
DNA glycosylases safeguard the genome by locating and excising a diverse array of aberrant nucleobases created from oxidation, alkylation, and deamination of DNA. Since the discovery 28years ago that these enzymes employ a base flipping mechanism to trap their substrates, six different protein architectures have been identified to perform the same basic task. Work over the past several years has unraveled details for how the various DNA glycosylases survey DNA, detect damage within the duplex, select for the correct modification, and catalyze base excision. Here, we provide a broad overview of these latest advances in glycosylase mechanisms gleaned from structural enzymology, highlighting features common to all glycosylases as well as key differences that define their particular substrate specificities.
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Affiliation(s)
- Sonja C Brooks
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
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15
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Hunter SE, Gustafson MA, Margillo KM, Lee SA, Ryde IT, Meyer JN. In vivo repair of alkylating and oxidative DNA damage in the mitochondrial and nuclear genomes of wild-type and glycosylase-deficient Caenorhabditis elegans. DNA Repair (Amst) 2012; 11:857-63. [PMID: 22959841 DOI: 10.1016/j.dnarep.2012.08.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 07/04/2012] [Accepted: 08/06/2012] [Indexed: 12/28/2022]
Abstract
Base excision repair (BER) is an evolutionarily conserved DNA repair pathway that is critical for repair of many of the most common types of DNA damage generated both by endogenous metabolic pathways and exposure to exogenous stressors such as pollutants. Caenorhabditis elegans is an increasingly important model organism for the study of DNA damage-related processes including DNA repair, genotoxicity, and apoptosis, but BER is not well understood in this organism, and has not previously been measured in vivo. We report robust BER in the nuclear genome and slightly slower damage removal from the mitochondrial genome; in both cases the removal rates are comparable to those observed in mammals. However we could detect no deficiency in BER in the nth-1 strain, which carries a deletion in the only glycosylase yet described in C. elegans that repairs oxidative DNA damage. We also failed to detect increased lethality or growth inhibition in nth-1 nematodes after exposure to oxidative or alkylating damage, suggesting the existence of at least one additional as-yet undetected glycosylase.
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Affiliation(s)
- Senyene E Hunter
- Nicholas School of the Environment and Center for the Environmental Implications of Nanotechnology, Duke University, Durham, NC 27708-0328, USA
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16
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Moréra S, Grin I, Vigouroux A, Couvé S, Henriot V, Saparbaev M, Ishchenko AA. Biochemical and structural characterization of the glycosylase domain of MBD4 bound to thymine and 5-hydroxymethyuracil-containing DNA. Nucleic Acids Res 2012; 40:9917-26. [PMID: 22848106 PMCID: PMC3479182 DOI: 10.1093/nar/gks714] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Active DNA demethylation in mammals occurs via hydroxylation of 5-methylcytosine to 5-hydroxymethylcytosine (5hmC) by the ten-eleven translocation family of proteins (TETs). 5hmC residues in DNA can be further oxidized by TETs to 5-carboxylcytosines and/or deaminated by the Activation Induced Deaminase/Apolipoprotein B mRNA-editing enzyme complex family proteins to 5-hydromethyluracil (5hmU). Excision and replacement of these intermediates is initiated by DNA glycosylases such as thymine-DNA glycosylase (TDG), methyl-binding domain protein 4 (MBD4) and single-strand specific monofunctional uracil-DNA glycosylase 1 in the base excision repair pathway. Here, we report detailed biochemical and structural characterization of human MBD4 which contains mismatch-specific TDG activity. Full-length as well as catalytic domain (residues 426–580) of human MBD4 (MBD4cat) can remove 5hmU when opposite to G with good efficiency. Here, we also report six crystal structures of human MBD4cat: an unliganded form and five binary complexes with duplex DNA containing a T•G, 5hmU•G or AP•G (apurinic/apyrimidinic) mismatch at the target base pair. These structures reveal that MBD4cat uses a base flipping mechanism to specifically recognize thymine and 5hmU. The recognition mechanism of flipped-out 5hmU bases in MBD4cat active site supports the potential role of MBD4, together with TDG, in maintenance of genome stability and active DNA demethylation in mammals.
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Affiliation(s)
- Solange Moréra
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Gif-sur-Yvette Cedex, F-91198, France.
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17
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Wallace SS, Murphy DL, Sweasy JB. Base excision repair and cancer. Cancer Lett 2012; 327:73-89. [PMID: 22252118 DOI: 10.1016/j.canlet.2011.12.038] [Citation(s) in RCA: 224] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 12/20/2011] [Accepted: 12/24/2011] [Indexed: 01/13/2023]
Abstract
Base excision repair is the system used from bacteria to man to remove the tens of thousands of endogenous DNA damages produced daily in each human cell. Base excision repair is required for normal mammalian development and defects have been associated with neurological disorders and cancer. In this paper we provide an overview of short patch base excision repair in humans and summarize current knowledge of defects in base excision repair in mouse models and functional studies on short patch base excision repair germ line polymorphisms and their relationship to cancer. The biallelic germ line mutations that result in MUTYH-associated colon cancer are also discussed.
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Affiliation(s)
- Susan S Wallace
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Burlington, 05405-0068, United States.
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18
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Guo JU, Su Y, Zhong C, Ming GL, Song H. Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell 2011; 145:423-34. [PMID: 21496894 DOI: 10.1016/j.cell.2011.03.022] [Citation(s) in RCA: 1013] [Impact Index Per Article: 77.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2010] [Revised: 01/23/2011] [Accepted: 03/11/2011] [Indexed: 12/31/2022]
Abstract
Cytosine methylation is the major covalent modification of mammalian genomic DNA and plays important roles in transcriptional regulation. The molecular mechanism underlying the enzymatic removal of this epigenetic mark, however, remains elusive. Here, we show that 5-methylcytosine (5mC) hydroxylase TET1, by converting 5mCs to 5-hydroxymethylcytosines (5hmCs), promotes DNA demethylation in mammalian cells through a process that requires the base excision repair pathway. Though expression of the 12 known human DNA glycosylases individually did not enhance removal of 5hmCs in mammalian cells, demethylation of both exogenously introduced and endogenous 5hmCs is promoted by the AID (activation-induced deaminase)/APOBEC (apolipoprotein B mRNA-editing enzyme complex) family of cytidine deaminases. Furthermore, Tet1 and Apobec1 are involved in neuronal activity-induced, region-specific, active DNA demethylation and subsequent gene expression in the dentate gyrus of the adult mouse brain in vivo. Our study suggests a TET1-induced oxidation-deamination mechanism for active DNA demethylation in mammals.
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Affiliation(s)
- Junjie U Guo
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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19
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Wang J, Yuan B, Guerrero C, Bahde R, Gupta S, Wang Y. Quantification of oxidative DNA lesions in tissues of Long-Evans Cinnamon rats by capillary high-performance liquid chromatography-tandem mass spectrometry coupled with stable isotope-dilution method. Anal Chem 2011; 83:2201-9. [PMID: 21323344 DOI: 10.1021/ac103099s] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The purpose of our study was to develop suitable methods to quantify oxidative DNA lesions in the setting of transition metal-related diseases. Transition metal-driven Fenton reactions constitute an important endogenous source of reactive oxygen species (ROS). In genetic diseases with accumulation of transition metal ions, excessive ROS production causes pathophysiological changes, including DNA damage. Wilson's disease is an autosomal recessive disorder with copper toxicosis due to deficiency of ATP7B protein needed for excreting copper into bile. The Long-Evans Cinnamon (LEC) rat bears a deletion in Atp7b gene and serves as an excellent model for hepatic Wilson's disease. We used a sensitive capillary liquid chromatography-electrospray-tandem mass spectrometry (LC-ESI-MS/MS/MS) method in conjunction with the stable isotope-dilution technique to quantify several types of oxidative DNA lesions in the liver and brain of LEC rats. These lesions included 5-formyl-2'-deoxyuridine, 5-hydroxymethyl-2'-deoxyuridine, and the 5'R and 5'S diastereomers of 8,5'-cyclo-2'-deoxyguanosine and 8,5'-cyclo-2'-deoxyadenosine. Moreover, the levels of these DNA lesions in the liver and brain increased with age and correlated with age-dependent regulation of the expression of DNA repair genes in LEC rats. These results provide significant new knowledge for better understanding the implications of oxidative DNA lesions in transition metal-induced diseases, such as Wilson's disease, as well as in aging and aging-related pathological conditions.
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Affiliation(s)
- Jin Wang
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
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20
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Natural history of eukaryotic DNA methylation systems. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 101:25-104. [PMID: 21507349 DOI: 10.1016/b978-0-12-387685-0.00002-0] [Citation(s) in RCA: 151] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Methylation of cytosines and adenines in DNA is a widespread epigenetic mark in both prokaryotes and eukaryotes. In eukaryotes, it has a profound influence on chromatin structure and dynamics. Recent advances in genomics and biochemistry have considerably elucidated the functions and provenance of these DNA modifications. DNA methylases appear to have emerged first in bacterial restriction-modification (R-M) systems from ancient RNA-modifying enzymes, in transitions that involved acquisition of novel catalytic residues and DNA-recognition features. DNA adenine methylases appear to have been acquired by ciliates, heterolobosean amoeboflagellates, and certain chlorophyte algae. Six distinct clades of cytosine methylases, including the DNMT1, DNMT2, and DNMT3 clades, were acquired by eukaryotes through independent lateral transfer of their precursors from bacteria or bacteriophages. In addition to these, multiple adenine and cytosine methylases were acquired by several families of eukaryotic transposons. In eukaryotes, the DNA-methylase module was often combined with distinct modified and unmodified peptide recognition domains and other modules mediating specialized interactions, for example, the RFD module of DNMT1 which contains a permuted Sm domain linked to a helix-turn-helix domain. In eukaryotes, the evolution of DNA methylases appears to have proceeded in parallel to the elaboration of histone-modifying enzymes and the RNAi system, with functions related to counter-viral and counter-transposon defense, and regulation of DNA repair and differential gene expression being their primary ancestral functions. Diverse DNA demethylation systems that utilize base-excision repair via DNA glycosylases and cytosine deaminases appear to have emerged in multiple eukaryotic lineages. Comparative genomics suggests that the link between cytosine methylation and DNA glycosylases probably emerged first in a novel R-M system in bacteria. Recent studies suggest that the 5mC is not a terminal DNA modification, with enzymes of the Tet/JBP family of 2-oxoglutarate- and iron-dependent dioxygenases further hydroxylating it to form 5-hydroxymethylcytosine (5hmC). These enzymes emerged first in bacteriophages and appear to have been transferred to eukaryotes on one or more occasions. Eukaryotes appear to have recruited three major types of DNA-binding domains (SRA/SAD, TAM/MBD, and CXXC) in discriminating DNA with methylated or unmethylated cytosines. Analysis of the domain architectures of these domains and the DNA methylases suggests that early in eukaryotic evolution they developed a close functional link with SET-domain methylases and Jumonji-related demethylases that operate on peptides in chromatin proteins. In several eukaryotes, other functional connections were elaborated in the form of various combinations between domains related to DNA methylation and those involved in ATP-dependent chromatin remodeling and RNAi. In certain eukaryotes, such as mammals and angiosperms, novel dependencies on the DNA methylation system emerged, which resulted in it affecting unexpected aspects of the biology of these organisms such as parent-offspring interactions. In genomic terms, this was reflected in the emergence of new proteins related to methylation, such as Stella. The well-developed methylation systems of certain heteroloboseans, stramenopiles, chlorophytes, and haptophyte indicate that these might be new model systems to explore the relevance of DNA modifications in eukaryotes.
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21
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Nemec AA, Wallace SS, Sweasy JB. Variant base excision repair proteins: contributors to genomic instability. Semin Cancer Biol 2010; 20:320-8. [PMID: 20955798 DOI: 10.1016/j.semcancer.2010.10.010] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cells sustain endogenous DNA damage at rates greater than 20,000 DNA lesions per cell per day. These damages occur largely as a result of the inherently unstable nature of DNA and the presence of reactive oxygen species within cells. The base excision repair system removes the majority of DNA lesions resulting from endogenous DNA damage. There are several enzymes that function during base excision repair. Importantly, there are over 100 germline single nucleotide polymorphisms in genes that function in base excision repair and that result in non-synonymous amino acid substitutions in the proteins they encode. Somatic variants of these enzymes are also found in human tumors. Variant repair enzymes catalyze aberrant base excision repair. Aberrant base excision repair combined with continuous endogenous DNA damage over time has the potential to lead to a mutator phenotype. Mutations that arise in key growth control genes, imbalances in chromosome number, chromosomal translocations, and loss of heterozygosity can result in the initiation of human cancer or its progression.
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Affiliation(s)
- Antonia A Nemec
- Department of Therapeutic Radiology, 15 York Street, New Haven, CT 06510, United States
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22
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Evans MD, Saparbaev M, Cooke MS. DNA repair and the origins of urinary oxidized 2'-deoxyribonucleosides. Mutagenesis 2010; 25:433-42. [PMID: 20522520 DOI: 10.1093/mutage/geq031] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Monitoring oxidative stress in vivo is made easier by the ability to use samples obtained non-invasively, such as urine. The analysis of DNA oxidation, by measurement of oxidized 2'-deoxyribonucleosides in urine, particularly 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG), has been reported extensively in the literature in many situations relating to various pathologies, populations and environmental exposures. Understanding the origins of urinary 8-oxodG, other than it simply being a marker of DNA oxidation or its synthetic precursors, is important to being able to effectively interpret differences in baseline urinary 8-oxodG levels between subject groups and changes in excretion. Diet and cell turnover play negligible roles in contributing to urinary 8-oxodG levels, leaving DNA repair as a primary source of this lesion. However, which repair processes contribute, and to what extent, to urinary 8-oxodG is still open to question. The most rational source would be the activity of selected members of the Nudix hydrolase family of enzymes, sanitizing the deoxyribonucleotide pool via the degradation of 8-oxo-7,8-dihydro-2'-deoxyguanosine-5'-triphosphate and 8-oxo-7,8-dihydro-2'-deoxyguanosine-5'-diphosphate, yielding mononucleotide products that can then be dephosphorylated to 8-oxodG and excreted. However, nucleotide excision repair (NER), transcription-coupled repair, nucleotide incision repair (NIR), mismatch repair and various exonuclease activities, such as proofreading function associated with DNA polymerases, can all feasibly generate initial products that could yield 8-oxodG after further metabolism. A recent study implying that a significant proportion of genomic 8-oxodG exists in the context of tandem lesions, refractory to repair by glycosylases, suggests the roles of NER and/or NIR remain to be further examined and defined as a source of 8-oxodG. 8-OxodG has been the primary focus of investigation, but other oxidized 2'-deoxyribonucleosides have been detected in urine, 2'-deoxythymidine glycol and 5-hydroxymethyl-2'-deoxyuridine; the origins of these compounds in urine, however, are presently even more speculative than for 8-oxodG.
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Affiliation(s)
- Mark D Evans
- Radiation and Oxidative Stress Section, Department of Cancer Studies and Molecular Medicine, University of Leicester, Leicester LE1 7RH, UK.
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23
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The oxidative DNA glycosylases of Mycobacterium tuberculosis exhibit different substrate preferences from their Escherichia coli counterparts. DNA Repair (Amst) 2009; 9:177-90. [PMID: 20031487 DOI: 10.1016/j.dnarep.2009.11.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Revised: 11/20/2009] [Accepted: 11/21/2009] [Indexed: 11/22/2022]
Abstract
The DNA glycosylases that remove oxidized DNA bases fall into two general families: the Fpg/Nei family and the Nth superfamily. Based on protein sequence alignments, we identified four putative Fpg/Nei family members, as well as a putative Nth protein in Mycobacterium tuberculosis H37Rv. All four Fpg/Nei proteins were successfully overexpressed using a bicistronic vector created in our laboratory. The MtuNth protein was also overexpressed in soluble form. The substrate specificities of the purified enzymes were characterized in vitro with oligodeoxynucleotide substrates containing single lesions. Some were further characterized by gas chromatography/mass spectrometry (GC/MS) analysis of products released from gamma-irradiated DNA. MtuFpg1 has substrate specificity similar to that of EcoFpg. Both EcoFpg and MtuFpg1 are more efficient at removing spiroiminodihydantoin (Sp) than 7,8-dihydro-8-oxoguanine (8-oxoG). However, MtuFpg1 shows a substantially increased opposite base discrimination compared to EcoFpg. MtuFpg2 contains only the C-terminal domain of an Fpg protein and has no detectable DNA binding activity or DNA glycosylase/lyase activity and thus appears to be a pseudogene. MtuNei1 recognizes oxidized pyrimidines on both double-stranded and single-stranded DNA and exhibits uracil DNA glycosylase activity. MtuNth recognizes a variety of oxidized bases, including urea, 5,6-dihydrouracil (DHU), 5-hydroxyuracil (5-OHU), 5-hydroxycytosine (5-OHC) and methylhydantoin (MeHyd). Both MtuNei1 and MtuNth excise thymine glycol (Tg); however, MtuNei1 strongly prefers the (5R) isomers, whereas MtuNth recognizes only the (5S) isomers. MtuNei2 did not demonstrate activity in vitro as a recombinant protein, but like MtuNei1 when expressed in Escherichia coli, it decreased the spontaneous mutation frequency of both the fpg mutY nei triple and nei nth double mutants, suggesting that MtuNei2 is functionally active in vivo recognizing both guanine and cytosine oxidation products. The kinetic parameters of the MtuFpg1, MtuNei1 and MtuNth proteins on selected substrates were also determined and compared to those of their E. coli homologs.
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Knaevelsrud I, Slupphaug G, Leiros I, Matsuda A, Ruoff P, Bjelland S. Opposite-base dependent excision of 5-formyluracil from DNA by hSMUG1. Int J Radiat Biol 2009; 85:413-20. [PMID: 19365746 DOI: 10.1080/09553000902818915] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
PURPOSE The aim of this study was to determine the excision efficiency of hSMUG1 (human single-strand-selective monofunctional uracil-DNA glycosylase) for 5-formyluracil (fU), a major thymine lesion formed by ionizing radiation, opposite all normal bases in DNA, to possibly explain mutation induction by fU in the DNA of mammalian cells. MATERIALS AND METHODS An enzymatically [(32)P]labelled fU-containing 36 nucleotide DNA sequence plus its complementary sequence (with an A, C, G or T residue inserted opposite fU) was subjected to hSMUG1 in a pH 7.5-buffer, followed by NaOH-mediated cleavage of the resultant abasic sites. Cleaved and uncleaved DNA were separated by denaturing electrophoresis and quantified by autoradiography. RESULTS The hSMUG1 excised fU from DNA opposite all normal bases with the highest activity when opposite non-cognate C or T followed by G and cognate A. CONCLUSIONS The predominant T --> G and T --> A transversions induced by fU in mammalian cells may be explained by replicative incorporation of C and T, respectively, opposite the lesion and subsequent SMUG1-initiated repair of fU.
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Affiliation(s)
- Ingeborg Knaevelsrud
- Faculty of Science and Technology, Department of Mathematics and Natural Sciences, University of Stavanger, Stavanger, Norway
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25
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Morinaga H, Yonekura SI, Nakamura N, Sugiyama H, Yonei S, Zhang-Akiyama QM. Purification and characterization of Caenorhabditis elegans NTH, a homolog of human endonuclease III: essential role of N-terminal region. DNA Repair (Amst) 2009; 8:844-51. [PMID: 19481506 DOI: 10.1016/j.dnarep.2009.04.020] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Revised: 04/28/2009] [Accepted: 04/28/2009] [Indexed: 11/26/2022]
Abstract
Oxidatively damaged bases in DNA cause many types of deleterious effects. The main enzyme that removes such lesions is DNA glycosylase, and accordingly, DNA glycosylase plays an important role in genome stability. Recently, a relationship between DNA glycosylases and aging has been suggested, but it remains controversial. Here, we investigated DNA glycosylases of C. elegans, which is a useful model organism for studying aging. We firstly identified a C. elegans homolog of endonuclease III (NTH), which is a well-conserved DNA glycosylase for oxidatively damaged pyrimidine bases, based on the activity and homology. Blast searching of the Wormbase database retrieved a sequence R10E4.5, highly homologous to the human NTH1. However, the R10E4.5-encoded protein did not have NTH activity, and this was considered to be due to lack of the N-terminal region crucial for the activity. Therefore, we purified the protein encoded by the sequence containing both R10E4.5 and the 117-bp region upstream from it, and found that the protein had the NTH activity. The endogenous CeNTH in the extract of C. elegans showed the same DNA glycosylase activity. Therefore, we concluded that the genuine C. elegans NTH gene is not the R10E4.5 but the sequence containing both R10E4.5 and the 117-bp upstream region. NTH-deficient C. elegans showed no difference from the wild-type in lifespan and was not more sensitive to two oxidizing agents, H2O2 and methyl viologen. This suggests that C. elegans has an alternative DNA glycosylase that repairs pyrimidine bases damaged by these agents. Indeed, DNA glycosylase activity that cleaved thymine glycol containing oligonucleotides was detected in the extract of the NTH-deficient C. elegans.
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Affiliation(s)
- Hironobu Morinaga
- Laboratory of Radiation Biology, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
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26
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Zhang-Akiyama QM, Morinaga H, Kikuchi M, Yonekura SI, Sugiyama H, Yamamoto K, Yonei S. KsgA, a 16S rRNA adenine methyltransferase, has a novel DNA glycosylase/AP lyase activity to prevent mutations in Escherichia coli. Nucleic Acids Res 2009; 37:2116-25. [PMID: 19223326 PMCID: PMC2673420 DOI: 10.1093/nar/gkp057] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The 5-formyluracil (5-foU), a major mutagenic oxidative damage of thymine, is removed from DNA by Nth, Nei and MutM in Escherichia coli. However, DNA polymerases can also replicate past the 5-foU by incorporating C and G opposite the lesion, although the mechanism of correction of the incorporated bases is still unknown. In this study, using a borohydride-trapping assay, we identified a protein trapped by a 5-foU/C-containing oligonucleotide in an extract from E. coli mutM nth nei mutant. The protein was subsequently purified from the E. coli mutM nth nei mutant and was identified as KsgA, a 16S rRNA adenine methyltransferase. Recombinant KsgA also formed the trapped complex with 5-foU/C- and thymine glycol (Tg)/C-containing oligonucleotides. Furthermore, KsgA excised C opposite 5-foU, Tg and 5-hydroxymethyluracil (5-hmU) from duplex oligonucleotides via a β-elimination reaction, whereas it could not remove the damaged base. In contrast, KsgA did not remove C opposite normal bases, 7,8-dihydro-8-oxoguanine and 2-hydroxyadenine. Finally, the introduction of the ksgA mutation increased spontaneous mutations in E. coli mutM mutY and nth nei mutants. These results demonstrate that KsgA has a novel DNA glycosylase/AP lyase activity for C mispaired with oxidized T that prevents the formation of mutations, which is in addition to its known rRNA adenine methyltransferase activity essential for ribosome biogenesis.
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Affiliation(s)
- Qiu-Mei Zhang-Akiyama
- Laboratory of Radiation Biology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan.
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Xu G, Herzig M, Rotrekl V, Walter CA. Base excision repair, aging and health span. Mech Ageing Dev 2008; 129:366-82. [PMID: 18423806 PMCID: PMC2526234 DOI: 10.1016/j.mad.2008.03.001] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Revised: 02/28/2008] [Accepted: 03/05/2008] [Indexed: 12/18/2022]
Abstract
DNA damage and mutagenesis are suggested to contribute to aging through their ability to mediate cellular dysfunction. The base excision repair (BER) pathway ameliorates a large number of DNA lesions that arise spontaneously. Many of these lesions are reported to increase with age. Oxidized guanine, repaired largely via base excision repair, is particularly well studied and shown to increase with age. Spontaneous mutant frequencies also increase with age which suggests that mutagenesis may contribute to aging. It is widely accepted that genetic instability contributes to age-related occurrences of cancer and potentially other age-related pathologies. BER activity decreases with age in multiple tissues. The specific BER protein that appears to limit activity varies among tissues. DNA polymerase-beta is reduced in brain from aged mice and rats while AP endonuclease is reduced in spermatogenic cells obtained from old mice. The differences in proteins that appear to limit BER activity among tissues may represent true tissue-specific differences in activity or may be due to differences in techniques, environmental conditions or other unidentified differences among the experimental approaches. Much remains to be addressed concerning the potential role of BER in aging and age-related health span.
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Affiliation(s)
- Guogang Xu
- Department of Cellular & Structural Biology, The University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900
| | - Maryanne Herzig
- Department of Cellular & Structural Biology, The University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900
| | - Vladimir Rotrekl
- Institute of Experimental Medicine, Department of Molecular Embryology, Masaryk University, Faculty of Medicine, Department of Biology, Kamenice 5, Building A6, 62500 Brno, Czech Republic
| | - Christi A. Walter
- Department of Cellular & Structural Biology, The University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900
- South Texas Veteran’s Health Care System, 7400 Merton Minter Blvd, San Antonio, TX 78229
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28
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Maiti AK, Boldogh I, Spratt H, Mitra S, Hazra TK. Mutator phenotype of mammalian cells due to deficiency of NEIL1 DNA glycosylase, an oxidized base-specific repair enzyme. DNA Repair (Amst) 2008; 7:1213-20. [PMID: 18495559 DOI: 10.1016/j.dnarep.2008.03.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Revised: 03/26/2008] [Accepted: 03/28/2008] [Indexed: 10/22/2022]
Abstract
The recently characterized NEIL1 and NEIL2 are distinct from the previously characterized mammalian DNA glycosylases (OGG1 and NTH1) involved in repair of oxidized bases because of the NEILs' preference for excising base lesions from single-stranded DNA present in bubble and fork structures. OGG1 and NTH1 are active only with duplex DNA. This raises the possibility that NEILs function in the repair of base lesions during DNA replication and/or transcription. S-phase-specific activation of only NEIL1 suggests its preferential involvement in repair during DNA replication. Here we show that antisense oligonucleotides specific for human or Chinese hamster NEIL1 decreased in vivo NEIL1 levels by 70-80%, concomitant with increased oxidative damage in the genome. Moreover, NEIL1 downregulation enhanced spontaneous mutation in the Hprt locus by about 3-fold in both Chinese hamster V79 and human bronchial A549 cell lines. The mutant frequency was further enhanced (7-8-fold) under oxidative stress. The majority of both spontaneous and induced mutations occurred at A.T base pairs, indicating that oxidized A and/or T are NEIL1's preferred in vivo substrates. NEIL1 thus plays a distinct and important role in repairing endogenous and induced mutagenic oxidized bases, and hence in maintaining the functional integrity of mammalian genomes.
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Affiliation(s)
- Amit K Maiti
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
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29
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Rogstad DK, Darwanto A, Herring JL, Rogstad KN, Burdzy A, Hadley S, Neidigh JW, Sowers LC. Measurement of the incorporation and repair of exogenous 5-hydroxymethyl-2'-deoxyuridine in human cells in culture using gas chromatography-negative chemical ionization-mass spectrometry. Chem Res Toxicol 2007; 20:1787-96. [PMID: 17914883 PMCID: PMC2532841 DOI: 10.1021/tx700221x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The DNA of all organisms is constantly damaged by oxidation. Among the array of damage products is 5-hydroxymethyluracil, derived from oxidation of the thymine methyl group. Previous studies have established that HmU can be a sensitive and valuable marker of DNA damage. More recently, the corresponding deoxynucleoside, 5-hydroxymethyl-2'-deoxyuridine (HmdU), has proven to be valuable for the introduction of controlled amounts of a single type of damage lesion into the DNA of replicating cells, which is subsequently repaired by the base excision repair pathway. Complicating the study of HmU formation and repair, however, is the known chemical reactivity of the hydroxymethyl group of HmU under conditions used to hydrolyze DNA. In the work reported here, this chemical property has been exploited by creating conditions that convert HmU to the corresponding methoxymethyluracil (MmU) derivative that can be further derivatized to the 3,5-bis-(trifluoromethyl)benzyl analogue. This derivatized compound can be detected by gas chromatography-negative chemical ionization-mass spectrometry (GC-NCI-MS) with good sensitivity. Using isotopically enriched exogenous HmdU and human osteosarcoma cells (U2OS) in culture, we demonstrate that this method allows for the measurement of HmU in DNA formed from the incorporation of exogenous HmdU. We further demonstrate that the addition of isotopically enriched uridine to the culture medium allows for the simultaneous measurement of DNA replication and repair kinetics. This sensitive and facile method should prove valuable for studies on DNA oxidation damage and repair in living cells.
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Affiliation(s)
| | | | | | | | | | | | | | - Lawrence C. Sowers
- *To whom correspondence should be addressed. Tel: 909-558-4480. Fax: 909-558-4035 E-mail:
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30
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Yonekura SI, Nakamura N, Doi T, Sugiyama H, Yamamoto K, Yonei S, Zhang QM. Recombinant Schizosaccharomyces pombe Nth1 protein exhibits DNA glycosylase activities for 8-oxo-7,8-dihydroguanine and thymine residues oxidized in the methyl group. JOURNAL OF RADIATION RESEARCH 2007; 48:417-24. [PMID: 17641464 DOI: 10.1269/jrr.07042] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Bacteria and eukaryotes possess redundant enzymes that recognize and remove oxidatively damaged bases from DNA through base excision repair. DNA glycosylases remove damaged bases to initiate the base excision repair. The exocyclic methyl group of thymine does not escape oxidative damage to produce 5-formyluracil (5-foU) and 5-hydroxymethyluracil (5-hmU). 5-foU is a potentially mutagenic lesion. A homolog of E. coli endonuclease III (SpNth1) had been identified and characterized in Schizosaccharomyces pombe. In this study, we found that SpNth1 recognizes and removes 5-foU and 5-hmU from DNA with similar efficiency. The specific activities for the removal of 5-foU and 5-hmU were comparable with that for thymine glycol. The expression of SpNth1 reduced the hydrogen peroxide toxicity and the frequency of spontaneous mutations in E. coli nth nei mutant. It was also revealed that SpNth1 had DNA glycosylase activity for removing 8-oxo-7,8-dihydroguanine (8-oxoG) from 8-oxoG/G and 8-oxoG/A mispairs. These results indicated that SpNth1 has a broad substrate specificity and is involved in the base excision repair of 8-oxoG and thymine residues oxidized in the methyl group in S. pombe.
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Affiliation(s)
- Shin-Ichiro Yonekura
- Laboratory of Radiation Biology, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, Japan
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31
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Bandaru V, Zhao X, Newton MR, Burrows CJ, Wallace SS. Human endonuclease VIII-like (NEIL) proteins in the giant DNA Mimivirus. DNA Repair (Amst) 2007; 6:1629-41. [PMID: 17627905 PMCID: PMC2096709 DOI: 10.1016/j.dnarep.2007.05.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Revised: 05/24/2007] [Accepted: 05/25/2007] [Indexed: 11/28/2022]
Abstract
Endonuclease VIII (Nei), which recognizes and repairs oxidized pyrimidines in the base excision repair (BER) pathway, is sparsely distributed among both the prokaryotes and eukaryotes. Recently, we and others identified three homologs of Escherichia coli endonuclease VIII-like (NEIL) proteins in humans. Here, we report identification of human NEIL homologs in Mimivirus, a giant DNA virus that infects Acanthamoeba. Characterization of the two mimiviral homologs, MvNei1 and MvNei2, showed that they share not only sequence homology but also substrate specificity with the human NEIL proteins, that is, they recognize oxidized pyrimidines in duplex DNA and in bubble substrates and as well show 5'2-deoxyribose-5-phosphate lyase (dRP lyase) activity. However, unlike MvNei1 and the human NEIL proteins, MvNei2 preferentially cleaves oxidized pyrimidines in single stranded DNA forming products with a different end chemistry. Interestingly, opposite base specificity of MvNei1 resembles human NEIL proteins for pyrimidine base damages whereas it resembles E. coli formamidopyrimidine DNA glycosylase (Fpg) for guanidinohydantoin (Gh), an oxidation product of 8-oxoguanine. Finally, a conserved arginine residue in the "zincless finger" motif, previously identified in human NEIL1, is required for the DNA glycosylase activity of MvNei1. Thus, Mimivirus represents the first example of a virus to carry oxidative DNA glycosylases with substrate specificities that resemble human NEIL proteins. Based on the sequence homology to the human NEIL homologs and novel bacterial NEIL homologs identified here, we predict that Mimivirus may have acquired the DNA glycosylases through the host-mediated lateral transfer from either a bacterium or from vertebrates.
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Affiliation(s)
- Viswanath Bandaru
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, The University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, Vermont 05405-0068
| | - Xiaobei Zhao
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt lake City, Utah 84112-0850
| | - Michael R. Newton
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt lake City, Utah 84112-0850
| | - Cynthia J. Burrows
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt lake City, Utah 84112-0850
| | - Susan S. Wallace
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, The University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, Vermont 05405-0068
- Address correspondence to: Susan S. Wallace, Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, The University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, Vermont 05405-0068, Tel. (802) 656-2164; Fax: (802) 656-8749; E-mail:
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32
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Lee HW, Lee HJ, Hong CM, Baker DJ, Bhatia R, O’Connor TR. Monitoring repair of DNA damage in cell lines and human peripheral blood mononuclear cells. Anal Biochem 2007; 365:246-59. [PMID: 17449003 PMCID: PMC3614353 DOI: 10.1016/j.ab.2007.03.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Revised: 03/13/2007] [Accepted: 03/16/2007] [Indexed: 11/20/2022]
Abstract
We introduce a method to follow DNA repair that is suitable for both clinical and laboratory samples. An episomal construct with a unique 8-oxoguanine (8-oxoG) base at a defined position was prepared in vitro using single-stranded phage harboring a 678-bp tract from exons 5 to 9 of the human P53 gene. Mixing curve experiments showed that the real-time PCR method has a linear response to damage, suggesting that it is useful for DNA repair studies. The episomal construct with a unique 8-oxoG base was introduced into AD293 cells or human peripheral blood mononuclear cells, and plasmids were recovered as a function of time. The quantitative real-time PCR assay demonstrated that repair of the 8-oxoG was 80% complete in less than 48 h in AD293 cells. Transfection of small interfering RNAs down-regulated OGG1 expression in AD293 cells and reduced the repair of 8-oxoG to 30%. Transfection of the episome into unstimulated white blood cells showed that 8-oxoG repair had a half-life of 2 to 5h. This method is a rapid, reproducible, and robust way to monitor repair of specific adducts in virtually any cell type.
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Affiliation(s)
- Hyun-Wook Lee
- Biology Department, Hematology Department, Beckman Research Institute, City of Hope National Medical Center, 1450 East Duarte Road, Duarte, CA 91010
| | - Hae-Jung Lee
- Biology Department, Hematology Department, Beckman Research Institute, City of Hope National Medical Center, 1450 East Duarte Road, Duarte, CA 91010
| | - Chong-mu Hong
- Biology Department, Hematology Department, Beckman Research Institute, City of Hope National Medical Center, 1450 East Duarte Road, Duarte, CA 91010
| | - David J. Baker
- Biology Department, Hematology Department, Beckman Research Institute, City of Hope National Medical Center, 1450 East Duarte Road, Duarte, CA 91010
| | - Ravi Bhatia
- Department of Hematology and Bone Marrow Transplantation, Beckman Research Institute, City of Hope National Medical Center, 1450 East Duarte Road, Duarte, CA 91010
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33
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Larsen E, Meza TJ, Kleppa L, Klungland A. Organ and cell specificity of base excision repair mutants in mice. Mutat Res 2007; 614:56-68. [PMID: 16765995 DOI: 10.1016/j.mrfmmm.2006.01.023] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2005] [Revised: 01/17/2006] [Accepted: 01/21/2006] [Indexed: 11/28/2022]
Abstract
Genetically modified mouse models are a powerful approach to study the relation of a single gene-deletion to processes such as mutagenesis and carcinogenesis. The generation of base excision repair (BER) deficient mouse models has resulted in a re-examination of the cellular defence mechanisms that exist to counteract DNA base damage. This review discusses novel insights into the relation between specific gene-deletions and the organ and cell specificity of visible and molecular phenotypes, including accumulation of base lesions in genomic DNA and carcinogenesis. Although promising models exist, there is still a need for new models. These models should comprise combined deficiencies of DNA glycosylases which initiate the BER pathway, to elaborate on the repair redundancy, as well as conditional models of the intermediate steps of BER.
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Affiliation(s)
- Elisabeth Larsen
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Rikshospitalet-Radiumhospitalet HF, 0027 Oslo, Norway.
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34
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Grin IR, Khodyreva SN, Nevinsky GA, Zharkov DO. Deoxyribophosphate lyase activity of mammalian endonuclease VIII-like proteins. FEBS Lett 2006; 580:4916-22. [PMID: 16920106 DOI: 10.1016/j.febslet.2006.08.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2006] [Revised: 08/04/2006] [Accepted: 08/07/2006] [Indexed: 11/28/2022]
Abstract
Base excision repair (BER) protects cells from nucleobase DNA damage. In eukaryotic BER, DNA glycosylases generate abasic sites, which are then converted to deoxyribo-5'-phosphate (dRP) and excised by a dRP lyase (dRPase) activity of DNA polymerase beta (Polbeta). Here, we demonstrate that NEIL1 and NEIL2, mammalian homologs of bacterial endonuclease VIII, excise dRP by beta-elimination with the efficiency similar to Polbeta. DNA duplexes imitating BER intermediates after insertion of a single nucleotide were better substrates. NEIL1 and NEIL2 supplied dRPase activity in BER reconstituted with dRPase-null Polbeta. Our results suggest a role for NEILs as backup dRPases in mammalian cells.
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Affiliation(s)
- Inga R Grin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
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35
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Jin G, Zhang QM, Satou Y, Satoh N, Kasai H, Yonei S. Cloning and characterization of an ascidian homolog of the human 8-oxoguanine DNA glycosylase (Ogg1) that is involved in the repair of 8-oxo-7,8-dihydroguanine in DNA in Ciona intestinalis. Int J Radiat Biol 2006; 82:241-50. [PMID: 16690592 DOI: 10.1080/09553000600649216] [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] [Indexed: 01/18/2023]
Abstract
PURPOSE It is of interest to perform a systematic comparative analysis of the conserved domains in DNA glycosylases and the evolution of DNA base excision repair systems. Furthermore, it is important to characterize the roles and regulation of base excision repair during the development of organisms. To address these issues, we first identified 8-oxo-7,8-dihydroguanine (8-oxoG)-DNA glycosylase (Ogg1) of the ascidian Ciona intestinalis as a good model system. MATERIALS AND METHODS A cDNA clone coding for a peptide with homology to human Ogg1 was identified in the expressed sequence tag (EST) database from the Ciona cDNA resources. We examined whether CiOgg1 has DNA glycosylase/AP (apurinic/apyrimidinic) lyase activities for 8-oxoG-containing oligonucleotide. Furthermore, the expression level of CiOgg1 was compared in various tissues of Ciona intestinalis. RESULTS The CiOgg1gene encoded a protein of 351 amino acids, which shows 37% identity of amino acid sequence with human Ogg1. The Helix-hairpin-Helix motif was highly conserved. The ascidian enzyme had functional 8-oxoG-DNA glycosylase/AP lyase activities, which removed 8-oxoG opposite cytosine from DNA. Expression of the CiOgg1 significantly reduced the frequency of spontaneous G:C to T:A transversions in E. coli mutM mutY. The highest expression level was observed in testis in Ciona intestinalis. CONCLUSIONS The structure and functions of Ogg1 are well conserved in Ciona intestinalis. CiOgg1 is involved in the repair of 8-oxoG in DNA in Ciona intestinalis.
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Affiliation(s)
- G Jin
- Laboratory of Radiation Biology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan
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