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Oswalt LE, Eichman BF. NEIL3: A unique DNA glycosylase involved in interstrand DNA crosslink repair. DNA Repair (Amst) 2024; 139:103680. [PMID: 38663144 PMCID: PMC11162926 DOI: 10.1016/j.dnarep.2024.103680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 05/09/2024]
Abstract
Endonuclease VIII-like 3 (NEIL3) is a versatile DNA glycosylase that repairs a diverse array of chemical modifications to DNA. Unlike other glycosylases, NEIL3 has a preference for lesions within single-strand DNA and at single/double-strand DNA junctions. Beyond its canonical role in base excision repair of oxidized DNA, NEIL3 initiates replication-dependent interstrand DNA crosslink repair as an alternative to the Fanconi Anemia pathway. This review outlines our current understanding of NEIL3's biological functions, role in disease, and three-dimensional structure as it pertains to substrate specificity and catalytic mechanism.
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Affiliation(s)
- Leah E Oswalt
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Brandt F Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA.
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2
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Eckenroth BE, Bumgarner JD, Matsumoto-Elliott O, David S, Doublié S. Structural and biochemical insights into NEIL2's preference for abasic sites. Nucleic Acids Res 2023; 51:12508-12521. [PMID: 37971311 PMCID: PMC10711445 DOI: 10.1093/nar/gkad1075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/17/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023] Open
Abstract
Cellular DNA is subject to damage from a multitude of sources and repair or bypass of sites of damage utilize an array of context or cell cycle dependent systems. The recognition and removal of oxidatively damaged bases is the task of DNA glycosylases from the base excision repair pathway utilizing two structural families that excise base lesions in a wide range of DNA contexts including duplex, single-stranded and bubble structures arising during transcription. The mammalian NEIL2 glycosylase of the Fpg/Nei family excises lesions from each of these DNA contexts favoring the latter two with a preference for oxidized cytosine products and abasic sites. We have determined the first liganded crystal structure of mammalian NEIL2 in complex with an abasic site analog containing DNA duplex at 2.08 Å resolution. Comparison to the unliganded structure revealed a large interdomain conformational shift upon binding the DNA substrate accompanied by local conformational changes in the C-terminal domain zinc finger and N-terminal domain void-filling loop necessary to position the enzyme on the DNA. The detailed biochemical analysis of NEIL2 with an array of oxidized base lesions indicates a significant preference for its lyase activity likely to be paramount when interpreting the biological consequences of variants.
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Affiliation(s)
- Brian E Eckenroth
- Department of Microbiology and Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405, USA
| | - Joshua D Bumgarner
- Department of Chemistry and Graduate Program in Chemistry and Chemical Biology, University of California Davis, Davis, CA 95616, USA
| | - Olivia Matsumoto-Elliott
- Department of Chemistry and Graduate Program in Chemistry and Chemical Biology, University of California Davis, Davis, CA 95616, USA
| | - Sheila S David
- Department of Chemistry and Graduate Program in Chemistry and Chemical Biology, University of California Davis, Davis, CA 95616, USA
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405, USA
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3
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Wallace SS. Consequences and repair of radiation-induced DNA damage: fifty years of fun questions and answers. Int J Radiat Biol 2021; 98:367-382. [PMID: 34187282 DOI: 10.1080/09553002.2021.1948141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
PURPOSE To summarize succinctly the 50 years of research undertaken in my laboratory and to provide an overview of my career in science. It is certainly a privilege to have been asked by Carmel Mothersill and Penny Jeggo to contribute to this special issue of the International Journal of Radiation Biology focusing on the work of women in the radiation sciences. CONCLUSION My students, post-docs and I identified and characterized a number of the enzymes that recognize and remove radiation-damaged DNA bases, the DNA glycosylases, which are the first enzymes in the Base Excision Repair (BER) pathway. Although this pathway actually evolved to repair oxidative and other endogenous DNA damages, it is also responsible for removing the vast majority of radiation-induced DNA damages including base damages, alkali-labile lesions and single strand breaks. However, because of its high efficiency, attempted BER of clustered lesions produced by ionizing radiation, can have disastrous effects on cellular DNA. We also evaluated the potential biological consequences of many of the radiation-induced DNA lesions. In addition, with collaborators, we employed computational techniques, x-ray crystallography and single molecule approaches to answer many questions at the molecular level.
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Affiliation(s)
- Susan S Wallace
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, USA
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5
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Wallace SS. Molecular radiobiology and the origins of the base excision repair pathway: an historical perspective. Int J Radiat Biol 2021; 99:891-902. [DOI: 10.1080/09553002.2021.1908639] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Susan S. Wallace
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, USA
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6
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Rodriguez AA, Wojtaszek JL, Greer BH, Haldar T, Gates KS, Williams RS, Eichman BF. An autoinhibitory role for the GRF zinc finger domain of DNA glycosylase NEIL3. J Biol Chem 2020; 295:15566-15575. [PMID: 32878989 PMCID: PMC7667957 DOI: 10.1074/jbc.ra120.015541] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/30/2020] [Indexed: 01/07/2023] Open
Abstract
The NEIL3 DNA glycosylase maintains genome integrity during replication by excising oxidized bases from single-stranded DNA (ssDNA) and unhooking interstrand cross-links (ICLs) at fork structures. In addition to its N-terminal catalytic glycosylase domain, NEIL3 contains two tandem C-terminal GRF-type zinc fingers that are absent in the other NEIL paralogs. ssDNA binding by the GRF-ZF motifs helps recruit NEIL3 to replication forks converged at an ICL, but the nature of DNA binding and the effect of the GRF-ZF domain on catalysis of base excision and ICL unhooking is unknown. Here, we show that the tandem GRF-ZFs of NEIL3 provide affinity and specificity for DNA that is greater than each individual motif alone. The crystal structure of the GRF domain shows that the tandem ZF motifs adopt a flexible head-to-tail configuration well-suited for binding to multiple ssDNA conformations. Functionally, we establish that the NEIL3 GRF domain inhibits glycosylase activity against monoadducts and ICLs. This autoinhibitory activity contrasts GRF-ZF domains of other DNA-processing enzymes, which typically use ssDNA binding to enhance catalytic activity, and suggests that the C-terminal region of NEIL3 is involved in both DNA damage recruitment and enzymatic regulation.
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Affiliation(s)
- Alyssa A Rodriguez
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Jessica L Wojtaszek
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Briana H Greer
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Tuhin Haldar
- Department of Chemistry, University of Missouri, Columbia, Missouri, USA
| | - Kent S Gates
- Department of Chemistry, University of Missouri, Columbia, Missouri, USA
| | - R Scott Williams
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA.
| | - Brandt F Eichman
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA.
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Tran OT, Tadesse S, Chu C, Kidane D. Overexpression of NEIL3 associated with altered genome and poor survival in selected types of human cancer. Tumour Biol 2020; 42:1010428320918404. [PMID: 32364878 DOI: 10.1177/1010428320918404] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Base excision repair, which is initiated by the DNA N-glycosylase proteins, is the frontline for repairing potentially mutagenic DNA base damage. Several base excision repair genes are deregulated in cancer and affect cellular outcomes to chemotherapy and carcinogenesis. Endonuclease VIII-like 3 (NEIL3) is a DNA glycosylase protein that is involved in oxidative and interstrand crosslink DNA damage repair. Our previous work has showed that NEIL3 is required to maintain replication fork integrity. It is unknown whether NEIL3 overexpression could contribute to cancer phenotypes, and its prognostic value and use as potential drug target remain unexplored. Our analysis of cancer genomics data sets reveals that NEIL3 frequently undergoes overexpression in several cancers. Furthermore, patients who exhibited NEIL3 overexpression with pancreatic adenocarcinoma, lung adenocarcinoma, lower grade glioma, kidney renal clear cell carcinoma, and kidney papillary cell carcinoma had worse overall survival. Importantly, NEIL3 overexpressed tumors accumulate mutation and chromosomal variations. Furthermore, NEIL3 overexpressed tumors exhibit simultaneous overexpression of homologous recombination genes (BRCA1/2) and mismatch repair genes (MSH2/MSH6). However, NEIL3 overexpression is negatively correlated with tumor overexpressing nucleotide excision repair genes (XPA, XPC, ERCC1/2). Our results suggest that NEIL3 might be a potential prognosis marker for high-risk patients, and/or an attractive therapeutic target for selected cancers.
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Affiliation(s)
- Oanh Tn Tran
- College of Natural Sciences, The University of Texas at Austin, Austin, TX, USA.,Department of Chemistry, University of California, Irvine, Irvine, CA, USA
| | - Serkalem Tadesse
- Division of Pharmacology and Toxicology, College of Pharmacy, Dell Pediatric Research Institute, The University of Texas at Austin, Austin, TX, USA
| | - Christopher Chu
- Division of Pharmacology and Toxicology, College of Pharmacy, Dell Pediatric Research Institute, The University of Texas at Austin, Austin, TX, USA
| | - Dawit Kidane
- Division of Pharmacology and Toxicology, College of Pharmacy, Dell Pediatric Research Institute, The University of Texas at Austin, Austin, TX, USA
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Unhooking of an interstrand cross-link at DNA fork structures by the DNA glycosylase NEIL3. DNA Repair (Amst) 2019; 86:102752. [PMID: 31923807 DOI: 10.1016/j.dnarep.2019.102752] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/16/2019] [Accepted: 11/19/2019] [Indexed: 01/06/2023]
Abstract
Interstrand DNA-DNA cross-links (ICLs) are generated by endogenous processes, drugs, and environmental toxins. Understanding the cellular pathways by which various ICLs are repaired is critical to understanding their biological effects. Recent studies showed that replication-dependent repair of an ICL derived from the reaction of an abasic (AP) site with an adenine residue (dA) on the opposing strand of duplex DNA proceeds via a novel mechanism in which the DNA glycosylase NEIL3 unhooks the ICL. Here we examined the ability of the glycosylase domain of murine NEIL3 (MmuNEIL3-GD) to unhook dA-AP ICLs. The enzyme selectively unhooks the dA-AP ICL located at the duplex/single-strand junction of splayed duplexes that model the strand-separated DNA at the leading edge of a replication fork. We show that the ability to unhook the dA-AP ICL is a specialized function of NEIL3 as this activity is not observed in other BER enzymes. Importantly, NEIL3 only unhooks the dA-AP ICL when the AP residue is located on what would be the leading template strand of a model replication fork. The same specificity for the leading template strand was observed with a 5,6-dihydrothymine monoadduct, demonstrating that this preference is a general feature of the glycosylase and independent of the type of DNA damage. Overall, the results show that the glycosylase domain of NEIL3, lacking the C-terminal NPL4 and GRF zinc finger motifs, is competent to unhook the dA-AP ICL in splayed substrates and independently enforces important substrate preferences on the repair process.
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Petri net-based model of the human DNA base excision repair pathway. PLoS One 2019; 14:e0217913. [PMID: 31518347 PMCID: PMC6743755 DOI: 10.1371/journal.pone.0217913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 05/21/2019] [Indexed: 12/14/2022] Open
Abstract
Cellular DNA is daily exposed to several damaging agents causing a plethora of DNA lesions. As a first aid to restore DNA integrity, several enzymes got specialized in damage recognition and lesion removal during the process called base excision repair (BER). A large number of DNA damage types and several different readers of nucleic acids lesions during BER pathway as well as two sub-pathways were considered in the definition of a model using the Petri net framework. The intuitive graphical representation in combination with precise mathematical analysis methods are the strong advantages of the Petri net-based representation of biological processes and make Petri nets a promising approach for modeling and analysis of human BER. The reported results provide new information that will aid efforts to characterize in silico knockouts as well as help to predict the sensitivity of the cell with inactivated repair proteins to different types of DNA damage. The results can also help in identifying the by-passing pathways that may lead to lack of pronounced phenotypes associated with mutations in some of the proteins. This knowledge is very useful when DNA damage-inducing drugs are introduced for cancer therapy, and lack of DNA repair is desirable for tumor cell death.
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Smatlikova P, Askeland G, Vaskovicova M, Klima J, Motlik J, Eide L, Ellederová Z. Age-Related Oxidative Changes in Primary Porcine Fibroblasts Expressing Mutated Huntingtin. NEURODEGENER DIS 2019; 19:22-34. [PMID: 31167196 DOI: 10.1159/000500091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 03/30/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Huntington's disease (HD) is a devastating neurodegenerative disorder caused by CAG triplet expansions in the huntingtin gene. Oxidative stress is linked to HD pathology, although it is not clear whether this is an effect or a mediator of disease. The transgenic (TgHD) minipig expresses the N-terminal part of human-mutated huntingtin and represents a unique model to investigate therapeutic strategies towards HD. A more detailed characterization of this model is needed to fully utilize its potential. METHODS In this study, we focused on the molecular and cellular features of fibroblasts isolated from TgHD minipigs and the wild-type (WT) siblings at different ages, pre-symptomatic at the age of 24-36 months and with the onset of behavioural symptoms at the age of 48 months. We measured oxidative stress, the expression of oxidative stress-related genes, proliferation capacity along with the expression of cyclin B1 and D1 proteins, cellular permeability, and the integrity of the nuclear DNA (nDNA) and mitochondrial DNA in these cells. RESULTS TgHD fibroblasts isolated from 48-month-old animals showed increased oxidative stress, which correlated with the overexpression of SOD2 encoding mitochondrial superoxide dismutase 2, and the NEIL3 gene encoding DNA glycosylase involved in replication-associated repair of oxidized DNA. TgHD cells displayed an abnormal proliferation capacity and permeability. We further demonstrated increased nDNA damage in pre-symptomatic TgHD fibroblasts (isolated from animals aged 24-36 months). CONCLUSIONS Our results unravel phenotypic alterations in primary fibroblasts isolated from the TgHD minipig model at the age of 48 months. Importantly, nDNA damage appears to precede these phenotypic alterations. Our results highlight the impact of fibroblasts from TgHD minipigs in studying the molecular mechanisms of HD pathophysiology that gradually occur with age.
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Affiliation(s)
- Petra Smatlikova
- Laboratory of Cell Regeneration and Plasticity, Research Center PIGMOD, Institute of Animal Physiology and Genetics, Czech Academy of Science, Libechov, Czechia.,Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague, Czechia
| | - Georgina Askeland
- Department of Medical Biochemistry, University of Oslo and Oslo University Hospital, Oslo, Norway.,Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Michaela Vaskovicova
- Laboratory of DNA Integrity, Research Center PIGMOD, Institute of Animal Physiology and Genetics, Czech Academy of Science, Libechov, Czechia.,Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague, Czechia
| | - Jiri Klima
- Laboratory of Cell Regeneration and Plasticity, Research Center PIGMOD, Institute of Animal Physiology and Genetics, Czech Academy of Science, Libechov, Czechia
| | - Jan Motlik
- Laboratory of Cell Regeneration and Plasticity, Research Center PIGMOD, Institute of Animal Physiology and Genetics, Czech Academy of Science, Libechov, Czechia
| | - Lars Eide
- Department of Medical Biochemistry, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Zdenka Ellederová
- Laboratory of Cell Regeneration and Plasticity, Research Center PIGMOD, Institute of Animal Physiology and Genetics, Czech Academy of Science, Libechov, Czechia,
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11
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Mullins EA, Rodriguez AA, Bradley NP, Eichman BF. Emerging Roles of DNA Glycosylases and the Base Excision Repair Pathway. Trends Biochem Sci 2019; 44:765-781. [PMID: 31078398 DOI: 10.1016/j.tibs.2019.04.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 12/20/2022]
Abstract
The base excision repair (BER) pathway historically has been associated with maintaining genome integrity by eliminating nucleobases with small chemical modifications. In the past several years, however, BER was found to play additional roles in genome maintenance and metabolism, including sequence-specific restriction modification and repair of bulky adducts and interstrand crosslinks. Central to this expanded biological utility are specialized DNA glycosylases - enzymes that selectively excise damaged, modified, or mismatched nucleobases. In this review we discuss the newly identified roles of the BER pathway and examine the structural and mechanistic features of the DNA glycosylases that enable these functions.
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Affiliation(s)
- Elwood A Mullins
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Alyssa A Rodriguez
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Noah P Bradley
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Brandt F Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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12
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Albelazi MS, Martin PR, Mohammed S, Mutti L, Parsons JL, Elder RH. The Biochemical Role of the Human NEIL1 and NEIL3 DNA Glycosylases on Model DNA Replication Forks. Genes (Basel) 2019; 10:genes10040315. [PMID: 31018584 PMCID: PMC6523847 DOI: 10.3390/genes10040315] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/15/2019] [Accepted: 04/17/2019] [Indexed: 12/22/2022] Open
Abstract
Endonuclease VIII-like (NEIL) 1 and 3 proteins eliminate oxidative DNA base damage and psoralen DNA interstrand crosslinks through initiation of base excision repair. Current evidence points to a DNA replication associated repair function of NEIL1 and NEIL3, correlating with induced expression of the proteins in S/G2 phases of the cell cycle. However previous attempts to express and purify recombinant human NEIL3 in an active form have been challenging. In this study, both human NEIL1 and NEIL3 have been expressed and purified from E. coli, and the DNA glycosylase activity of these two proteins confirmed using single- and double-stranded DNA oligonucleotide substrates containing the oxidative bases, 5-hydroxyuracil, 8-oxoguanine and thymine glycol. To determine the biochemical role that NEIL1 and NEIL3 play during DNA replication, model replication fork substrates were designed containing the oxidized bases at one of three specific sites relative to the fork. Results indicate that whilst specificity for 5- hydroxyuracil and thymine glycol was observed, NEIL1 acts preferentially on double-stranded DNA, including the damage upstream to the replication fork, whereas NEIL3 preferentially excises oxidized bases from single stranded DNA and within open fork structures. Thus, NEIL1 and NEIL3 act in concert to remove oxidized bases from the replication fork.
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Affiliation(s)
- Mustafa S Albelazi
- Biomedical Research Centre, School of Environment and Life Sciences, Peel Building, University of Salford, Salford, M5 4NT, UK.
| | - Peter R Martin
- Biomedical Research Centre, School of Environment and Life Sciences, Peel Building, University of Salford, Salford, M5 4NT, UK.
| | - Soran Mohammed
- Biomedical Research Centre, School of Environment and Life Sciences, Peel Building, University of Salford, Salford, M5 4NT, UK.
- Chemical Biology, Diagnostics and Therapeutics Group, Chemistry Faculty, University of Southampton, Southampton, SO17 1BJ, UK.
| | - Luciano Mutti
- Biomedical Research Centre, School of Environment and Life Sciences, Peel Building, University of Salford, Salford, M5 4NT, UK.
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA.
| | - Jason L Parsons
- Cancer Research Centre, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 200 London Road, Liverpool L3 9TA, UK.
| | - Rhoderick H Elder
- Biomedical Research Centre, School of Environment and Life Sciences, Peel Building, University of Salford, Salford, M5 4NT, UK.
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Wu RA, Semlow DR, Kamimae-Lanning AN, Kochenova OV, Chistol G, Hodskinson MR, Amunugama R, Sparks JL, Wang M, Deng L, Mimoso CA, Low E, Patel KJ, Walter JC. TRAIP is a master regulator of DNA interstrand crosslink repair. Nature 2019; 567:267-272. [PMID: 30842657 PMCID: PMC6417926 DOI: 10.1038/s41586-019-1002-0] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 02/01/2019] [Indexed: 12/24/2022]
Abstract
Cells often use multiple pathways to repair the same DNA lesion, and the choice of pathway has substantial implications for the fidelity of genome maintenance. DNA interstrand crosslinks covalently link the two strands of DNA, and thereby block replication and transcription; the cytotoxicity of these crosslinks is exploited for chemotherapy. In Xenopus egg extracts, the collision of replication forks with interstrand crosslinks initiates two distinct repair pathways. NEIL3 glycosylase can cleave the crosslink1; however, if this fails, Fanconi anaemia proteins incise the phosphodiester backbone that surrounds the interstrand crosslink, generating a double-strand-break intermediate that is repaired by homologous recombination2. It is not known how the simpler NEIL3 pathway is prioritized over the Fanconi anaemia pathway, which can cause genomic rearrangements. Here we show that the E3 ubiquitin ligase TRAIP is required for both pathways. When two replisomes converge at an interstrand crosslink, TRAIP ubiquitylates the replicative DNA helicase CMG (the complex of CDC45, MCM2-7 and GINS). Short ubiquitin chains recruit NEIL3 through direct binding, whereas longer chains are required for the unloading of CMG by the p97 ATPase, which enables the Fanconi anaemia pathway. Thus, TRAIP controls the choice between the two known pathways of replication-coupled interstrand-crosslink repair. These results, together with our other recent findings3,4 establish TRAIP as a master regulator of CMG unloading and the response of the replisome to obstacles.
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Affiliation(s)
- R Alex Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Daniel R Semlow
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | | | - Olga V Kochenova
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Gheorghe Chistol
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | | | - Ravindra Amunugama
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Justin L Sparks
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Meng Wang
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Lin Deng
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Claudia A Mimoso
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Emily Low
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ketan J Patel
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
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Minko IG, Christov PP, Li L, Stone MP, McCullough AK, Lloyd RS. Processing of N 5-substituted formamidopyrimidine DNA adducts by DNA glycosylases NEIL1 and NEIL3. DNA Repair (Amst) 2018; 73:49-54. [PMID: 30448017 DOI: 10.1016/j.dnarep.2018.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/02/2018] [Accepted: 11/02/2018] [Indexed: 12/29/2022]
Abstract
A variety of agents cause DNA base alkylation damage, including the known hepatocarcinogen aflatoxin B1 (AFB1) and chemotherapeutic drugs derived from nitrogen mustard (NM). The N7 site of guanine is the primary site of alkylation, with some N7-deoxyguanosine adducts undergoing imidazole ring-opening to stable mutagenic N5-alkyl formamidopyrimidine (Fapy-dG) adducts. These adducts exist as a mixture of canonical β- and unnatural α-anomeric forms. The β species are predominant in double-stranded (ds) DNA. Recently, we have demonstrated that the DNA glycosylase NEIL1 can initiate repair of AFB1-Fapy-dG adducts both in vitro and in vivo, with Neil1-/- mice showing an increased susceptibility to AFB1-induced hepatocellular carcinoma. Here, we hypothesized that NEIL1 could excise NM-Fapy-dG and that NEIL3, a closely related DNA glycosylase, could excise both NM-Fapy-dG and AFB1-Fapy-dG. Product formation from the reaction of human NEIL1 with ds oligodeoxynucleotides containing a unique NM-Fapy-dG followed a bi-component exponential function under single turnover conditions. Thus, two adduct conformations were differentially recognized by hNEIL1. The excision rate of the major form (∼13.0 min-1), presumed to be the β-anomer, was significantly higher than that previously reported for 5-hydroxycytosine, 5-hydroxyuracil, thymine glycol (Tg), and AFB1-Fapy-dG. Product generation from the minor form was much slower (∼0.4 min-1), likely reflecting the rate of conversion of the α anomer into the β anomer. Mus musculus NEIL3 (MmuNEIL3Δ324) excised NM-Fapy-dG from single-stranded (ss) DNA (turnover rate of ∼0.4 min-1), but not from ds DNA. Product formation from ss substrate was incomplete, presumably because of a substantial presence of the α anomer. MmuNEIL3Δ324 could not initiate repair of AFB1-Fapy-dG in either ds or ss DNA. Overall, the data suggest that both NEIL1 and NEIL3 may protect cells against cytotoxic and mutagenic effects of NM-Fapy-dG, but NEIL1 may have a unique role in initiation of base excision repair of AFB1-Fapy-dG.
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Affiliation(s)
- Irina G Minko
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, United States
| | - Plamen P Christov
- Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Vanderbilt University, Nashville, TN 37235, United States
| | - Liang Li
- Department of Chemistry and Biochemistry, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, United States
| | - Michael P Stone
- Department of Chemistry and Biochemistry, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, United States
| | - Amanda K McCullough
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, United States; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, United States
| | - R Stephen Lloyd
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, United States; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, United States; Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, OR 97239, United States.
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15
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Zhou J, Chan J, Lambelé M, Yusufzai T, Stumpff J, Opresko PL, Thali M, Wallace SS. NEIL3 Repairs Telomere Damage during S Phase to Secure Chromosome Segregation at Mitosis. Cell Rep 2018; 20:2044-2056. [PMID: 28854357 DOI: 10.1016/j.celrep.2017.08.020] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/05/2017] [Accepted: 08/01/2017] [Indexed: 12/28/2022] Open
Abstract
Oxidative damage to telomere DNA compromises telomere integrity. We recently reported that the DNA glycosylase NEIL3 preferentially repairs oxidative lesions in telomere sequences in vitro. Here, we show that loss of NEIL3 causes anaphase DNA bridging because of telomere dysfunction. NEIL3 expression increases during S phase and reaches maximal levels in late S/G2. NEIL3 co-localizes with TRF2 and associates with telomeres during S phase, and this association increases upon oxidative stress. Mechanistic studies reveal that NEIL3 binds to single-stranded DNA via its intrinsically disordered C terminus in a telomere-sequence-independent manner. Moreover, NEIL3 is recruited to telomeres through its interaction with TRF1, and this interaction enhances the enzymatic activity of purified NEIL3. Finally, we show that NEIL3 interacts with AP Endonuclease 1 (APE1) and the long-patch base excision repair proteins PCNA and FEN1. Taken together, we propose that NEIL3 protects genome stability through targeted repair of oxidative damage in telomeres during S/G2 phase.
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Affiliation(s)
- Jia Zhou
- Department of Microbiology and Molecular Genetics, College of Medicine and College of Agriculture and Life Sciences, University of Vermont, Burlington, VT 05405, USA; Graduate Program in Cell and Molecular Biology, University of Vermont, Burlington, VT 05405, USA; Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jany Chan
- Department of Microbiology and Molecular Genetics, College of Medicine and College of Agriculture and Life Sciences, University of Vermont, Burlington, VT 05405, USA
| | - Marie Lambelé
- Department of Microbiology and Molecular Genetics, College of Medicine and College of Agriculture and Life Sciences, University of Vermont, Burlington, VT 05405, USA
| | - Timur Yusufzai
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jason Stumpff
- Department of Molecular Physiology and Biophysics, College of Medicine, University of Vermont, Burlington, VT 05405, USA; Graduate Program in Cell and Molecular Biology, University of Vermont, Burlington, VT 05405, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Markus Thali
- Department of Microbiology and Molecular Genetics, College of Medicine and College of Agriculture and Life Sciences, University of Vermont, Burlington, VT 05405, USA; Graduate Program in Cell and Molecular Biology, University of Vermont, Burlington, VT 05405, USA.
| | - Susan S Wallace
- Department of Microbiology and Molecular Genetics, College of Medicine and College of Agriculture and Life Sciences, University of Vermont, Burlington, VT 05405, USA; Graduate Program in Cell and Molecular Biology, University of Vermont, Burlington, VT 05405, USA.
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16
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Martin PR, Couvé S, Zutterling C, Albelazi MS, Groisman R, Matkarimov BT, Parsons JL, Elder RH, Saparbaev MK. The Human DNA glycosylases NEIL1 and NEIL3 Excise Psoralen-Induced DNA-DNA Cross-Links in a Four-Stranded DNA Structure. Sci Rep 2017; 7:17438. [PMID: 29234069 PMCID: PMC5727206 DOI: 10.1038/s41598-017-17693-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/29/2017] [Indexed: 01/09/2023] Open
Abstract
Interstrand cross-links (ICLs) are highly cytotoxic DNA lesions that block DNA replication and transcription by preventing strand separation. Previously, we demonstrated that the bacterial and human DNA glycosylases Nei and NEIL1 excise unhooked psoralen-derived ICLs in three-stranded DNA via hydrolysis of the glycosidic bond between the crosslinked base and deoxyribose sugar. Furthermore, NEIL3 from Xenopus laevis has been shown to cleave psoralen- and abasic site-induced ICLs in Xenopus egg extracts. Here we report that human NEIL3 cleaves psoralen-induced DNA-DNA cross-links in three-stranded and four-stranded DNA substrates to generate unhooked DNA fragments containing either an abasic site or a psoralen-thymine monoadduct. Furthermore, while Nei and NEIL1 also cleave a psoralen-induced four-stranded DNA substrate to generate two unhooked DNA duplexes with a nick, NEIL3 targets both DNA strands in the ICL without generating single-strand breaks. The DNA substrate specificities of these Nei-like enzymes imply the occurrence of long uninterrupted three- and four-stranded crosslinked DNA-DNA structures that may originate in vivo from DNA replication fork bypass of an ICL. In conclusion, the Nei-like DNA glycosylases unhook psoralen-derived ICLs in various DNA structures via a genuine repair mechanism in which complex DNA lesions can be removed without generation of highly toxic double-strand breaks.
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Affiliation(s)
- Peter R Martin
- Biomedical Research Centre, Cockcroft Building, University of Salford, Salford, M5 4NT, UK
| | - Sophie Couvé
- Ecole Pratique des Hautes Etudes, Paris, France Laboratoire de Génétique Oncologique EPHE, INSERM U753, Villejuif, France; Faculté de Médecine, Université Paris-Sud, Kremlin-Bicêtre, France
| | - Caroline Zutterling
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale Contre le Cancer, CNRS UMR8200, Université Paris-Sud, Gustave Roussy Cancer Campus, F-94805, Villejuif Cedex, France
| | - Mustafa S Albelazi
- Biomedical Research Centre, Cockcroft Building, University of Salford, Salford, M5 4NT, UK
| | - Regina Groisman
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale Contre le Cancer, CNRS UMR8200, Université Paris-Sud, Gustave Roussy Cancer Campus, F-94805, Villejuif Cedex, France
| | - Bakhyt T Matkarimov
- National Laboratory Astana, Nazarbayev University, Astana, 010000, Kazakhstan
| | - Jason L Parsons
- Cancer Research Centre, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 200 London Road, Liverpool, L3 9TA, UK
| | - Rhoderick H Elder
- Biomedical Research Centre, Cockcroft Building, University of Salford, Salford, M5 4NT, UK.
| | - Murat K Saparbaev
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale Contre le Cancer, CNRS UMR8200, Université Paris-Sud, Gustave Roussy Cancer Campus, F-94805, Villejuif Cedex, France.
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17
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Olsen MB, Hildrestrand GA, Scheffler K, Vinge LE, Alfsnes K, Palibrk V, Wang J, Neurauter CG, Luna L, Johansen J, Øgaard JDS, Ohm IK, Slupphaug G, Kuśnierczyk A, Fiane AE, Brorson SH, Zhang L, Gullestad L, Louch WE, Iversen PO, Østlie I, Klungland A, Christensen G, Sjaastad I, Sætrom P, Yndestad A, Aukrust P, Bjørås M, Finsen AV. NEIL3-Dependent Regulation of Cardiac Fibroblast Proliferation Prevents Myocardial Rupture. Cell Rep 2017; 18:82-92. [PMID: 28052262 DOI: 10.1016/j.celrep.2016.12.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/06/2016] [Accepted: 12/01/2016] [Indexed: 12/15/2022] Open
Abstract
Myocardial infarction (MI) triggers a reparative response involving fibroblast proliferation and differentiation driving extracellular matrix modulation necessary to form a stabilizing scar. Recently, it was shown that a genetic variant of the base excision repair enzyme NEIL3 was associated with increased risk of MI in humans. Here, we report elevated myocardial NEIL3 expression in heart failure patients and marked myocardial upregulation of Neil3 after MI in mice, especially in a fibroblast-enriched cell fraction. Neil3-/- mice show increased mortality after MI caused by myocardial rupture. Genome-wide analysis of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) reveals changes in the cardiac epigenome, including in genes related to the post-MI transcriptional response. Differentially methylated genes are enriched in pathways related to proliferation and myofibroblast differentiation. Accordingly, Neil3-/- ruptured hearts show increased proliferation of fibroblasts and myofibroblasts. We propose that NEIL3-dependent modulation of DNA methylation regulates cardiac fibroblast proliferation and thereby affects extracellular matrix modulation after MI.
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Affiliation(s)
- Maria B Olsen
- Research Institute of Internal Medicine, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Center for Heart Failure Research, University of Oslo, 0317 Oslo, Norway; K.G. Jebsen Inflammation Research Centre, University of Oslo, 0317 Oslo, Norway
| | - Gunn A Hildrestrand
- Department of Microbiology, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway
| | - Katja Scheffler
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Leif Erik Vinge
- Research Institute of Internal Medicine, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Department of Cardiology, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Center for Heart Failure Research, University of Oslo, 0317 Oslo, Norway
| | - Katrine Alfsnes
- Research Institute of Internal Medicine, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Center for Heart Failure Research, University of Oslo, 0317 Oslo, Norway; K.G. Jebsen Inflammation Research Centre, University of Oslo, 0317 Oslo, Norway
| | - Vuk Palibrk
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Junbai Wang
- Department of Pathology, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway
| | - Christine G Neurauter
- Department of Microbiology, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway
| | - Luisa Luna
- Department of Microbiology, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway
| | - Jostein Johansen
- Bioinformatics Core Facility-BioCore , Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Jonas D S Øgaard
- Research Institute of Internal Medicine, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway
| | - Ingrid K Ohm
- Research Institute of Internal Medicine, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Center for Heart Failure Research, University of Oslo, 0317 Oslo, Norway
| | - Geir Slupphaug
- Proteomics and Metabolomics Core Facility-PROMEC, Norwegian University of Science and Technology, 7491 Trondheim, Norway; Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Anna Kuśnierczyk
- Proteomics and Metabolomics Core Facility-PROMEC, Norwegian University of Science and Technology, 7491 Trondheim, Norway; Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Arnt E Fiane
- Department of Cardiothoracic Surgery, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway
| | - Sverre-Henning Brorson
- Department of Pathology, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway
| | - Lili Zhang
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway
| | - Lars Gullestad
- Research Institute of Internal Medicine, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Department of Cardiology, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Center for Heart Failure Research, University of Oslo, 0317 Oslo, Norway
| | - William E Louch
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Center for Heart Failure Research, University of Oslo, 0317 Oslo, Norway
| | - Per Ole Iversen
- Department of Haematology, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Department of Nutrition, University of Oslo, 0317 Oslo, Norway
| | - Ingunn Østlie
- Department of Pathology, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway
| | - Geir Christensen
- Department of Cardiology, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Center for Heart Failure Research, University of Oslo, 0317 Oslo, Norway
| | - Ivar Sjaastad
- Department of Cardiology, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Center for Heart Failure Research, University of Oslo, 0317 Oslo, Norway
| | - Pål Sætrom
- Bioinformatics Core Facility-BioCore , Norwegian University of Science and Technology, 7491 Trondheim, Norway; Department of Computer and Information Science, Norwegian University of Science and Technology, 7491 Trondheim, Norway; Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Arne Yndestad
- Research Institute of Internal Medicine, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Center for Heart Failure Research, University of Oslo, 0317 Oslo, Norway; K.G. Jebsen Inflammation Research Centre, University of Oslo, 0317 Oslo, Norway
| | - Pål Aukrust
- Research Institute of Internal Medicine, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; K.G. Jebsen Inflammation Research Centre, University of Oslo, 0317 Oslo, Norway
| | - Magnar Bjørås
- Department of Microbiology, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway.
| | - Alexandra V Finsen
- Research Institute of Internal Medicine, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Department of Cardiology, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Center for Heart Failure Research, University of Oslo, 0317 Oslo, Norway
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18
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Fleming AM, Burrows CJ. Formation and processing of DNA damage substrates for the hNEIL enzymes. Free Radic Biol Med 2017; 107:35-52. [PMID: 27880870 PMCID: PMC5438787 DOI: 10.1016/j.freeradbiomed.2016.11.030] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/13/2016] [Accepted: 11/16/2016] [Indexed: 12/13/2022]
Abstract
Reactive oxygen species (ROS) are harnessed by the cell for signaling at the same time as being detrimental to cellular components such as DNA. The genome and transcriptome contain instructions that can alter cellular processes when oxidized. The guanine (G) heterocycle in the nucleotide pool, DNA, or RNA is the base most prone to oxidation. The oxidatively-derived products of G consistently observed in high yields from hydroxyl radical, carbonate radical, or singlet oxygen oxidations under conditions modeling the cellular reducing environment are discussed. The major G base oxidation products are 8-oxo-7,8-dihydroguanine (OG), 5-carboxamido-5-formamido-2-iminohydantoin (2Ih), spiroiminodihydantoin (Sp), and 5-guanidinohydantoin (Gh). The yields of these products show dependency on the oxidant and the reaction context that includes nucleoside, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), and G-quadruplex DNA (G4-DNA) structures. Upon formation of these products in cells, they are recognized by the DNA glycosylases in the base excision repair (BER) pathway. This review focuses on initiation of BER by the mammalian Nei-like1-3 (NEIL1-3) glycosylases for removal of 2Ih, Sp, and Gh. The unique ability of the human NEILs to initiate removal of the hydantoins in ssDNA, bulge-DNA, bubble-DNA, dsDNA, and G4-DNA is outlined. Additionally, when Gh exists in a G4 DNA found in a gene promoter, NEIL-mediated repair is modulated by the plasticity of the G4-DNA structure provided by additional G-runs flanking the sequence. On the basis of these observations and cellular studies from the literature, the interplay between DNA oxidation and BER to alter gene expression is discussed.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, UT 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, UT 84112-0850, United States.
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19
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Repair of oxidatively induced DNA damage by DNA glycosylases: Mechanisms of action, substrate specificities and excision kinetics. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 771:99-127. [PMID: 28342455 DOI: 10.1016/j.mrrev.2017.02.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Indexed: 02/07/2023]
Abstract
Endogenous and exogenous reactive species cause oxidatively induced DNA damage in living organisms by a variety of mechanisms. As a result, a plethora of mutagenic and/or cytotoxic products are formed in cellular DNA. This type of DNA damage is repaired by base excision repair, although nucleotide excision repair also plays a limited role. DNA glycosylases remove modified DNA bases from DNA by hydrolyzing the glycosidic bond leaving behind an apurinic/apyrimidinic (AP) site. Some of them also possess an accompanying AP-lyase activity that cleaves the sugar-phosphate chain of DNA. Since the first discovery of a DNA glycosylase, many studies have elucidated the mechanisms of action, substrate specificities and excision kinetics of these enzymes present in all living organisms. For this purpose, most studies used single- or double-stranded oligodeoxynucleotides with a single DNA lesion embedded at a defined position. High-molecular weight DNA with multiple base lesions has been used in other studies with the advantage of the simultaneous investigation of many DNA base lesions as substrates. Differences between the substrate specificities and excision kinetics of DNA glycosylases have been found when these two different substrates were used. Some DNA glycosylases possess varying substrate specificities for either purine-derived lesions or pyrimidine-derived lesions, whereas others exhibit cross-activity for both types of lesions. Laboratory animals with knockouts of the genes of DNA glycosylases have also been used to provide unequivocal evidence for the substrates, which had previously been found in in vitro studies, to be the actual substrates in vivo as well. On the basis of the knowledge gained from the past studies, efforts are being made to discover small molecule inhibitors of DNA glycosylases that may be used as potential drugs in cancer therapy.
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20
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Abstract
DNA methylation plays important roles in development and disease. Yet, only recently has the dynamic nature of this epigenetic mark via oxidation and DNA repair-mediated demethylation been recognized. A major conceptual challenge to the model that DNA methylation is reversible is the risk of genomic instability, which may come with widespread DNA repair activity. Here, we focus on recent advances in mechanisms of TET-TDG mediated demethylation and cellular strategies that avoid genomic instability. We highlight the recently discovered involvement of NEIL DNA glycosylases, which cooperate with TDG in oxidative demethylation to accelerate substrate turnover and promote the organized handover of harmful repair intermediates to maintain genome stability.
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Affiliation(s)
| | - Christof Niehrs
- Institute of Molecular Biology (IMB), Mainz, Germany.,Division of Molecular Embryology, German Cancer Research Center-Zentrum für Molekulare Biologie der Universität Heidelberg (DKFZ-ZMBH) Alliance, Heidelberg, Germany
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21
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Li X, Cornelis MC, Liang L, Song F, De Vivo I, Giovannucci E, Tang JY, Han J. A genome-wide analysis of gene-caffeine consumption interaction on basal cell carcinoma. Carcinogenesis 2016; 37:1138-1143. [PMID: 27797824 PMCID: PMC5137266 DOI: 10.1093/carcin/bgw107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/16/2016] [Accepted: 10/06/2016] [Indexed: 12/21/2022] Open
Abstract
Animal models have suggested that oral or topical administration of caffeine could inhibit ultraviolet-induced carcinogenesis via the ataxia telangiectasia and rad3 (ATR)-related apoptosis. Previous epidemiological studies have demonstrated that increased caffeine consumption is associated with reduced risk of basal cell carcinoma (BCC). To identify common genetic markers that may modify this association, we tested gene-caffeine intake interaction on BCC risk in a genome-wide analysis. We included 3383 BCC cases and 8528 controls of European ancestry from the Nurses' Health Study and Health Professionals Follow-up Study. Single nucleotide polymorphism (SNP) rs142310826 near the NEIL3 gene showed a genome-wide significant interaction with caffeine consumption (P = 1.78 × 10-8 for interaction) on BCC risk. There was no gender difference for this interaction (P = 0.64 for heterogeneity). NEIL3, a gene belonging to the base excision DNA repair pathway, encodes a DNA glycosylase that recognizes and removes lesions produced by oxidative stress. In addition, we identified several loci with P value for interaction <5 × 10-7 in gender-specific analyses (P for heterogeneity between genders < 0.001) including those mapping to the genes LRRTM4, ATF3 and DCLRE1C in women and POTEA in men. Finally, we tested the associations between caffeine consumption-related SNPs reported by previous genome-wide association studies and risk of BCC, both individually and jointly, but found no significant association. In sum, we identified a DNA repair gene that could be involved in caffeine-mediated skin tumor inhibition. Further studies are warranted to confirm these findings.
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Affiliation(s)
- Xin Li
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston MA 02115, USA
| | - Marilyn C Cornelis
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago IL 60611, USA
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston MA 02115, USA
| | - Fengju Song
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Hospital and Institute, Tianjin 300060, China
- National Clinical Research Center for Cancer and Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China
| | - Immaculata De Vivo
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston MA 02115, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Edward Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston MA 02115, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Jean Y Tang
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA 94063, USA
| | - Jiali Han
- Department of Epidemiology, Fairbanks School of Public Health, Indiana University, Indianapolis, IN 46202, USA
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN 46202, USA
- Center for Pharmacoepidemiology, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, IN 46202, USA
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22
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Massaad MJ, Zhou J, Tsuchimoto D, Chou J, Jabara H, Janssen E, Glauzy S, Olson BG, Morbach H, Ohsumi TK, Schmitz K, Kyriacos M, Kane J, Torisu K, Nakabeppu Y, Notarangelo LD, Chouery E, Megarbane A, Kang PB, Al-Idrissi E, Aldhekri H, Meffre E, Mizui M, Tsokos GC, Manis JP, Al-Herz W, Wallace SS, Geha RS. Deficiency of base excision repair enzyme NEIL3 drives increased predisposition to autoimmunity. J Clin Invest 2016; 126:4219-4236. [PMID: 27760045 DOI: 10.1172/jci85647] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 09/06/2016] [Indexed: 12/17/2022] Open
Abstract
Alterations in the apoptosis of immune cells have been associated with autoimmunity. Here, we have identified a homozygous missense mutation in the gene encoding the base excision repair enzyme Nei endonuclease VIII-like 3 (NEIL3) that abolished enzymatic activity in 3 siblings from a consanguineous family. The NEIL3 mutation was associated with fatal recurrent infections, severe autoimmunity, hypogammaglobulinemia, and impaired B cell function in these individuals. The same homozygous NEIL3 mutation was also identified in an asymptomatic individual who exhibited elevated levels of serum autoantibodies and defective peripheral B cell tolerance, but normal B cell function. Further analysis of the patients revealed an absence of LPS-responsive beige-like anchor (LRBA) protein expression, a known cause of immunodeficiency. We next examined the contribution of NEIL3 to the maintenance of self-tolerance in Neil3-/- mice. Although Neil3-/- mice displayed normal B cell function, they exhibited elevated serum levels of autoantibodies and developed nephritis following treatment with poly(I:C) to mimic microbial stimulation. In Neil3-/- mice, splenic T and B cells as well as germinal center B cells from Peyer's patches showed marked increases in apoptosis and cell death, indicating the potential release of self-antigens that favor autoimmunity. These findings demonstrate that deficiency in NEIL3 is associated with increased lymphocyte apoptosis, autoantibodies, and predisposition to autoimmunity.
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23
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Replication-Dependent Unhooking of DNA Interstrand Cross-Links by the NEIL3 Glycosylase. Cell 2016; 167:498-511.e14. [PMID: 27693351 DOI: 10.1016/j.cell.2016.09.008] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 07/28/2016] [Accepted: 09/02/2016] [Indexed: 12/19/2022]
Abstract
During eukaryotic DNA interstrand cross-link (ICL) repair, cross-links are resolved ("unhooked") by nucleolytic incisions surrounding the lesion. In vertebrates, ICL repair is triggered when replication forks collide with the lesion, leading to FANCI-FANCD2-dependent unhooking and formation of a double-strand break (DSB) intermediate. Using Xenopus egg extracts, we describe here a replication-coupled ICL repair pathway that does not require incisions or FANCI-FANCD2. Instead, the ICL is unhooked when one of the two N-glycosyl bonds forming the cross-link is cleaved by the DNA glycosylase NEIL3. Cleavage by NEIL3 is the primary unhooking mechanism for psoralen and abasic site ICLs. When N-glycosyl bond cleavage is prevented, unhooking occurs via FANCI-FANCD2-dependent incisions. In summary, we identify an incision-independent unhooking mechanism that avoids DSB formation and represents the preferred pathway of ICL repair in a vertebrate cell-free system.
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24
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Cipollini M, Figlioli G, Maccari G, Garritano S, De Santi C, Melaiu O, Barone E, Bambi F, Ermini S, Pellegrini G, Cristaudo A, Foddis R, Bonotti A, Romei C, Vivaldi A, Agate L, Molinari E, Barale R, Forsti A, Hemminki K, Elisei R, Gemignani F, Landi S. Polymorphisms within base and nucleotide excision repair pathways and risk of differentiated thyroid carcinoma. DNA Repair (Amst) 2016; 41:27-31. [PMID: 27062014 DOI: 10.1016/j.dnarep.2016.03.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 03/02/2016] [Accepted: 03/08/2016] [Indexed: 12/21/2022]
Abstract
The thyrocytes are exposed to high levels of oxidative stress which could induce DNA damages. Base excision repair (BER) is one of the principal mechanisms of defense against oxidative DNA damage, however recent evidences suggest that also nucleotide excision repair (NER) could be involved. The aim of present work was to identify novel differentiated thyroid cancer (DTC) risk variants in BER and NER genes. For this purpose, the most strongly associated SNPs within NER and BER genes found in our previous GWAS on DTC were selected and replicated in an independent series of samples for a new case-control study. Although a positive signal was detected at the nominal level of 0.05 for rs7689099 (encoding for an aminoacid change proline to arginine at codon 117 within NEIL3), none of the considered SNPs (i.e. rs7990340 and rs690860 within RFC3, rs3744767 and rs1131636 within RPA1, rs16962916 and rs3136166 in ERCC4, and rs17739370 and rs7689099 in NEIL3) was associated with the risk of DTC when the correction of multiple testing was applied. In conclusion, a role of NER and BER pathways was evoked in the susceptibility to DTC. However, this seemed to be limited to few polymorphic genes and the overall effect size appeared weak.
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Affiliation(s)
| | | | - Giuseppe Maccari
- Center for Nanotechnology and Innovation @NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro Pisa, Italy
| | - Sonia Garritano
- Center for Integrated Biology, University of Trento, Trento, Italy
| | | | | | - Elisa Barone
- Department of Biology, University of Pisa, Pisa, Italy
| | - Franco Bambi
- Blood Centre of University Hospital of Meyer, Florence, Italy
| | - Stefano Ermini
- Blood Centre of University Hospital of Meyer, Florence, Italy
| | - Giovanni Pellegrini
- Operative Unit of laboratory of Clinical Chemistry Analyses, University Hospital of Cisanello, Pisa, Italy
| | - Alfonso Cristaudo
- Department of Endocrinology and Metabolism, Orthopaedics and Traumatology, Occupational Medicine, University of Pisa, Pisa, Italy
| | - Rudy Foddis
- Department of Endocrinology and Metabolism, Orthopaedics and Traumatology, Occupational Medicine, University of Pisa, Pisa, Italy
| | - Alessandra Bonotti
- Department of Endocrinology and Metabolism, Orthopaedics and Traumatology, Occupational Medicine, University of Pisa, Pisa, Italy
| | - Cristina Romei
- Department of Endocrinology and Metabolism, Orthopaedics and Traumatology, Occupational Medicine, University of Pisa, Pisa, Italy
| | - Agnese Vivaldi
- Operative Unit of laboratory of Clinical Chemistry Analyses, University Hospital of Cisanello, Pisa, Italy
| | - Laura Agate
- Department of Endocrinology and Metabolism, Orthopaedics and Traumatology, Occupational Medicine, University of Pisa, Pisa, Italy
| | - Eleonora Molinari
- Department of Endocrinology and Metabolism, Orthopaedics and Traumatology, Occupational Medicine, University of Pisa, Pisa, Italy
| | | | - Asta Forsti
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany; Center for Primary Health Care Research, Clinical Research Center, Lund University, Malmö, Sweden
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany; Center for Primary Health Care Research, Clinical Research Center, Lund University, Malmö, Sweden
| | - Rossella Elisei
- Department of Endocrinology and Metabolism, Orthopaedics and Traumatology, Occupational Medicine, University of Pisa, Pisa, Italy
| | | | - Stefano Landi
- Department of Biology, University of Pisa, Pisa, Italy.
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Zhou J, Fleming AM, Averill AM, Burrows CJ, Wallace SS. The NEIL glycosylases remove oxidized guanine lesions from telomeric and promoter quadruplex DNA structures. Nucleic Acids Res 2015; 43:4039-54. [PMID: 25813041 PMCID: PMC4417164 DOI: 10.1093/nar/gkv252] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 03/11/2015] [Indexed: 12/31/2022] Open
Abstract
G-quadruplex is a four-stranded G-rich DNA structure that is highly susceptible to oxidation. Despite the important roles that G-quadruplexes play in telomere biology and gene transcription, neither the impact of guanine lesions on the stability of quadruplexes nor their repair are well understood. Here, we show that the oxidized guanine lesions 8-oxo-7,8-dihydroguanine (8-oxoG), guanidinohydantoin (Gh) and spiroiminodihydantoin (Sp) reduce the thermostability and alter the folding of telomeric quadruplexes in a location-dependent manner. Also, the NEIL1 and NEIL3 DNA glycosylases can remove hydantoin lesions but none of the glycosylases, including OGG1, are able to remove 8-oxoG from telomeric quadruplexes. Interestingly, a hydantoin lesion at the site most prone to oxidation in quadruplex DNA is not efficiently removed by NEIL1 or NEIL3. However, NEIL1, NEIL2 and NEIL3 remove hydantoins from telomeric quadruplexes formed by five TTAGGG repeats much more rapidly than the commonly studied four-repeat quadruplex structures. We also show that APE1 cleaves furan in selected positions in Na+-coordinated telomeric quadruplexes. In promoter G-quadruplex DNA, the NEIL glycosylases primarily remove Gh from Na+-coordinated antiparallel quadruplexes but not K+-coordinated parallel quadruplexes containing VEGF or c-MYC promoter sequences. Thus, the NEIL DNA glycosylases may be involved in both telomere maintenance and in gene regulation.
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Affiliation(s)
- Jia Zhou
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - April M Averill
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Susan S Wallace
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
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Oxidatively induced DNA damage and its repair in cancer. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2014; 763:212-45. [PMID: 25795122 DOI: 10.1016/j.mrrev.2014.11.002] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 11/03/2014] [Accepted: 11/04/2014] [Indexed: 12/28/2022]
Abstract
Oxidatively induced DNA damage is caused in living organisms by endogenous and exogenous reactive species. DNA lesions resulting from this type of damage are mutagenic and cytotoxic and, if not repaired, can cause genetic instability that may lead to disease processes including carcinogenesis. Living organisms possess DNA repair mechanisms that include a variety of pathways to repair multiple DNA lesions. Mutations and polymorphisms also occur in DNA repair genes adversely affecting DNA repair systems. Cancer tissues overexpress DNA repair proteins and thus develop greater DNA repair capacity than normal tissues. Increased DNA repair in tumors that removes DNA lesions before they become toxic is a major mechanism for development of resistance to therapy, affecting patient survival. Accumulated evidence suggests that DNA repair capacity may be a predictive biomarker for patient response to therapy. Thus, knowledge of DNA protein expressions in normal and cancerous tissues may help predict and guide development of treatments and yield the best therapeutic response. DNA repair proteins constitute targets for inhibitors to overcome the resistance of tumors to therapy. Inhibitors of DNA repair for combination therapy or as single agents for monotherapy may help selectively kill tumors, potentially leading to personalized therapy. Numerous inhibitors have been developed and are being tested in clinical trials. The efficacy of some inhibitors in therapy has been demonstrated in patients. Further development of inhibitors of DNA repair proteins is globally underway to help eradicate cancer.
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Scott TL, Rangaswamy S, Wicker CA, Izumi T. Repair of oxidative DNA damage and cancer: recent progress in DNA base excision repair. Antioxid Redox Signal 2014; 20:708-26. [PMID: 23901781 PMCID: PMC3960848 DOI: 10.1089/ars.2013.5529] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
SIGNIFICANCE Reactive oxygen species (ROS) are generated by exogenous and environmental genotoxins, but also arise from mitochondria as byproducts of respiration in the body. ROS generate DNA damage of which pathological consequence, including cancer is well established. Research efforts are intense to understand the mechanism of DNA base excision repair, the primary mechanism to protect cells from genotoxicity caused by ROS. RECENT ADVANCES In addition to the notion that oxidative DNA damage causes transformation of cells, recent studies have revealed how the mitochondrial deficiencies and ROS generation alter cell growth during the cancer transformation. CRITICAL ISSUES The emphasis of this review is to highlight the importance of the cellular response to oxidative DNA damage during carcinogenesis. Oxidative DNA damage, including 7,8-dihydro-8-oxoguanine, play an important role during the cellular transformation. It is also becoming apparent that the unusual activity and subcellular distribution of apurinic/apyrimidinic endonuclease 1, an essential DNA repair factor/redox sensor, affect cancer malignancy by increasing cellular resistance to oxidative stress and by positively influencing cell proliferation. FUTURE DIRECTIONS Technological advancement in cancer cell biology and genetics has enabled us to monitor the detailed DNA repair activities in the microenvironment. Precise understanding of the intracellular activities of DNA repair proteins for oxidative DNA damage should provide help in understanding how mitochondria, ROS, DNA damage, and repair influence cancer transformation.
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Affiliation(s)
- Timothy L Scott
- Graduate Center for Toxicology, University of Kentucky , Lexington, Kentucky
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Wallace SS. DNA glycosylases search for and remove oxidized DNA bases. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2013; 54:691-704. [PMID: 24123395 PMCID: PMC3997179 DOI: 10.1002/em.21820] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 09/04/2013] [Accepted: 09/05/2013] [Indexed: 05/19/2023]
Abstract
This review article presents, an overview of the DNA glycosylases that recognize oxidized DNA bases using the Fpg/Nei family of DNA glycosylases as models for how structure can inform function. For example, even though human NEIL1 and the plant and fungal orthologs lack the zinc finger shown to be required for binding, DNA crystal structures revealed a "zincless finger" with the same properties. Moreover, the "lesion recognition loop" is not involved in lesion recognition, rather, it stabilizes 8-oxoG in the active site pocket. Unlike the other Fpg/Nei family members, Neil3 lacks two of the three void-filling residues that stabilize the DNA duplex and interact with the opposite strand to the damage which may account for its preference for lesions in single-stranded DNA. Also single-molecule approaches show that DNA glycosylases search for their substrates in a sea of undamaged DNA by using a wedge residue that is inserted into the DNA helix to probe for the presence of damage.
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Affiliation(s)
- 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, VT 05405-0068, USA Tel: (802) 656-2164; Fax: (802) 656-8749
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29
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McKibbin PL, Fleming AM, Towheed MA, Van Houten B, Burrows CJ, David SS. Repair of hydantoin lesions and their amine adducts in DNA by base and nucleotide excision repair. J Am Chem Soc 2013; 135:13851-61. [PMID: 23930966 PMCID: PMC3906845 DOI: 10.1021/ja4059469] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
An important feature of the common DNA oxidation product 8-oxo-7,8-dihydroguanine (OG) is its susceptibility to further oxidation that produces guanidinohydantoin (Gh) and spiroiminodihydantoin (Sp) lesions. In the presence of amines, G or OG oxidation produces hydantoin amine adducts. Such adducts may form in cells via interception of oxidized intermediates by protein-derived nucleophiles or naturally occurring amines that are tightly associated with DNA. Gh and Sp are known to be substrates for base excision repair (BER) glycosylases; however, large Sp-amine adducts would be expected to be more readily repaired by nucleotide excision repair (NER). A series of Sp adducts differing in the size of the attached amine were synthesized to evaluate the relative processing by NER and BER. The UvrABC complex excised Gh, Sp, and the Sp-amine adducts from duplex DNA, with the greatest efficiency for the largest Sp-amine adducts. The affinity of UvrA for all of the lesion duplexes was found to be similar, whereas the efficiency of UvrB loading tracked with the efficiency of UvrABC excision. In contrast, the human BER glycosylase NEIL1 exhibited robust activity for all Sp-amine adducts irrespective of size. These studies suggest that both NER and BER pathways mediate repair of a diverse set of hydantoin lesions in cells.
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Affiliation(s)
- Paige L. McKibbin
- Department of Chemistry, One Shields Avenue, University of California, Davis, Davis, California 95616 United States
| | - Aaron M. Fleming
- Department of Chemistry, 315 S. 1400 East, University of Utah, Salt Lake City, Utah, 84112, United States
| | - Mohammad Atif Towheed
- Department of Pharmacology and Chemical Biology, 5117 Centre Avenue, University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, 15213 United States,
| | - Bennett Van Houten
- Department of Pharmacology and Chemical Biology, 5117 Centre Avenue, University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, 15213 United States,
| | - Cynthia J. Burrows
- Department of Chemistry, 315 S. 1400 East, University of Utah, Salt Lake City, Utah, 84112, United States
| | - Sheila S. David
- Department of Chemistry, One Shields Avenue, University of California, Davis, Davis, California 95616 United States
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30
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Zhou J, Liu M, Fleming AM, Burrows CJ, Wallace SS. Neil3 and NEIL1 DNA glycosylases remove oxidative damages from quadruplex DNA and exhibit preferences for lesions in the telomeric sequence context. J Biol Chem 2013; 288:27263-27272. [PMID: 23926102 DOI: 10.1074/jbc.m113.479055] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The telomeric DNA of vertebrates consists of d(TTAGGG)n tandem repeats, which can form quadruplex DNA structures in vitro and likely in vivo. Despite the fact that the G-rich telomeric DNA is susceptible to oxidation, few biochemical studies of base excision repair in telomeric DNA and quadruplex structures have been done. Here, we show that telomeric DNA containing thymine glycol (Tg), 8-oxo-7,8-dihydroguanine (8-oxoG), guanidinohydantoin (Gh), or spiroiminodihydantoin (Sp) can form quadruplex DNA structures in vitro. We have tested the base excision activities of five mammalian DNA glycosylases (NEIL1, NEIL2, mNeil3, NTH1, and OGG1) on these lesion-containing quadruplex substrates and found that only mNeil3 had excision activity on Tg in quadruplex DNA and that the glycosylase exhibited a strong preference for Tg in the telomeric sequence context. Although Sp and Gh in quadruplex DNA were good substrates for mNeil3 and NEIL1, none of the glycosylases had activity on quadruplex DNA containing 8-oxoG. In addition, NEIL1 but not mNeil3 showed enhanced glycosylase activity on Gh in the telomeric sequence context. These data suggest that one role for Neil3 and NEIL1 is to repair DNA base damages in telomeres in vivo and that Neil3 and Neil1 may function in quadruplex-mediated cellular events, such as gene regulation via removal of damaged bases from quadruplex DNA.
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Affiliation(s)
- Jia Zhou
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, The University of Vermont, Burlington, Vermont 05405-0068
| | - Minmin Liu
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, The University of Vermont, Burlington, Vermont 05405-0068
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 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, Burlington, Vermont 05405-0068.
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31
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Krokeide SZ, Laerdahl JK, Salah M, Luna L, Cederkvist FH, Fleming AM, Burrows CJ, Dalhus B, Bjørås M. Human NEIL3 is mainly a monofunctional DNA glycosylase removing spiroimindiohydantoin and guanidinohydantoin. DNA Repair (Amst) 2013; 12:1159-64. [PMID: 23755964 DOI: 10.1016/j.dnarep.2013.04.026] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Revised: 04/23/2013] [Accepted: 04/25/2013] [Indexed: 10/26/2022]
Abstract
Base excision repair is the major pathway for removal of oxidative DNA base damage. This pathway is initiated by DNA glycosylases, which recognize and excise damaged bases from DNA. In this work, we have purified the glycosylase domain (GD) of human DNA glycosylase NEIL3. The substrate specificity has been characterized and we have elucidated the catalytic mechanisms. GD NEIL3 excised the hydantoin lesions spiroiminodihydantoin (Sp) and guanidinohydantoin (Gh) in single-stranded (ss) and double-stranded (ds) DNA efficiently. NEIL3 also removed 5-hydroxy-2'-deoxycytidine (5OHC) and 5-hydroxy-2'-deoxyuridine (5OHU) in ssDNA, but less efficiently than hydantoins. Unlike NEIL1 and NEIL2, which possess a β,δ-elimination activity, NEIL3 mainly incised damaged DNA by β-elimination. Further, the base excision and strand incision activities of NEIL3 exhibited a non-concerted action, indicating that NEIL3 mainly operate as a monofunctional DNA glycosylase. The site-specific NEIL3 mutant V2P, however, showed a concerted action, suggesting that the N-terminal amino group in Val2 is critical for the monofunctional modus. Finally, we demonstrated that residue Lys81 is essential for catalysis.
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Affiliation(s)
- Silje Z Krokeide
- Department of Microbiology, University of Oslo, Oslo University Hospital, Rikshospitalet, PO Box 4950, Nydalen, NO-0424 Oslo, Norway
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Liu M, Imamura K, Averill AM, Wallace SS, Doublié S. Structural characterization of a mouse ortholog of human NEIL3 with a marked preference for single-stranded DNA. Structure 2013; 21:247-56. [PMID: 23313161 DOI: 10.1016/j.str.2012.12.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 12/07/2012] [Accepted: 12/08/2012] [Indexed: 12/21/2022]
Abstract
Endonuclease VIII-like 3 (Neil3) is a DNA glycosylase of the base excision repair pathway that protects cells from oxidative DNA damage by excising a broad spectrum of cytotoxic and mutagenic base lesions. Interestingly, Neil3 exhibits an unusual preference for DNA with single-stranded regions. Here, we report the 2.0 Å crystal structure of a Neil3 enzyme. Although the glycosylase region of mouse Neil3 (MmuNeil3Δ324) exhibits the same overall fold as that of other Fpg/Nei proteins, it presents distinct structural features. First, MmuNeil3Δ324 lacks the αF-β9/10 loop that caps the flipped-out 8-oxoG in bacterial Fpg, which is consistent with its inability to cleave 8-oxoguanine. Second, Neil3 not only lacks two of the three void-filling residues that stabilize the opposite strand, but it also harbors negatively charged residues that create an unfavorable electrostatic environment for the phosphate backbone of that strand. These structural features provide insight into the substrate specificity and marked preference of Neil3 for ssDNA.
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Affiliation(s)
- Minmin Liu
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405-0068, USA
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Loss of Neil3, the major DNA glycosylase activity for removal of hydantoins in single stranded DNA, reduces cellular proliferation and sensitizes cells to genotoxic stress. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:1157-64. [PMID: 23305905 DOI: 10.1016/j.bbamcr.2012.12.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 12/13/2012] [Accepted: 12/26/2012] [Indexed: 11/21/2022]
Abstract
7,8-Dihydro-8-oxoguanine (8-oxoG) is one of the most common oxidative base lesions in normal tissues induced by a variety of endogenous and exogenous agents. Hydantoins are products of 8-oxoG oxidation and as 8-oxoG, they have been shown to be mutagenic lesions. Oxidative DNA damage has been implicated in the etiology of various age-associated pathologies, such as cancer, cardiovascular diseases, arthritis, and several neurodegenerative diseases. The mammalian endonuclease VIII-like 3 (Neil3) is one of the four DNA glycosylases found to recognize and remove hydantoins in the first step of base excision repair (BER) pathway. We have generated mice lacking Neil3 and by using total cell extracts we demonstrate that Neil3 is the main DNA glycosylase that incises hydantoins in single stranded DNA in tissues. Using the neurosphere culture system as a model to study neural stem/progenitor (NSPC) cells we found that lack of Neil3 impaired self renewal but did not affect differentiation capacity. Proliferation was also reduced in mouse embryonic fibroblasts (MEFs) derived from Neil3(-/-) embryos and these cells were sensitive to both the oxidative toxicant paraquat and interstrand cross-link (ICL)-inducing agent cisplatin. Our data support the involvement of Neil3 in removal of replication blocks in proliferating cells.
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34
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Liu M, Doublié S, Wallace SS. Neil3, the final frontier for the DNA glycosylases that recognize oxidative damage. Mutat Res 2012; 743-744:4-11. [PMID: 23274422 DOI: 10.1016/j.mrfmmm.2012.12.003] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 12/18/2012] [Indexed: 11/17/2022]
Abstract
DNA glycosylases are the enzymes that initiate the Base Excision Repair (BER) process that protects all organisms from the mutagenic and/or cytotoxic effects of DNA base lesions. Endonuclease VIII like proteins (Neil1, Neil2 and Neil3) are found in vertebrate genomes and are homologous to the well-characterized bacterial DNA glycosylases, Formamidopyrimidine DNA glycosylase (Fpg) and Endonuclease VIII (Nei). Since the initial discovery of the Neil proteins, much progress has been made on characterizing Neil1 and Neil2. It was not until recently, however, that Neil3 was shown to be a functional DNA glycosylase having a different substrate specificity and unusual structural features compared with other Fpg/Nei homologs. Although the biological functions of Neil3 still remain an enigma, this review highlights recent biochemical and structural data that may ultimately shed light on its biological role.
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Affiliation(s)
- Minmin Liu
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Dr., Burlington, VT 05405-0086, United States.
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Dr., Burlington, VT 05405-0086, United States
| | - Susan S Wallace
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Dr., Burlington, VT 05405-0086, United States.
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