151
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Billon P, Li J, Lambert JP, Chen Y, Tremblay V, Brunzelle JS, Gingras AC, Verreault A, Sugiyama T, Couture JF, Côté J. Acetylation of PCNA Sliding Surface by Eco1 Promotes Genome Stability through Homologous Recombination. Mol Cell 2016; 65:78-90. [PMID: 27916662 DOI: 10.1016/j.molcel.2016.10.033] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 10/09/2016] [Accepted: 10/24/2016] [Indexed: 11/19/2022]
Abstract
During DNA replication, proliferating cell nuclear antigen (PCNA) adopts a ring-shaped structure to promote processive DNA synthesis, acting as a sliding clamp for polymerases. Known posttranslational modifications function at the outer surface of the PCNA ring to favor DNA damage bypass. Here, we demonstrate that acetylation of lysine residues at the inner surface of PCNA is induced by DNA lesions. We show that cohesin acetyltransferase Eco1 targets lysine 20 at the sliding surface of the PCNA ring in vitro and in vivo in response to DNA damage. Mimicking constitutive acetylation stimulates homologous recombination and robustly suppresses the DNA damage sensitivity of mutations in damage tolerance pathways. In comparison to the unmodified trimer, structural differences are observed at the interface between protomers in the crystal structure of the PCNA-K20ac ring. Thus, acetylation regulates PCNA sliding on DNA in the presence of DNA damage, favoring homologous recombination linked to sister-chromatid cohesion.
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Affiliation(s)
- Pierre Billon
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Centre de Recherche du CHU de Québec-Axe Oncologie, Quebec City, QC G1R 3S3, Canada
| | - Jian Li
- Department of Biological Sciences and Molecular and Cellular Biology Graduate Program, Ohio University, Athens, OH 45701, USA
| | - Jean-Philippe Lambert
- The Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Yizhang Chen
- Department of Biological Sciences and Molecular and Cellular Biology Graduate Program, Ohio University, Athens, OH 45701, USA
| | - Véronique Tremblay
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Joseph S Brunzelle
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Anne-Claude Gingras
- The Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Alain Verreault
- Institute for Research in Immunology and Cancer and Département de Pathologie et Biologie Cellulaire, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Tomohiko Sugiyama
- Department of Biological Sciences and Molecular and Cellular Biology Graduate Program, Ohio University, Athens, OH 45701, USA
| | - Jean-Francois Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Centre de Recherche du CHU de Québec-Axe Oncologie, Quebec City, QC G1R 3S3, Canada.
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152
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Burin-des-Roziers C, Rothschild PR, Layet V, Chen JM, Ghiotti T, Leroux C, Cremers FPM, Brézin AP, Valleix S. Deletions Overlapping VCAN Exon 8 Are New Molecular Defects for Wagner Disease. Hum Mutat 2016; 38:43-47. [PMID: 27667122 DOI: 10.1002/humu.23124] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/31/2016] [Accepted: 09/19/2016] [Indexed: 01/01/2023]
Abstract
Wagner disease is a rare nonsyndromic autosomal-dominant vitreoretinopathy, associated with splice mutations specifically targeting VCAN exon 8. We report the extensive genetic analysis of two Wagner probands, previously found negative for disease-associated splice mutations. Next-generation sequencing (NGS), quantitative real-time PCR, and long-range PCR identified two deletions (3.4 and 10.5 kb) removing at least one exon-intron boundary of exon 8, and both correlating with an imbalance of VCAN mRNA isoforms. We showed that the 10.5-kb deletion occurred de novo, causing somatic mosaicism in the proband's mother who had an unusually mild asymmetrical phenotype. Therefore, exon 8 deletions are novel VCAN genetic defects responsible for Wagner disease, and VCAN mosaic mutations may be involved in the pathogenesis of Wagner disease with attenuated phenotype. NGS is then an effective screening tool for genetic diagnosis of Wagner disease, improving the chance of identifying all disease-causative variants as well as mosaic mutations in VCAN.
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Affiliation(s)
- Cyril Burin-des-Roziers
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 1163, Institut Imagine, Laboratoire de Génétique Ophtalmologique, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Pierre-Raphael Rothschild
- Service d'ophtalmologie, Groupe Hospitalier Cochin-Hôtel-Dieu, Assistance Publique-Hôpitaux de Paris, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Valérie Layet
- Service de Génétique Médicale, Hôpital Jacques Monod, Le Havre, France
| | - Jian-Min Chen
- Institut National de la Santé et de la Recherche Médicale (INSERM), France Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale (UBO), France Etablissement Français du sang (EFS)-Bretagne, Brest, France
| | - Tiffany Ghiotti
- Service de Biochimie et de Génétique Moléculaire, Groupe Hospitalier Cochin-Hôtel-Dieu, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Céline Leroux
- Service de Biochimie et de Génétique Moléculaire, Groupe Hospitalier Cochin-Hôtel-Dieu, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Antoine P Brézin
- Service d'ophtalmologie, Groupe Hospitalier Cochin-Hôtel-Dieu, Assistance Publique-Hôpitaux de Paris, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Sophie Valleix
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 1163, Institut Imagine, Laboratoire de Génétique Ophtalmologique, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Laboratoire de Génétique Moléculaire, Service de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
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153
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Kim JK, Yeom M, Hong JK, Song I, Lee YS, Guengerich FP, Choi JY. Six Germline Genetic Variations Impair the Translesion Synthesis Activity of Human DNA Polymerase κ. Chem Res Toxicol 2016; 29:1741-1754. [PMID: 27603496 DOI: 10.1021/acs.chemrestox.6b00244] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
DNA polymerase (pol) κ efficiently catalyzes error-free translesion DNA synthesis (TLS) opposite bulky N2-guanyl lesions induced by carcinogens such as polycyclic aromatic hydrocarbons. We investigated the biochemical effects of nine human nonsynonymous germline POLK variations on the TLS properties of pol κ, utilizing recombinant pol κ (residues 1-526) enzymes and DNA templates containing an N2-CH2(9-anthracenyl)G (N2-AnthG), 8-oxo-7,8-dihydroguanine (8-oxoG), O6-methyl(Me)G, or an abasic site. In steady-state kinetic analyses, the R246X, R298H, T473A, and R512W variants displayed 7- to 18-fold decreases in kcat/Km for dCTP insertion opposite G and N2-AnthG, with 2- to 3-fold decreases in DNA binding affinity, compared to that of the wild-type, and further showed 5- to 190-fold decreases in kcat/Km for next-base extension from C paired with N2-AnthG. The A471V variant showed 2- to 4-fold decreases in kcat/Km for correct nucleotide insertion opposite and beyond G (or N2-AnthG) compared to that of the wild-type. These five hypoactive variants also showed similar patterns of attenuation of TLS activity opposite 8-oxoG, O6-MeG, and abasic lesions. By contrast, the T44M variant exhibited 7- to 11-fold decreases in kcat/Km for dCTP insertion opposite N2-AnthG and O6-MeG (as well as for dATP insertion opposite an abasic site) but not opposite both G and 8-oxoG, nor beyond N2-AnthG, compared to that of the wild-type. These results suggest that the R246X, R298H, T473A, R512W, and A471V variants cause a general catalytic impairment of pol κ opposite G and all four lesions, whereas the T44M variant induces opposite lesion-dependent catalytic impairment, i.e., only opposite O6-MeG, abasic, and bulky N2-G lesions but not opposite G and 8-oxoG, in pol κ, which might indicate that these hypoactive pol κ variants are genetic factors in modifying individual susceptibility to genotoxic carcinogens in certain subsets of populations.
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Affiliation(s)
- Jae-Kwon Kim
- Division of Pharmacology, Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine , Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Mina Yeom
- Division of Pharmacology, Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine , Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Jin-Kyung Hong
- Division of Pharmacology, Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine , Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Insil Song
- Division of Pharmacology, Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine , Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Young-Sam Lee
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology , Daegu 42988, Republic of Korea
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine , Nashville, Tennessee 37232-0146, United States
| | - Jeong-Yun Choi
- Division of Pharmacology, Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine , Suwon, Gyeonggi-do 16419, Republic of Korea
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154
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Bose A, Millsap AD, DeLeon A, Rizzo C, Basu AK. Translesion Synthesis of the N(2)-2'-Deoxyguanosine Adduct of the Dietary Mutagen IQ in Human Cells: Error-Free Replication by DNA Polymerase κ and Mutagenic Bypass by DNA Polymerases η, ζ, and Rev1. Chem Res Toxicol 2016; 29:1549-59. [PMID: 27490094 PMCID: PMC5031085 DOI: 10.1021/acs.chemrestox.6b00221] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Indexed: 12/18/2022]
Abstract
Translesion synthesis (TLS) of the N(2)-2'-deoxyguanosine (dG-N(2)-IQ) adduct of the carcinogen 2-amino-3-methylimidazo[4,5-f]quinoline (IQ) was investigated in human embryonic kidney 293T cells by replicating plasmid constructs in which the adduct was individually placed at each guanine (G1, G2, or G3) of the NarI sequence (5'-CG1G2CG3CC-3'). TLS efficiency was 38%, 29%, and 25% for the dG-N(2)-IQ located at G1, G2, and G3, respectively, which suggests that dG-N(2)-IQ is bypassed more efficiently by one or more DNA polymerases at G1 than at either G2 or G3. TLS efficiency was decreased 8-35% in cells with knockdown of pol η, pol κ, pol ι, pol ζ, or Rev1. Up to 75% reduction in TLS occurred when pol η, pol ζ, and Rev1 were simultaneously knocked down, suggesting that these three polymerases play important roles in dG-N(2)-IQ bypass. Mutation frequencies (MFs) of dG-N(2)-IQ at G1, G2, and G3 were 23%, 17%, and 11%, respectively, exhibiting a completely reverse trend of the previously reported MF of the C8-dG adduct of IQ (dG-C8-IQ), which is most mutagenic at G3 ( ( 2015 ) Nucleic Acids Res. 43 , 8340 - 8351 ). The major type of mutation induced by dG-N(2)-IQ was targeted G → T, as was reported for dG-C8-IQ. In each site, knockdown of pol κ resulted in an increase in MF, whereas MF was reduced when pol η, pol ι, pol ζ, or Rev1 was knocked down. The reduction in MF was most pronounced when pol η, pol ζ, and Rev1 were simultaneously knocked down and especially when the adduct was located at G3, where MF was reduced by 90%. We conclude that pol κ predominantly performs error-free TLS of the dG-N(2)-IQ adduct, whereas pols η, pol ζ, and Rev1 cooperatively carry out the error-prone TLS. However, in vitro experiments using yeast pol ζ and κ showed that the former was inefficient in full-length primer extension on dG-N(2)-IQ templates, whereas the latter was efficient in both error-free and error-prone extensions. We believe that the observed differences between the in vitro experiments using purified DNA polymerases, and the cellular results may arise from several factors including the crucial roles played by the accessory proteins in TLS.
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Affiliation(s)
- Arindam Bose
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Amy D. Millsap
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Arnie DeLeon
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Carmelo
J. Rizzo
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Ashis K. Basu
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
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155
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Abstract
It has been long understood that mutation distribution is not completely random across genomic space and in time. Indeed, recent surprising discoveries identified multiple simultaneous mutations occurring in tiny regions within chromosomes while the rest of the genome remains relatively mutation-free. Mechanistic elucidation of these phenomena, called mutation showers, mutation clusters, or kataegis, in parallel with findings of abundant clustered mutagenesis in cancer genomes, is ongoing. So far, the combination of factors most important for clustered mutagenesis is the induction of DNA lesions within unusually long and persistent single-strand DNA intermediates. In addition to being a fascinating phenomenon, clustered mutagenesis also became an indispensable tool for identifying a previously unrecognized major source of mutation in cancer, APOBEC cytidine deaminases. Future research on clustered mutagenesis may shed light onto important mechanistic details of genome maintenance, with potentially profound implications for human health.
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Affiliation(s)
- Kin Chan
- Mechanisms of Genome Dynamics Group, National Institute of Environmental Health Sciences, Department of Health and Human Services, National Institutes of Health, Durham, North Carolina 27709; ,
| | - Dmitry A Gordenin
- Mechanisms of Genome Dynamics Group, National Institute of Environmental Health Sciences, Department of Health and Human Services, National Institutes of Health, Durham, North Carolina 27709; ,
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156
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Cho JE, Jinks-Robertson S. Ribonucleotides and Transcription-Associated Mutagenesis in Yeast. J Mol Biol 2016; 429:3156-3167. [PMID: 27511624 DOI: 10.1016/j.jmb.2016.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 08/01/2016] [Accepted: 08/03/2016] [Indexed: 12/26/2022]
Abstract
High levels of transcription stimulate mutation rates in microorganisms, and this occurs primarily through an enhanced accumulation of DNA damage. The major source of transcription-associated damage in yeast is Topoisomerase I (Top1), an enzyme that removes torsional stress that accumulates when DNA strands are separated. Top1 relieves torsional stress by nicking and resealing one DNA strand, and some Top1-dependent mutations are due to trapping and processing of the covalent cleavage intermediate. Most, however, reflect enzyme incision at ribonucleotides, which are the most abundant noncanonical component of DNA. In either case, Top1 generates a distinctive mutation signature composed of short deletions in tandem repeats; in the specific case of ribonucleotide-initiated events, mutations reflect sequential cleavage by the enzyme. Top1-dependent mutations do not require highly activated transcription, but their levels are greatly increased by transcription, which partially reflects an interaction of Top1 with RNA polymerase. Recent studies have demonstrated that Top1-dependent mutations exhibit a strand bias, with the nature of the bias differing depending on the transcriptional status of the underlying DNA. Under low-transcription conditions, most Top1-dependent mutations arise in the context of replication and reflect incision at ribonucleotides incorporated during leading-strand synthesis. Under high-transcription conditions, most Top1-dependent events arise when the enzyme cleaves the non-transcribed strand of DNA. In addition to increasing genetic instability in growing cells, Top1 activity in transcriptionally active regions may be a source of mutations in quiescent cells.
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Affiliation(s)
- Jang-Eun Cho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA.
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157
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Kobayashi K, Guilliam TA, Tsuda M, Yamamoto J, Bailey LJ, Iwai S, Takeda S, Doherty AJ, Hirota K. Repriming by PrimPol is critical for DNA replication restart downstream of lesions and chain-terminating nucleosides. Cell Cycle 2016; 15:1997-2008. [PMID: 27230014 PMCID: PMC4968974 DOI: 10.1080/15384101.2016.1191711] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/12/2016] [Accepted: 05/14/2016] [Indexed: 01/28/2023] Open
Abstract
PrimPol is a DNA damage tolerance enzyme possessing both translesion synthesis (TLS) and primase activities. To uncover its potential role in TLS-mediated IgVλ hypermutation and define its interplay with other TLS polymerases, PrimPol(-/-) and PrimPol(-/-)/Polη(-/-)/Polζ (-/-) gene knockouts were generated in avian cells. Loss of PrimPol had no significant impact on the rate of hypermutation or the mutation spectrum of IgVλ. However, PrimPol(-/-) cells were sensitive to methylmethane sulfonate, suggesting that it may bypass abasic sites at the IgVλ segment by repriming DNA synthesis downstream of these sites. PrimPol(-/-) cells were also sensitive to cisplatin and hydroxyurea, indicating that it assists in maintaining / restarting replication at a variety of lesions. To accurately measure the relative contribution of the TLS and primase activities, we examined DNA damage sensitivity in PrimPol(-/-) cells complemented with polymerase or primase-deficient PrimPol. Polymerase-defective, but not primase-deficient, PrimPol suppresses the hypersensitivity of PrimPol(-/-) cells. This indicates that its primase, rather than TLS activity, is pivotal for DNA damage tolerance. Loss of TLS polymerases, Polη and Polζ has an additive effect on the sensitivity of PrimPol(-/-) cells. Moreover, we found that PrimPol and Polη-Polζ redundantly prevented cell death and facilitated unperturbed cell cycle progression. PrimPol(-/-) cells also exhibited increased sensitivity to a wide variety of chain-terminating nucleoside analogs (CTNAs). PrimPol could perform close-coupled repriming downstream of CTNAs and oxidative damage in vitro. Together, these results indicate that PrimPol's repriming activity plays a central role in reinitiating replication downstream from CTNAs and other specific DNA lesions.
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Affiliation(s)
- Kaori Kobayashi
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-shi, Tokyo, Japan
| | - Thomas A. Guilliam
- Genome Damage and Stability Center, School of Life Sciences, University of Sussex, Brighton, UK
| | - Masataka Tsuda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto, Japan
| | - Junpei Yamamoto
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan
| | - Laura J. Bailey
- Genome Damage and Stability Center, School of Life Sciences, University of Sussex, Brighton, UK
| | - Shigenori Iwai
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto, Japan
| | - Aidan J. Doherty
- Genome Damage and Stability Center, School of Life Sciences, University of Sussex, Brighton, UK
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-shi, Tokyo, Japan
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158
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Y-family DNA polymerase-independent gap-filling translesion synthesis across aristolochic acid-derived adenine adducts in mouse cells. DNA Repair (Amst) 2016; 46:55-60. [PMID: 27497692 DOI: 10.1016/j.dnarep.2016.07.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 07/25/2016] [Accepted: 07/27/2016] [Indexed: 12/16/2022]
Abstract
Translesion DNA synthesis (TLS) operates when replicative polymerases are blocked by DNA lesions. To investigate the mechanism of mammalian TLS, we employed a plasmid bearing a single 7-(deoxyadenosine-N6-yl)-aristolactam I (dA-AL-I) adduct, which is generated by the human carcinogen, aristolochic acid I, and genetically engineered mouse embryonic fibroblasts. This lesion induces A to T transversions at a high frequency. The simultaneous knockouts of the Polh, Poli and Polk genes did not influence the TLS efficiency or the coding property of dA-AL-I, indicating that an unknown DNA polymerase(s) can efficiently catalyze the insertion of a nucleotide opposite the adduct and subsequent extension. Similarly, knockout of the Rev1 gene did not significantly affect TLS. However, knockout of the Rev3l gene, coding for the catalytic subunit of polζ, drastically suppressed TLS and abolished dA-AL-I to T transversions. The results support the idea that Rev1 is not essential for the cellular TLS functions of polζ in mammalian cells. Furthermore, the frequency of dA-AL-I to T transversion was affected by a sequence context, suggesting that TLS, at least in part, contributes to the formation of mutational hot and cold spots observed in aristolochic acid-induced cancers.
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159
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Loss of BRCA1 or BRCA2 markedly increases the rate of base substitution mutagenesis and has distinct effects on genomic deletions. Oncogene 2016; 36:746-755. [PMID: 27452521 PMCID: PMC5096687 DOI: 10.1038/onc.2016.243] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 04/20/2016] [Accepted: 05/26/2016] [Indexed: 12/23/2022]
Abstract
Loss-of-function mutations in the BRCA1 and BRCA2 genes increase the risk of cancer. Owing to their function in homologous recombination repair, much research has focused on the unstable genomic phenotype of BRCA1/2 mutant cells manifest mainly as large-scale rearrangements. We used whole-genome sequencing of multiple isogenic chicken DT40 cell clones to precisely determine the consequences of BRCA1/2 loss on all types of genomic mutagenesis. Spontaneous base substitution mutation rates increased sevenfold upon the disruption of either BRCA1 or BRCA2, and the arising mutation spectra showed strong and specific correlation with a mutation signature associated with BRCA1/2 mutant tumours. To model endogenous alkylating damage, we determined the mutation spectrum caused by methyl methanesulfonate (MMS), and showed that MMS also induces more base substitution mutations in BRCA1/2-deficient cells. Spontaneously arising and MMS-induced insertion/deletion mutations and large rearrangements were also more common in BRCA1/2 mutant cells compared with the wild-type control. A difference in the short deletion phenotypes of BRCA1 and BRCA2 suggested distinct roles for the two proteins in the processing of DNA lesions, as BRCA2 mutants contained more short deletions, with a wider size distribution, which frequently showed microhomology near the breakpoints resembling repair by non-homologous end joining. An increased and prolonged gamma-H2AX signal in MMS-treated BRCA1/2 cells suggested an aberrant processing of stalled replication forks as the cause of increased mutagenesis. The high rate of base substitution mutagenesis demonstrated by our experiments is likely to significantly contribute to the oncogenic effect of the inactivation of BRCA1 or BRCA2.
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160
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Hirota K, Tsuda M, Mohiuddin, Tsurimoto T, Cohen IS, Livneh Z, Kobayashi K, Narita T, Nishihara K, Murai J, Iwai S, Guilbaud G, Sale JE, Takeda S. In vivo evidence for translesion synthesis by the replicative DNA polymerase δ. Nucleic Acids Res 2016; 44:7242-50. [PMID: 27185888 PMCID: PMC5009730 DOI: 10.1093/nar/gkw439] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 05/06/2016] [Indexed: 12/17/2022] Open
Abstract
The intolerance of DNA polymerase δ (Polδ) to incorrect base pairing contributes to its extremely high accuracy during replication, but is believed to inhibit translesion synthesis (TLS). However, chicken DT40 cells lacking the POLD3 subunit of Polδ are deficient in TLS. Previous genetic and biochemical analysis showed that POLD3 may promote lesion bypass by Polδ itself independently of the translesion polymerase Polζ of which POLD3 is also a subunit. To test this hypothesis, we have inactivated Polδ proofreading in pold3 cells. This significantly restored TLS in pold3 mutants, enhancing dA incorporation opposite abasic sites. Purified proofreading-deficient human Polδ holoenzyme performs TLS of abasic sites in vitro much more efficiently than the wild type enzyme, with over 90% of TLS events resulting in dA incorporation. Furthermore, proofreading deficiency enhances the capability of Polδ to continue DNA synthesis over UV lesions both in vivo and in vitro. These data support Polδ contributing to TLS in vivo and suggest that the mutagenesis resulting from loss of Polδ proofreading activity may in part be explained by enhanced lesion bypass.
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Affiliation(s)
- Kouji Hirota
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minami-Osawa 1-1, Hachioji- shi, Tokyo 192-0397, Japan
| | - Masataka Tsuda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Mohiuddin
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Toshiki Tsurimoto
- Department of Biology, School of Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Isadora S Cohen
- Weizmann Institute of Science, Department of Biological Chemistry, Rehovot 76100, Israel
| | - Zvi Livneh
- Weizmann Institute of Science, Department of Biological Chemistry, Rehovot 76100, Israel
| | - Kaori Kobayashi
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minami-Osawa 1-1, Hachioji- shi, Tokyo 192-0397, Japan
| | - Takeo Narita
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kana Nishihara
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Junko Murai
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shigenori Iwai
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Guillaume Guilbaud
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Julian E Sale
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
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161
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Abstract
The HORMA domain is a multifunctional protein–protein interaction module found in diverse eukaryotic signaling pathways including the spindle assembly checkpoint, numerous DNA recombination/repair pathways, and the initiation of autophagy. In all of these pathways, HORMA domain proteins occupy key signaling junctures and function through the controlled assembly and disassembly of signaling complexes using a stereotypical “safety belt” peptide interaction mechanism. A recent explosion of structural and functional work has shed new light on these proteins, illustrating how strikingly similar structural mechanisms give rise to radically different functional outcomes in each family of HORMA domain proteins.
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Affiliation(s)
- Scott C Rosenberg
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, CA 92093
| | - Kevin D Corbett
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, CA 92093 Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093
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162
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Yeom M, Kim IH, Kim JK, Kang K, Eoff RL, Guengerich FP, Choi JY. Effects of Twelve Germline Missense Variations on DNA Lesion and G-Quadruplex Bypass Activities of Human DNA Polymerase REV1. Chem Res Toxicol 2016; 29:367-79. [PMID: 26914252 DOI: 10.1021/acs.chemrestox.5b00513] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The Y-family DNA polymerase REV1 is involved in replicative bypass of damaged DNA and G-quadruplex (G4) DNA. In addition to a scaffolding role in the replicative bypass, REV1 acts in a catalytic role as a deoxycytidyl transferase opposite some replication stall sites, e.g., apurinic/apyrimidinic (AP) sites, N(2)-guanyl lesions, and G4 sites. We characterized the biochemical properties of 12 reported germline missense variants of human REV1, including the N373S variant associated with high risk of cervical cancer, using the recombinant REV1 (residues 330-833) proteins and DNA templates containing a G, AP site, N(2)-CH2(2-naphthyl)G (N(2)-NaphG), or G4. In steady-state kinetic analyses, the F427L, R434Q, M656V, D700N, R704Q, and P831L variants displayed 2- to 8-fold decreases in kcat/Km for dCTP insertion opposite all four templates, compared to that of wild-type, while the N373S, M407L, and N497S showed 2- to 3-fold increases with all four and the former three or two templates, respectively. The F427L, R434Q, M656V, and R704Q variants also had 2- to 3-fold lower binding affinities to DNA substrates containing G, an AP site, and/or N(2)-NaphG than wild-type. Distinctively, the N373S variant had a 3-fold higher binding affinity to G4 DNA than the wild-type, as well as a 2-fold higher catalytic activity opposite the first tetrad G, suggesting a facilitating effect of this variation on replication of G4 DNA sequences in certain human papillomavirus genomes. Our results suggest that the catalytic function of REV1 is moderately or slightly altered by at least nine genetic variations, and the G4 DNA processing function of REV1 is slightly enhanced by the N373S variation, which might provide the possibility that certain germline missense REV1 variations affect the individual susceptibility to carcinogenesis by modifying the capability of REV1 for replicative bypass past DNA lesions and G4 motifs derived from chemical and viral carcinogens.
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Affiliation(s)
| | | | | | | | - Robert L Eoff
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine , Nashville, Tennessee 37232-0146, United States
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163
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Su WP, Hsu SH, Wu CK, Chang SB, Lin YJ, Yang WB, Hung JJ, Chiu WT, Tzeng SF, Tseng YL, Chang JY, Su WC, Liaw H. Chronic treatment with cisplatin induces replication-dependent sister chromatid recombination to confer cisplatin-resistant phenotype in nasopharyngeal carcinoma. Oncotarget 2015; 5:6323-37. [PMID: 25051366 PMCID: PMC4171633 DOI: 10.18632/oncotarget.2210] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Cisplatin can cause intrastrand and interstrand crosslinks between purine bases and is a chemotherapeutic drug widely used to treat cancer. However, the major barrier to the efficacy of the treatment is drug resistance. Homologous recombination (HR) plays a central role in restoring stalled forks caused by DNA lesions. Here, we report that chronic treatment with cisplatin induces HR to confer cisplatin resistance in nasopharyngeal carcinoma (NPC) cells. A high frequency of sister chromatid exchanges (SCE) occurs in the cisplatin-resistant NPC cells. In addition, several genes in the Fanconi anemia (FA) and template switching (TS) pathways show elevated expression. Significantly, depletion of HR gene BRCA1, TS gene UBC13, or FA gene FANCD2 suppresses SCE and causes cells to accumulate in the S phase, concomitantly with high γH2AX foci formation in the presence of low-dose cisplatin. Consistent with this result, depletion of several genes in the HR, TS, or FA pathway sensitizes the cisplatin-resistant NPC cells to cisplatin. Our results suggest that the enhanced HR, in coordination with the FA and TS pathways, underlies the cisplatin resistance. Targeting the HR, TS, or FA pathways could be a potential therapeutic strategy for treating cisplatin-resistant cancer.
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Affiliation(s)
- Wen-Pin Su
- Departments of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University; Graduate Institutes of Clinical Medicine, College of Medicine, National Cheng Kung University
| | - Sen-Huei Hsu
- Department of Life Sciences, National Cheng Kung University, No.1 University Road, Tainan City 701, Taiwan; These authors contributed equally to this work
| | - Cheng-Kuei Wu
- Department of Life Sciences, National Cheng Kung University, No.1 University Road, Tainan City 701, Taiwan; These authors contributed equally to this work
| | - Song-Bin Chang
- Department of Life Sciences, National Cheng Kung University, No.1 University Road, Tainan City 701, Taiwan
| | - Yi-Ju Lin
- Department of Life Sciences, National Cheng Kung University, No.1 University Road, Tainan City 701, Taiwan
| | - Wen-Bin Yang
- Institute of Bioinformatics and Biosignal Transduction, National Cheng Kung University
| | - Jan-Jong Hung
- Institute of Bioinformatics and Biosignal Transduction, National Cheng Kung University
| | - Wen-Tai Chiu
- Department of Biomedical Engineering, National Cheng Kung University
| | - Shun-Fen Tzeng
- Department of Life Sciences, National Cheng Kung University, No.1 University Road, Tainan City 701, Taiwan
| | - Yau-Lin Tseng
- Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University
| | - Jang-Yang Chang
- Departments of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University; National Institute of Cancer Research, National Health Research Institutes, Taiwan
| | - Wu-Chou Su
- Cancer Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University
| | - Hungjiun Liaw
- Department of Life Sciences, National Cheng Kung University, No.1 University Road, Tainan City 701, Taiwan
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164
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Princz LN, Gritenaite D, Pfander B. The Slx4-Dpb11 scaffold complex: coordinating the response to replication fork stalling in S-phase and the subsequent mitosis. Cell Cycle 2015; 14:488-94. [PMID: 25496009 DOI: 10.4161/15384101.2014.989126] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Replication fork stalling at DNA lesions is a common problem during the process of DNA replication. One way to allow the bypass of these lesions is via specific recombination-based mechanisms that involve switching of the replication template to the sister chromatid. Inherent to these mechanisms is the formation of DNA joint molecules (JMs) between sister chromatids. Such JMs need to be disentangled before chromatid separation in mitosis and the activity of JM resolution enzymes, which is under stringent cell cycle control, is therefore up-regulated in mitosis. An additional layer of control is facilitated by scaffold proteins. In budding yeast, specifically during mitosis, Slx4 and Dpb11 form a cell cycle kinase-dependent complex with the Mus81-Mms4 structure-selective endonuclease, which allows efficient JM resolution by Mus81. Furthermore, Slx4 and Dpb11 interact even prior to joining Mus81 and respond to replication fork stalling in S-phase. This S-phase complex is involved in the regulation of the DNA damage checkpoint as well as in early steps of template switch recombination. Similar interactions and regulatory principles are found in human cells suggesting that Slx4 and Dpb11 may have an evolutionary conserved role organizing the cellular response to replication fork stalling.
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Affiliation(s)
- Lissa N Princz
- a Max-Planck Institute of Biochemistry ; DNA Replication and Genome Integrity ; Martinsried , Germany
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165
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Yagi T, Fujikawa Y, Sawai T, Takamura-Enya T, Ito-Harashima S, Kawanishi M. Error-Prone and Error-Free Translesion DNA Synthesis over Site-Specifically Created DNA Adducts of Aryl Hydrocarbons (3-Nitrobenzanthrone and 4-Aminobiphenyl). Toxicol Res 2015; 33:265-272. [PMID: 29071010 PMCID: PMC5654197 DOI: 10.5487/tr.2017.33.4.265] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 09/20/2017] [Accepted: 09/25/2017] [Indexed: 01/05/2023] Open
Abstract
Aryl hydrocarbons such as 3-nitrobenzanthrone (NBA), 4-aminobiphenyl (ABP), acetylaminofluorene (AAF), benzo(a)pyrene (BaP), and 1-nitropyrene (NP) form bulky DNA adducts when absorbed by mammalian cells. These chemicals are metabolically activated to reactive forms in mammalian cells and preferentially get attached covalently to the N2 or C8 positions of guanine or the N6 position of adenine. The proportion of N2 and C8 guanine adducts in DNA differs among chemicals. Although these adducts block DNA replication, cells have a mechanism allowing to continue replication by bypassing these adducts: translesion DNA synthesis (TLS). TLS is performed by translesion DNA polymerases—Pol η, κ, ι, and ζ and Rev1—in an error-free or error-prone manner. Regarding the NBA adducts, namely, 2-(2′-deoxyguanosin-N2-yl)-3-aminobenzanthrone (dG-N2-ABA) and N-(2′-deoxyguanosin-8-yl)-3-aminobenzanthrone (dG-C8-ABA), dG-N2-ABA is produced more often than dG-C8-ABA, whereas dG-C8-ABA blocks DNA replication more strongly than dG-N2-ABA. dG-N2-ABA allows for a less error-prone bypass than dG-C8-ABA does. Pol η and κ are stronger contributors to TLS over dG-C8-ABA, and Pol κ bypasses dG-C8-ABA in an error-prone manner. TLS efficiency and error-proneness are affected by the sequences surrounding the adduct, as demonstrated in our previous study on an ABP adduct, N-(2′-deoxyguanosine-8-yl)-4-aminobiphenyl (dG-C8-ABP). Elucidation of the general mechanisms determining efficiency, error-proneness, and the polymerases involved in TLS over various adducts is the next step in the research on TLS. These TLS studies will clarify the mechanisms underlying aryl hydrocarbon mutagenesis and carcinogenesis in more detail.
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Affiliation(s)
- Takashi Yagi
- Department of Biology, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Yoshihiro Fujikawa
- Department of Biology, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Tomoko Sawai
- Department of Biology, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Takeji Takamura-Enya
- Department of Applied Chemistry, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
| | - Sayoko Ito-Harashima
- Department of Biology, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Masanobu Kawanishi
- Department of Biology, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka, Japan
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166
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Abstract
Fanconi anemia (FA) is a rare recessive genetic disease characterized by congenital abnormalities, bone marrow failure and heightened cancer susceptibility in early adulthood. FA is caused by biallelic germ-line mutation of any one of 16 genes. While several functions for the FA proteins have been ascribed, the prevailing hypothesis is that the FA proteins function cooperatively in the FA-BRCA pathway to repair damaged DNA. A pivotal step in the activation of the FA-BRCA pathway is the monoubiquitination of the FANCD2 and FANCI proteins. Despite their importance for DNA repair, the domain structure, regulation, and function of FANCD2 and FANCI remain poorly understood. In this review, we provide an overview of our current understanding of FANCD2 and FANCI, with an emphasis on their posttranslational modification and common and unique functions.
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Key Words
- AML , acute myeloid leukemia
- APC/C, anaphase-promoting complex/cyclosome
- APH, aphidicolin
- ARM, armadillo repeat domain
- AT, ataxia-telangiectasia
- ATM, ataxia-telangiectasia mutated
- ATR, ATM and Rad3-related
- BAC, bacterial-artificial-chromosome
- BS, Bloom syndrome
- CUE, coupling of ubiquitin conjugation to endoplasmic reticulum degradation
- ChIP-seq, CHIP sequencing
- CtBP, C-terminal binding protein
- CtIP, CtBP-interacting protein
- DNA interstrand crosslink repair
- DNA repair
- EPS15, epidermal growth factor receptor pathway substrate 15
- FA, Fanconi anemia
- FAN1, FANCD2-associated nuclease1
- FANCD2
- FANCI
- FISH, fluorescence in situ hybridization
- Fanconi anemia
- HECT, homologous to E6-AP Carboxy Terminus
- HJ, Holliday junction
- HR, homologous recombination
- MCM2-MCM7, minichromosome maintenance 2–7
- MEFs, mouse embryonic fibroblasts
- MMC, mitomycin C
- MRN, MRE11/RAD50/NBS1
- NLS, nuclear localization signal
- PCNA, proliferating cell nuclear antigen
- PIKK, phosphatidylinositol-3-OH-kinase-like family of protein kinases
- PIP-box, PCNA-interacting protein motif
- POL κ, DNA polymerase κ
- RACE, rapid amplification of cDNA ends
- RING, really interesting new gene
- RTK, receptor tyrosine kinase
- SCF, Skp1/Cullin/F-box protein complex
- SCKL1, seckel syndrome
- SILAC, stable isotope labeling with amino acids in cell culture
- SLD1/SLD2, SUMO-like domains
- SLIM, SUMO-like domain interacting motif
- TIP60, 60 kDa Tat-interactive protein
- TLS, Translesion DNA synthesis
- UAF1, USP1-associated factor 1
- UBD, ubiquitin-binding domain
- UBZ, ubiquitin-binding zinc finger
- UFB, ultra-fine DNA bridges
- UIM, ubiquitin-interacting motif
- ULD, ubiquitin-like domain
- USP1, ubiquitin-specific protease 1
- VRR-nuc, virus-type replication repair nuclease
- iPOND, isolation of proteins on nascent DNA
- ubiquitin
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Affiliation(s)
- Rebecca A Boisvert
- a Department of Cell and Molecular Biology ; University of Rhode Island ; Kingston , RI USA
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167
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Chen JM, Férec C, Cooper DN. Complex Multiple-Nucleotide Substitution Mutations Causing Human Inherited Disease Reveal Novel Insights into the Action of Translesion Synthesis DNA Polymerases. Hum Mutat 2015; 36:1034-8. [PMID: 26172832 DOI: 10.1002/humu.22831] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 06/23/2015] [Indexed: 01/01/2023]
Abstract
Translesion synthesis (TLS) DNA polymerases allow the bypass of unrepaired lesions during DNA replication. Based upon mutational signatures of a subtype of multiple-nucleotide substitution (MNS) mutations causing human inherited disease, we have recently postulated two properties of TLS DNA polymerases in DNA repair, namely, the generation of neo-microhomologies potentiating strand-misalignment, and additional microlesions within the templated inserts when recruited to stalled replication forks. To provide further support for this postulate, we analyzed the mutational signatures of a new and complex subtype of pathogenic MNS mutation. Several mutations containing long templated inserts (8-19 bp) that are highly informative with regard to their underlying mutational mechanisms, harbor imprints of TLS DNA polymerase action. Dissecting the mechanism underlying the generation of the 19-bp insert implicated repeated participation of TLS DNA polymerases in the conversion of a damaged base into a complex MNS lesion through a process of successive template switching and bypass repair.
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Affiliation(s)
- Jian-Min Chen
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1078, Brest, France.,Etablissement Français du Sang (EFS) - Bretagne, Brest, France.,Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale (UBO), Brest, France
| | - Claude Férec
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1078, Brest, France.,Etablissement Français du Sang (EFS) - Bretagne, Brest, France.,Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale (UBO), Brest, France.,Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Centre Hospitalier Universitaire (CHU) Brest, Hôpital Morvan, Brest, France
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
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168
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Bose A, Pande P, Jasti VP, Millsap AD, Hawkins EK, Rizzo CJ, Basu AK. DNA polymerases κ and ζ cooperatively perform mutagenic translesion synthesis of the C8-2'-deoxyguanosine adduct of the dietary mutagen IQ in human cells. Nucleic Acids Res 2015. [PMID: 26220181 PMCID: PMC4787813 DOI: 10.1093/nar/gkv750] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The roles of translesion synthesis (TLS) DNA polymerases in bypassing the C8-2'-deoxyguanosine adduct (dG-C8-IQ) formed by 2-amino-3-methylimidazo[4,5-f]quinoline (IQ), a highly mutagenic and carcinogenic heterocyclic amine found in cooked meats, were investigated. Three plasmid vectors containing the dG-C8-IQ adduct at the G1-, G2- or G3-positions of the NarI site (5'-G1G2CG3CC-3') were replicated in HEK293T cells. Fifty percent of the progeny from the G3 construct were mutants, largely G→T, compared to 18% and 24% from the G1 and G2 constructs, respectively. Mutation frequency (MF) of dG-C8-IQ was reduced by 38-67% upon siRNA knockdown of pol κ, whereas it was increased by 10-24% in pol η knockdown cells. When pol κ and pol ζ were simultaneously knocked down, MF of the G1 and G3 constructs was reduced from 18% and 50%, respectively, to <3%, whereas it was reduced from 24% to <1% in the G2 construct. In vitro TLS using yeast pol ζ showed that it can extend G3*:A pair more efficiently than G3*:C pair, but it is inefficient at nucleotide incorporation opposite dG-C8-IQ. We conclude that pol κ and pol ζ cooperatively carry out the majority of the error-prone TLS of dG-C8-IQ, whereas pol η is involved primarily in its error-free bypass.
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Affiliation(s)
- Arindam Bose
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
| | - Paritosh Pande
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
| | - Vijay P Jasti
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
| | - Amy D Millsap
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Edward K Hawkins
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Carmelo J Rizzo
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Ashis K Basu
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
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169
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Ahmed-Seghir S, Pouvelle C, Despras E, Cordonnier A, Sarasin A, Kannouche PL. Aberrant C-terminal domain of polymerase η targets the functional enzyme to the proteosomal degradation pathway. DNA Repair (Amst) 2015; 29:154-65. [PMID: 25766642 DOI: 10.1016/j.dnarep.2015.02.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 02/14/2015] [Accepted: 02/16/2015] [Indexed: 12/22/2022]
Abstract
Xeroderma pigmentosum variant (XP-V) is a rare genetic disease, characterized by sunlight sensitivity and predisposition to cutaneous malignancies. XP-V is caused by a deficiency in DNA polymerase eta (Polη) that plays a pivotal role in translesion synthesis by bypassing UV-induced pyrimidine dimers. Previously we identified a new Polη variant containing two missense mutations, one mutation within the bipartite NLS (T692A) and a second mutation on the stop codon (X714W) leading to a longer protein with an extra 8 amino acids (721 instead of 713 AA). First biochemical analysis revealed that this Polη missense variant was barely detectable by western blot. As this mutant is extremely unstable and is nearly undetectable, a definitive measure of its functional deficit in cells has not been explored. Here we report the molecular and cellular characterization of this missense variant. In cell free extracts, the extra 8 amino acids in the C-terminal of Polη(721) only slightly reduce the bypass efficiency through CPD lesions. In vivo, Polη(721) accumulates in replication factories and interacts with mUb-PCNA albeit at lower level than Polη(wt). XP-V cells overexpressing Polη(721) were only slightly UV-sensitive. Altogether, our data strongly suggest that Polη(721) is functional and that the patient displays a XP-V phenotype because the mutant protein is excessively unstable. We then investigated the molecular mechanisms involved in this excessive proteolysis. We showed that Polη(721) is degraded by the proteasome in an ubiquitin-dependent manner and that this proteolysis is independent of the E3 ligases, CRL4(cdt2) and Pirh2, reported to promote Polη degradation. We then demonstrated that the extra 8 amino acids of Polη(721) do not act as a degron but rather induce a conformational change of the Polη C-terminus exposing its bipartite NLS as well as a sequence close to its UBZ to the ubiquitin/proteasome system. Interestingly we showed that the clinically approved proteasome inhibitor, Bortezomib restores the levels of Polη(721) suggesting that this might be a therapeutic approach to preventing tumor development in certain XP-V patients harboring missense mutations.
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Affiliation(s)
- Sana Ahmed-Seghir
- Université Paris-Sud, CNRS-UMR8200, Equipe labellisée Ligue Contre le Cancer, Gustave Roussy, Villejuif, France
| | - Caroline Pouvelle
- Université Paris-Sud, CNRS-UMR8200, Equipe labellisée Ligue Contre le Cancer, Gustave Roussy, Villejuif, France
| | - Emmanuelle Despras
- Université Paris-Sud, CNRS-UMR8200, Equipe labellisée Ligue Contre le Cancer, Gustave Roussy, Villejuif, France
| | | | - Alain Sarasin
- Université Paris-Sud, CNRS-UMR8200, Equipe labellisée Ligue Contre le Cancer, Gustave Roussy, Villejuif, France
| | - Patricia L Kannouche
- Université Paris-Sud, CNRS-UMR8200, Equipe labellisée Ligue Contre le Cancer, Gustave Roussy, Villejuif, France.
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170
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Wickramasinghe CM, Arzouk H, Frey A, Maiter A, Sale JE. Contributions of the specialised DNA polymerases to replication of structured DNA. DNA Repair (Amst) 2015; 29:83-90. [PMID: 25704659 DOI: 10.1016/j.dnarep.2015.01.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 01/16/2015] [Indexed: 01/06/2023]
Abstract
It is becoming increasingly clear that processive DNA replication is threatened not only by DNA damage but also by secondary structures that can form in the DNA template. Failure to resolve these structures promptly leads to both genetic instability, for instance DNA breaks and rearrangements, and to epigenetic instability, in which inaccurate propagation of the parental chromatin state leads to unscheduled changes in gene expression. Multiple overlapping mechanisms are needed to deal with the wide range of potential DNA structural challenges to replication. This review focuses on the emerging mechanisms by which specialised DNA polymerases, best known for their role in the replication of damaged DNA, contribute to the replication of undamaged but structured DNA, particularly G quadruplexes.
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Affiliation(s)
| | - Hayat Arzouk
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Alexander Frey
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Ahmed Maiter
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Julian E Sale
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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171
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Bugay AN, Krasavin EA, Parkhomenko AY, Vasilyeva MA. Modeling nucleotide excision repair and its impact on UV-induced mutagenesis during SOS-response in bacterial cells. J Theor Biol 2015; 364:7-20. [DOI: 10.1016/j.jtbi.2014.08.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 07/31/2014] [Accepted: 08/22/2014] [Indexed: 02/01/2023]
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172
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Abstract
A role for somatic mutations in carcinogenesis is well accepted, but the degree to which mutation rates influence cancer initiation and development is under continuous debate. Recently accumulated genomic data have revealed that thousands of tumour samples are riddled by hypermutation, broadening support for the idea that many cancers acquire a mutator phenotype. This major expansion of cancer mutation data sets has provided unprecedented statistical power for the analysis of mutation spectra, which has confirmed several classical sources of mutation in cancer, highlighted new prominent mutation sources (such as apolipoprotein B mRNA editing enzyme catalytic polypeptide-like (APOBEC) enzymes) and empowered the search for cancer drivers. The confluence of cancer mutation genomics and mechanistic insight provides great promise for understanding the basic development of cancer through mutations.
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173
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Ortiz-Bazán MÁ, Gallo-Fernández M, Saugar I, Jiménez-Martín A, Vázquez MV, Tercero JA. Rad5 plays a major role in the cellular response to DNA damage during chromosome replication. Cell Rep 2014; 9:460-8. [PMID: 25310987 DOI: 10.1016/j.celrep.2014.09.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 08/13/2014] [Accepted: 08/29/2014] [Indexed: 10/24/2022] Open
Abstract
The RAD6/RAD18 pathway of DNA damage tolerance overcomes unrepaired lesions that block replication forks. It is subdivided into two branches: translesion DNA synthesis, which is frequently error prone, and the error-free DNA-damage-avoidance subpathway. Here, we show that Rad5(HLTF/SHPRH), which mediates the error-free branch, has a major role in the response to DNA damage caused by methyl methanesulfonate (MMS) during chromosome replication, whereas translesion synthesis polymerases make only a minor contribution. Both the ubiquitin-ligase and the ATPase/helicase activities of Rad5 are necessary for this cellular response. We show that Rad5 is required for the progression of replication forks through MMS-damaged DNA. Moreover, supporting its role during replication, this protein reaches maximum levels during S phase and forms subnuclear foci when replication occurs in the presence of DNA damage. Thus, Rad5 ensures the completion of chromosome replication under DNA-damaging conditions while minimizing the risk of mutagenesis, thereby contributing significantly to genome integrity maintenance.
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Affiliation(s)
| | - María Gallo-Fernández
- Centro de Biología Molecular Severo Ochoa (CSIC/UAM), Cantoblanco, 28049 Madrid, Spain
| | - Irene Saugar
- Centro de Biología Molecular Severo Ochoa (CSIC/UAM), Cantoblanco, 28049 Madrid, Spain
| | | | | | - José Antonio Tercero
- Centro de Biología Molecular Severo Ochoa (CSIC/UAM), Cantoblanco, 28049 Madrid, Spain.
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174
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Histone H3.3 is required to maintain replication fork progression after UV damage. Curr Biol 2014; 24:2195-2201. [PMID: 25201682 PMCID: PMC4175177 DOI: 10.1016/j.cub.2014.07.077] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 07/11/2014] [Accepted: 07/30/2014] [Indexed: 11/22/2022]
Abstract
Unlike histone H3, which is present only in S phase, the variant histone H3.3 is expressed throughout the cell cycle [1] and is incorporated into chromatin independent of replication [2]. Recently, H3.3 has been implicated in the cellular response to ultraviolet (UV) light [3]. Here, we show that chicken DT40 cells completely lacking H3.3 are hypersensitive to UV light, a defect that epistasis analysis suggests may result from less-effective nucleotide excision repair. Unexpectedly, H3.3-deficient cells also exhibit a substantial defect in maintaining replication fork progression on UV-damaged DNA, which is independent of nucleotide excision repair, demonstrating a clear requirement for H3.3 during S phase. Both the UV hypersensitivity and replication fork slowing are reversed by expression of H3.3 and require the specific residues in the α2 helix that are responsible for H3.3 binding its dedicated chaperones. However, expression of an H3.3 mutant in which serine 31 is replaced with alanine, the equivalent residue in H3.2, restores normal fork progression but not UV resistance, suggesting that H3.3[S31A] may be incorporated at UV-damaged forks but is unable to help cells tolerate UV lesions. Similar behavior was observed with expression of H3.3 carrying mutations at K27 and G34, which have been reported in pediatric brain cancers. We speculate that incorporation of H3.3 during replication may mark sites of lesion bypass and, possibly through an as-yet-unidentified function of the N-terminal tail, facilitate subsequent processing of the damage. We report a vertebrate cell line completely lacking the histone variant H3.3 H3.3-deficient cells are hypersensitive to DNA damage A supply of H3.3 is required to maintain fork progression after UV damage This S phase role requires the distinct chaperone-binding patch of H3.3
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175
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Bryan DS, Ransom M, Adane B, York K, Hesselberth JR. High resolution mapping of modified DNA nucleobases using excision repair enzymes. Genome Res 2014; 24:1534-42. [PMID: 25015380 PMCID: PMC4158761 DOI: 10.1101/gr.174052.114] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 07/08/2014] [Indexed: 12/20/2022]
Abstract
The incorporation and creation of modified nucleobases in DNA have profound effects on genome function. We describe methods for mapping positions and local content of modified DNA nucleobases in genomic DNA. We combined in vitro nucleobase excision with massively parallel DNA sequencing (Excision-seq) to determine the locations of modified nucleobases in genomic DNA. We applied the Excision-seq method to map uracil in E. coli and budding yeast and discovered significant variation in uracil content, wherein uracil is excluded from the earliest and latest replicating regions of the genome, possibly driven by changes in nucleotide pool composition. We also used Excision-seq to identify sites of pyrimidine dimer formation induced by UV light exposure, where the method could distinguish between sites of cyclobutane and 6-4 photoproduct formation. These UV mapping data enabled analysis of local sequence bias around pyrimidine dimers and suggested a preference for an adenosine downstream from 6-4 photoproducts. The Excision-seq method is broadly applicable for high precision, genome-wide mapping of modified nucleobases with cognate repair enzymes.
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Affiliation(s)
- D Suzi Bryan
- Department of Biochemistry and Molecular Genetics, Program in Molecular Biology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Monica Ransom
- Department of Biochemistry and Molecular Genetics, Program in Molecular Biology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Biniam Adane
- Department of Biochemistry and Molecular Genetics, Program in Molecular Biology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Kerri York
- Department of Biochemistry and Molecular Genetics, Program in Molecular Biology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Jay R Hesselberth
- Department of Biochemistry and Molecular Genetics, Program in Molecular Biology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
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176
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Pande P, Malik CK, Bose A, Jasti VP, Basu AK. Mutational analysis of the C8-guanine adduct of the environmental carcinogen 3-nitrobenzanthrone in human cells: critical roles of DNA polymerases η and κ and Rev1 in error-prone translesion synthesis. Biochemistry 2014; 53:5323-31. [PMID: 25080294 PMCID: PMC4139159 DOI: 10.1021/bi5007805] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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3-Nitrobenzanthrone (3-NBA), a potent
mutagen and suspected human
carcinogen, is a common environmental pollutant. The genotoxicity
of 3-NBA has been associated with its ability to form DNA adducts,
including N-(2′-deoxyguanosin-8-yl)-3-aminobenzanthrone
(C8-dG-ABA). To investigate the molecular mechanism of C8-dG-ABA mutagenesis
in human cells, we have replicated a plasmid containing a single C8-dG-ABA
in human embryonic kidney 293T (HEK293T) cells, which yielded 14%
mutant progeny. The major types of mutations induced by C8-dG-ABA
were G → T > G → A > G → C. siRNA knockdown
of
the translesion synthesis (TLS) DNA polymerases (pols) in HEK293T
cells indicated that pol η, pol κ, pol ι, pol ζ,
and Rev1 each have a role in replication across this adduct. The extent
of TLS was reduced with each pol knockdown, but the largest decrease
(of ∼55% reduction) in the level of TLS occurred in cells with
knockdown of pol ζ. Pol η and pol κ were considered
the major contributors of the mutagenic TLS, because the mutation
frequency (MF) decreased by 70%, when these pols were simultaneously
knocked down. Rev1 also is important for mutagenesis, as reflected
by the 60% reduction in MF upon Rev1 knockdown, but it probably plays
a noncatalytic role by physically interacting with the other two Y-family
pols. In contrast, pol ζ appeared to be involved in the error-free
bypass of the lesion, because MF increased by 60% in pol ζ knockdown
cells. These results provide important mechanistic insight into the
bypass of the C8-dG-ABA adduct.
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Affiliation(s)
- Paritosh Pande
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
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177
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Tolerating DNA damage during eukaryotic chromosome replication. Exp Cell Res 2014; 329:170-7. [PMID: 25038291 DOI: 10.1016/j.yexcr.2014.07.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 07/03/2014] [Indexed: 11/23/2022]
Abstract
In eukaryotes, the evolutionarily conserved RAD6/RAD18 pathway of DNA damage tolerance overcomes unrepaired DNA lesions that interfere with the progression of replication forks, helping to ensure the completion of chromosome replication and the maintenance of genome stability in every cell cycle. This pathway uses two different strategies for damage bypass: translesion DNA synthesis, which is carried out by specialized polymerases that can replicate across the lesions, and DNA damage avoidance, a process that relies on a switch to an undamaged-DNA template for synthesis past the lesion. In this review, we summarise the current knowledge on DNA damage tolerance mechanisms mediated by RAD6/RAD18 that are used by eukaryotic cells to cope with DNA lesions during chromosome replication.
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178
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A DNA-Dependent Protease Involved in DNA-Protein Crosslink Repair. Cell 2014; 158:327-338. [DOI: 10.1016/j.cell.2014.04.053] [Citation(s) in RCA: 186] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 03/28/2014] [Accepted: 04/21/2014] [Indexed: 12/20/2022]
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179
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Babu VMP, Sutton MD. A dnaN plasmid shuffle strain for rapid in vivo analysis of mutant Escherichia coli β clamps provides insight into the role of clamp in umuDC-mediated cold sensitivity. PLoS One 2014; 9:e98791. [PMID: 24896652 PMCID: PMC4045847 DOI: 10.1371/journal.pone.0098791] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 05/07/2014] [Indexed: 12/05/2022] Open
Abstract
The E. coli umuDC gene products participate in two temporally distinct roles: UmuD2C acts in a DNA damage checkpoint control, while UmuD'2C, also known as DNA polymerase V (Pol V), catalyzes replication past DNA lesions via a process termed translesion DNA synthesis. These different roles of the umuDC gene products are managed in part by the dnaN-encoded β sliding clamp protein. Co-overexpression of the β clamp and Pol V severely blocked E. coli growth at 30°C. We previously used a genetic assay that was independent of the ability of β clamp to support E. coli viability to isolate 8 mutant clamp proteins (βQ61K, βS107L, βD150N, βG157S, βV170M, βE202K, βM204K and βP363S) that failed to block growth at 30°C when co-overexpressed with Pol V. It was unknown whether these mutant clamps were capable of supporting E. coli viability and normal umuDC functions in vivo. The goals of this study were to answer these questions. To this end, we developed a novel dnaN plasmid shuffle assay. Using this assay, βD150N and βP363S were unable to support E. coli viability. The remaining 6 mutant clamps, each of which supported viability, were indistinguishable from β+ with respect to umuDC functions in vivo. In light of these findings, we analyzed phenotypes of strains overexpressing either β clamp or Pol V alone. The strain overexpressing β+, but not those expressing mutant β clamps, displayed slowed growth irrespective of the incubation temperature. Moreover, growth of the Pol V-expressing strain was modestly slowed at 30°, but not 42°C. Taken together, these results suggest the mutant clamps were identified due to their inability to slow growth rather than an inability to interact with Pol V. They further suggest that cold sensitivity is due, at least in part, to the combination of their individual effects on growth at 30°C.
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Affiliation(s)
- Vignesh M. P. Babu
- Department of Biochemistry, School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, New York, United States of America
- Witebsky Center for Microbial Pathogenesis & Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, New York, United States of America
| | - Mark D. Sutton
- Department of Biochemistry, School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, New York, United States of America
- Witebsky Center for Microbial Pathogenesis & Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, New York, United States of America
- Genetics, Genomics and Bioinformatics Program, School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, New York, United States of America
- * E-mail:
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180
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Siebler HM, Lada AG, Baranovskiy AG, Tahirov TH, Pavlov YI. A novel variant of DNA polymerase ζ, Rev3ΔC, highlights differential regulation of Pol32 as a subunit of polymerase δ versus ζ in Saccharomyces cerevisiae. DNA Repair (Amst) 2014; 24:138-149. [PMID: 24819597 DOI: 10.1016/j.dnarep.2014.04.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 04/17/2014] [Accepted: 04/24/2014] [Indexed: 10/25/2022]
Abstract
Unrepaired DNA lesions often stall replicative DNA polymerases and are bypassed by translesion synthesis (TLS) to prevent replication fork collapse. Mechanisms of TLS are lesion- and species-specific, with a prominent role of specialized DNA polymerases with relaxed active sites. After nucleotide(s) are incorporated across from the altered base(s), the aberrant primer termini are typically extended by DNA polymerase ζ (pol ζ). As a result, pol ζ is responsible for most DNA damage-induced mutations. The mechanisms of sequential DNA polymerase switches in vivo remain unclear. The major replicative DNA polymerase δ (pol δ) shares two accessory subunits, called Pol31/Pol32 in yeast, with pol ζ. Inclusion of Pol31/Pol32 in the pol δ/pol ζ holoenzymes requires a [4Fe-4S] cluster in C-termini of the catalytic subunits. Disruption of this cluster in Pol ζ or deletion of POL32 attenuates induced mutagenesis. Here we describe a novel mutation affecting the catalytic subunit of pol ζ, rev3ΔC, which provides insight into the regulation of pol switches. Strains with Rev3ΔC, lacking the entire C-terminal domain and therefore the platform for Pol31/Pol32 binding, are partially proficient in Pol32-dependent UV-induced mutagenesis. This suggests an additional role of Pol32 in TLS, beyond being a pol ζ subunit, related to pol δ. In search for members of this regulatory pathway, we examined the effects of Maintenance of Genome Stability 1 (Mgs1) protein on mutagenesis in the absence of Rev3-Pol31/Pol32 interaction. Mgs1 may compete with Pol32 for binding to PCNA. Mgs1 overproduction suppresses induced mutagenesis, but had no effect on UV-mutagenesis in the rev3ΔC strain, suggesting that Mgs1 exerts its inhibitory effect by acting specifically on Pol32 bound to pol ζ. The evidence for differential regulation of Pol32 in pol δ and pol ζ emphasizes the complexity of polymerase switches.
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Affiliation(s)
- Hollie M Siebler
- Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA.
| | - Artem G Lada
- Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA.
| | - Andrey G Baranovskiy
- Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA.
| | - Tahir H Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA.
| | - Youri I Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA.
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181
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Bacolla A, Cooper DN, Vasquez KM. Mechanisms of base substitution mutagenesis in cancer genomes. Genes (Basel) 2014; 5:108-46. [PMID: 24705290 PMCID: PMC3978516 DOI: 10.3390/genes5010108] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 02/07/2014] [Accepted: 02/11/2014] [Indexed: 01/24/2023] Open
Abstract
Cancer genome sequence data provide an invaluable resource for inferring the key mechanisms by which mutations arise in cancer cells, favoring their survival, proliferation and invasiveness. Here we examine recent advances in understanding the molecular mechanisms responsible for the predominant type of genetic alteration found in cancer cells, somatic single base substitutions (SBSs). Cytosine methylation, demethylation and deamination, charge transfer reactions in DNA, DNA replication timing, chromatin status and altered DNA proofreading activities are all now known to contribute to the mechanisms leading to base substitution mutagenesis. We review current hypotheses as to the major processes that give rise to SBSs and evaluate their relative relevance in the light of knowledge acquired from cancer genome sequencing projects and the study of base modifications, DNA repair and lesion bypass. Although gene expression data on APOBEC3B enzymes provide support for a role in cancer mutagenesis through U:G mismatch intermediates, the enzyme preference for single-stranded DNA may limit its activity genome-wide. For SBSs at both CG:CG and YC:GR sites, we outline evidence for a prominent role of damage by charge transfer reactions that follow interactions of the DNA with reactive oxygen species (ROS) and other endogenous or exogenous electron-abstracting molecules.
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Affiliation(s)
- Albino Bacolla
- Dell Pediatric Research Institute, Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA.
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK.
| | - Karen M Vasquez
- Dell Pediatric Research Institute, Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA.
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182
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Abstract
The discovery of DNA repair defects in human syndromes, initially in xeroderma pigmentosum (XP) but later in many others, led to striking observations on the association of molecular defects and patients' clinical phenotypes. For example, patients with syndromes resulting from defective nucleotide excision repair (NER) or translesion synthesis (TLS) present high levels of skin cancer in areas exposed to sunlight. However, some defects in NER also lead to more severe symptoms, such as developmental and neurological impairment and signs of premature aging. Skin cancer in XP patients is clearly associated with increased mutagenesis and genomic instability, reflecting the defective repair of DNA lesions. By analogy, more severe symptoms observed in NER-defective patients have also been associated with defective repair, likely involving cell death after transcription blockage of damaged templates. Endogenously induced DNA lesions, particularly through oxidative stress, have been identified as responsible for these severe pathologies. However, this association is not that clear and alternative explanations have been proposed. Despite high levels of exposure to intense sunlight, patients from tropical countries receive little attention or care, which likely also reflects the lack of understanding of how DNA damage causes cancer and premature aging.
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Affiliation(s)
- Carlos FM Menck
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP,
Brazil
| | - Veridiana Munford
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP,
Brazil
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183
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Phytoagents for cancer management: regulation of nucleic acid oxidation, ROS, and related mechanisms. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2013; 2013:925804. [PMID: 24454991 PMCID: PMC3886269 DOI: 10.1155/2013/925804] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 09/27/2013] [Accepted: 10/05/2013] [Indexed: 12/28/2022]
Abstract
Accumulation of oxidized nucleic acids causes genomic instability leading to senescence, apoptosis, and tumorigenesis. Phytoagents are known to reduce the risk of cancer development; whether such effects are through regulating the extent of nucleic acid oxidation remains unclear. Here, we outlined the role of reactive oxygen species in nucleic acid oxidation as a driving force in cancer progression. The consequential relationship between genome instability and cancer progression highlights the importance of modulation of cellular redox level in cancer management. Current epidemiological and experimental evidence demonstrate the effects and modes of action of phytoagents in nucleic acid oxidation and provide rationales for the use of phytoagents as chemopreventive or therapeutic agents. Vitamins and various phytoagents antagonize carcinogen-triggered oxidative stress by scavenging free radicals and/or activating endogenous defence systems such as Nrf2-regulated antioxidant genes or pathways. Moreover, metal ion chelation by phytoagents helps to attenuate oxidative DNA damage caused by transition metal ions. Besides, the prooxidant effects of some phytoagents pose selective cytotoxicity on cancer cells and shed light on a new strategy of cancer therapy. The “double-edged sword” role of phytoagents as redox regulators in nucleic acid oxidation and their possible roles in cancer prevention or therapy are discussed in this review.
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184
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Abstract
DNA damage is one of many possible perturbations that challenge the mechanisms that preserve genetic stability during the copying of the eukaryotic genome in S phase. This short review provides, in the first part, a general introduction to the topic and an overview of checkpoint responses. In the second part, the mechanisms of error-free tolerance in response to fork-arresting DNA damage will be discussed in some detail.
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Affiliation(s)
- Nimrat Chatterjee
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030
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185
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Listovsky T, Sale JE. Sequestration of CDH1 by MAD2L2 prevents premature APC/C activation prior to anaphase onset. ACTA ACUST UNITED AC 2013; 203:87-100. [PMID: 24100295 PMCID: PMC3798251 DOI: 10.1083/jcb.201302060] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
MAD2L2 is rapidly degraded by APC/CCDC20 at the onset of anaphase, allowing release of sequestered CDH1 to activate the dephosphorylated APC/C. The switch from activation of the anaphase-promoting complex/cyclosome (APC/C) by CDC20 to CDH1 during anaphase is crucial for accurate mitosis. APC/CCDC20 ubiquitinates a limited set of substrates for subsequent degradation, including Cyclin B1 and Securin, whereas APC/CCDH1 has a broader specificity. This switch depends on dephosphorylation of CDH1 and the APC/C, and on the degradation of CDC20. Here we show, in human cells, that the APC/C inhibitor MAD2L2 also contributes to ensuring the sequential activation of the APC/C by CDC20 and CDH1. In prometaphase, MAD2L2 sequestered free CDH1 away from the APC/C. At the onset of anaphase, MAD2L2 was rapidly degraded by APC/CCDC20, releasing CDH1 to activate the dephosphorylated APC/C. Loss of MAD2L2 led to premature association of CDH1 with the APC/C, early destruction of APC/CCDH1 substrates, and accelerated mitosis with frequent mitotic aberrations. Thus, MAD2L2 helps to ensure a robustly bistable switch between APC/CCDC20 and APC/CCDH1 during the metaphase-to-anaphase transition, thereby contributing to mitotic fidelity.
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Affiliation(s)
- Tamar Listovsky
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, England, UK
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186
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Chan K, Resnick MA, Gordenin DA. The choice of nucleotide inserted opposite abasic sites formed within chromosomal DNA reveals the polymerase activities participating in translesion DNA synthesis. DNA Repair (Amst) 2013; 12:878-89. [PMID: 23988736 DOI: 10.1016/j.dnarep.2013.07.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 07/19/2013] [Accepted: 07/20/2013] [Indexed: 10/26/2022]
Abstract
Abasic sites in genomic DNA can be a significant source of mutagenesis in biological systems, including human cancers. Such mutagenesis requires translesion DNA synthesis (TLS) bypass of the abasic site by specialized DNA polymerases. The abasic site bypass specificity of TLS proteins had been studied by multiple means in vivo and in vitro, although the generality of the conclusions reached have been uncertain. Here, we introduce a set of yeast reporter strains for investigating the in vivo specificity of abasic site bypass at numerous random positions within chromosomal DNA. When shifted to 37°C, these strains underwent telomere uncapping and resection that exposed reporter genes within a long 3' ssDNA overhang. Human APOBEC3G cytosine deaminase was expressed to create uracils in ssDNA, which were excised by uracil-DNA N-glycosylase. During repair synthesis, error-prone TLS bypassed the resulting abasic sites. Because of APOBEC3G's strict motif specificity and the restriction of abasic site formation to only one DNA strand, this system provides complete information about the location of abasic sites that led to mutations. We recapitulated previous findings on the roles of REV1 and REV3. Further, we found that sequence context can strongly influence the relative frequency of A or C insertion. We also found that deletion of Pol32, a non-essential common subunit of Pols δ and ζ, resulted in residual low-frequency C insertion dependent on Rev1 catalysis. We summarize our results in a detailed model of the interplay between TLS components leading to error-prone bypass of abasic sites. Our results underscore the utility of this system for studying TLS bypass of many types of lesions within genomic DNA.
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Affiliation(s)
- Kin Chan
- Chromosome Stability Section, Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, USA.
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