1
|
Daskalova SM, Eisenhauer BM, Gao M, Feng X, Ji X, Cheng Q, Fahmi N, Khdour OM, Chen S, Hecht SM. An assay for DNA polymerase β lyase inhibitors that engage the catalytic nucleophile for binding. Bioorg Med Chem 2020; 28:115642. [PMID: 32773093 DOI: 10.1016/j.bmc.2020.115642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/03/2020] [Accepted: 07/05/2020] [Indexed: 11/16/2022]
Abstract
DNA polymerase β (Pol β) repairs cellular DNA damage. When such damage is inflicted upon the DNA in tumor cells treated with DNA targeted antitumor agents, Pol β thus diminishes their efficacy. Accordingly, this enzyme has long been a target for antitumor therapy. Although numerous inhibitors of the lyase activity of the enzyme have been reported, none has yet proven adequate for development as a therapeutic agent. In the present study, we developed a new strategy to identify lyase inhibitors that critically engage the lyase active site primary nucleophile Lys72 as part of the binding interface. This involves a parallel evaluation of the effect of the inhibitors on the wild-type DNA polymerase β (Pol β) and Pol β modified with a lysine analogue at position 72. A model panel of five structurally diverse lyase inhibitors identified in our previous studies (only one of which has been published) with unknown modes of binding were used for testing, and one compound, cis-9,10-epoxyoctadecanoic acid, was found to have the desired characteristics. This finding was further corroborated by in silico docking, demonstrating that the predominant mode of binding of the inhibitor involves an important electrostatic interaction between the oxygen atom of the epoxy group and Nε of the main catalytic nucleophile, Lys72. The strategy, which is designed to identify compounds that engage certain structural elements of the target enzyme, could find broader application for identification of ligands with predetermined sites of binding.
Collapse
Affiliation(s)
- Sasha M Daskalova
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Brian M Eisenhauer
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, VA 22904, United States
| | - Mingxuan Gao
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Xizhi Feng
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, VA 22904, United States
| | - Xun Ji
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Qi Cheng
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - NourEddine Fahmi
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, VA 22904, United States
| | - Omar M Khdour
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Shengxi Chen
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States; Departments of Chemistry and Biology, University of Virginia, Charlottesville, VA 22904, United States
| |
Collapse
|
2
|
Khodyreva S, Lavrik O. Non-canonical interaction of DNA repair proteins with intact and cleaved AP sites. DNA Repair (Amst) 2020; 90:102847. [DOI: 10.1016/j.dnarep.2020.102847] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/06/2020] [Accepted: 03/24/2020] [Indexed: 02/01/2023]
|
3
|
Hoitsma NM, Whitaker AM, Schaich MA, Smith MR, Fairlamb MS, Freudenthal BD. Structure and function relationships in mammalian DNA polymerases. Cell Mol Life Sci 2020; 77:35-59. [PMID: 31722068 PMCID: PMC7050493 DOI: 10.1007/s00018-019-03368-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/11/2019] [Accepted: 10/31/2019] [Indexed: 12/19/2022]
Abstract
DNA polymerases are vital for the synthesis of new DNA strands. Since the discovery of DNA polymerase I in Escherichia coli, a diverse library of mammalian DNA polymerases involved in DNA replication, DNA repair, antibody generation, and cell checkpoint signaling has emerged. While the unique functions of these DNA polymerases are differentiated by their association with accessory factors and/or the presence of distinctive catalytic domains, atomic resolution structures of DNA polymerases in complex with their DNA substrates have revealed mechanistic subtleties that contribute to their specialization. In this review, the structure and function of all 15 mammalian DNA polymerases from families B, Y, X, and A will be reviewed and discussed with special emphasis on the insights gleaned from recently published atomic resolution structures.
Collapse
Affiliation(s)
- Nicole M Hoitsma
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Amy M Whitaker
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Matthew A Schaich
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Mallory R Smith
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Max S Fairlamb
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
| |
Collapse
|
4
|
Abstract
Base excision repair (BER) is one of the most active DNA repair pathways in cells correcting DNA damage from oxidation, deamination, alkylation, and damages induced by free radicals and ionizing radiation. Deregulation or deficiencies in BER mechanisms increase the level of mutations leading to carcinogenesis, and single-strand DNA break formation, which may be converted to double-strand breaks and induce apoptosis. BER deficiency is associated with development of diseases causing neurodegenerative disorders, such as Alzheimer's disease (AD) and amyotrophic lateral sclerosis (ALS). In addition, BER mechanisms can be affected by viral infections, such as HPV, HTLV-1, and HIV-1. Deficiencies in DNA repair in cells can be analyzed using a very convenient and effective approach, where mammalian cells are transfected with plasmids carrying a reporter gene of fluorescent protein that contain inactivating damages. The repair of DNA damages depends on the cellular machinery and is reflected by expression of the reporter gene measured by flow cytometry. In this chapter, we describe this plasmid-based reporter gene system to investigate in cell the repairs of DNA damages involving BER mechanisms.
Collapse
Affiliation(s)
- Dorota Piekna-Przybylska
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA.
| |
Collapse
|
5
|
Ahmed AA, Smoczer C, Pace B, Patterson D, Cress Cabelof D. Loss of DNA polymerase β induces cellular senescence. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2018; 59:603-612. [PMID: 29968395 PMCID: PMC6203593 DOI: 10.1002/em.22206] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 04/28/2018] [Accepted: 04/30/2018] [Indexed: 06/01/2023]
Abstract
We aim to establish that accelerated aging and premature cellular senescence seen in individuals with Down syndrome is related to reduced DNA polymeraseβ. We report here that primary fibroblasts from Down syndrome individuals exhibit greater SA-β-gal staining (fourfold increase, P < 0.001), increased p16 transcript abundance (threefold increase, P < 0.01), and reduced HMGB1 nuclear localization (1.5-fold lower, P < 0.01). We also find that DNA polymerase β expression is significantly reduced in Down syndrome primary fibroblasts (53% decline, P < 0.01). To evaluate whether DNA polymerase β might be causative in senescence induction, we evaluated the impact of murine DNA polymerase β nullizygosity on senescence. We find that unexposed DNA polymerase β -null primary fibroblasts exhibit a robust increase in the number of senescent cells compared to wild-type (11-fold, P < 0.001), demonstrating that loss DNA polymerase β is sufficient to induce senescence. We also see an additional increase in response to hydroxyurea (threefold greater than WT-HU, P < 0.05). These data demonstrate that loss of DNA polymerase β is sufficient to induce senescence. Additionally, we report a significant induction in spontaneous DNA double strand breaks in DNA polymerase β null MEFs (fivefold increase from wild-type, P < 0.0001). Our findings strongly suggest that DNA polymerase β is causative in senescence induction, reasonably pointing to DNA polymerase β as a likely factor driving the premature senescence in Down syndrome. Environ. Mol. Mutagen. 59:603-612, 2018. © 2018 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Aqila A. Ahmed
- Department of Nutrition and Food Science, Wayne State University, Detroit, MI, United States
| | - Cristine Smoczer
- Department of Nutrition and Food Science, Wayne State University, Detroit, MI, United States
| | - Brianna Pace
- Department of Nutrition and Food Science, Wayne State University, Detroit, MI, United States
| | - David Patterson
- Eleanor Roosevelt Institute, University of Denver, Denver, Colorado, United States
- Knoebel Institute for Healthy Aging and Department of Biological Sciences, University of Denver, Denver, Colorado, United States
| | - Diane Cress Cabelof
- Department of Nutrition and Food Science, Wayne State University, Detroit, MI, United States
| |
Collapse
|
6
|
Variable termination sites of DNA polymerases encountering a DNA-protein cross-link. PLoS One 2018; 13:e0198480. [PMID: 29856874 PMCID: PMC5983568 DOI: 10.1371/journal.pone.0198480] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/18/2018] [Indexed: 11/19/2022] Open
Abstract
DNA-protein cross-links (DPCs) are important DNA lesions induced by endogenous crosslinking agents such as formaldehyde or acetaldehyde, as well as ionizing radiation, cancer chemotherapeutic drugs, and abortive action of some enzymes. Due to their very bulky nature, they are expected to interfere with DNA and RNA synthesis and DNA repair. DPCs are highly genotoxic and the ability of cells to deal with them is relevant for many chemotherapeutic interventions. However, interactions of DNA polymerases with DPCs have been poorly studied due to the lack of a convenient experimental model. We have used NaBH4-induced trapping of E. coli formamidopyrimidine-DNA glycosylase with DNA to construct model DNA polymerase substrates containing a DPC in single-stranded template, or in the template strand of double-stranded DNA, or in the non-template (displaced) strand of double-stranded DNA. Nine DNA polymerases belonging to families A, B, X, and Y were studied with respect to their behavior upon encountering a DPC: Klenow fragment of E. coli DNA polymerase I, Thermus aquaticus DNA polymerase I, Pyrococcus furiosus DNA polymerase, Sulfolobus solfataricus DNA polymerase IV, human DNA polymerases β, κ and λ, and DNA polymerases from bacteriophages T4 and RB69. Although none were able to fully bypass DPCs in any context, Family B DNA polymerases (T4, RB69) and Family Y DNA polymerase IV were able to elongate the primer up to the site of the cross-link if a DPC was located in single-stranded template or in the displaced strand. In other cases, DNA synthesis stopped 4-5 nucleotides before the site of the cross-link in single-stranded template or in double-stranded DNA if the polymerases could displace the downstream strand. We suggest that termination of DNA polymerases on a DPC is mostly due to the unrelieved conformational strain experienced by the enzyme when pressing against the cross-linked protein molecule.
Collapse
|
7
|
Klvaňa M, Bren U, Florián J. Uniform Free-Energy Profiles of the P-O Bond Formation and Cleavage Reactions Catalyzed by DNA Polymerases β and λ. J Phys Chem B 2016; 120:13017-13030. [PMID: 27992186 PMCID: PMC5217713 DOI: 10.1021/acs.jpcb.6b08581] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
Human
X-family DNA polymerases β (Polβ) and λ
(Polλ) catalyze the nucleotidyl-transfer reaction in the base
excision repair pathway of the cellular DNA damage response. Using
empirical valence bond and free-energy perturbation simulations, we
explore the feasibility of various mechanisms for the deprotonation
of the 3′-OH group of the primer DNA strand, and the subsequent
formation and cleavage of P–O bonds in four Polβ, two
truncated Polλ (tPolλ), and two tPolλ Loop1 mutant
(tPolλΔL1) systems differing in the initial X-ray crystal
structure and nascent base pair. The average calculated activation
free energies of 14, 18, and 22 kcal mol–1 for Polβ,
tPolλ, and tPolλΔL1, respectively, reproduce the
trend in the observed catalytic rate constants. The most feasible
reaction pathway consists of two successive steps: specific base (SB)
proton transfer followed by rate-limiting concerted formation and
cleavage of the P–O bonds. We identify linear free-energy relationships
(LFERs) which show that the differences in the overall activation
and reaction free energies among the eight studied systems are determined
by the reaction free energy of the SB proton transfer. We discuss
the implications of the LFERs and suggest pKa of the 3′-OH group as a predictor of the catalytic
rate of X-family DNA polymerases.
Collapse
Affiliation(s)
- Martin Klvaňa
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Technology, University of Maribor , Smetanova ulica 17, 2000 Maribor, Slovenia.,Department of Chemistry and Biochemistry, Loyola University Chicago , 1032 W. Sheridan Road, Chicago, Illinois 60660, United States
| | - Urban Bren
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Technology, University of Maribor , Smetanova ulica 17, 2000 Maribor, Slovenia.,Laboratory for Molecular Modeling, National Institute of Chemistry , Hajdrihova ulica 19, 1001 Ljubljana, Slovenia
| | - Jan Florián
- Department of Chemistry and Biochemistry, Loyola University Chicago , 1032 W. Sheridan Road, Chicago, Illinois 60660, United States
| |
Collapse
|
8
|
Dietary Calorie Restriction from Adulthood Through Old Age in Rats: Improved DNA Polymerase β and DNA Gap Repair Activity in Cortical Neurons. Neurochem Res 2016; 41:270-7. [PMID: 26801173 DOI: 10.1007/s11064-015-1787-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 11/21/2015] [Accepted: 11/24/2015] [Indexed: 10/22/2022]
Abstract
It is well established now that dietary calorie restriction (CR) leads to extension of life span in many species, although the exact mechanism of this effect is still eluding. In the present study, we examined the effect of 40 % CR imposed during a prolonged period of life span (from 6 to 30 months) of rats on the activity of DNA polymerase β (pol β) in view of its role in short gap base excision DNA repair and template driven primer extension. DNA pol β activity is very low at this late age. However, cortical neuronal extracts prepared from CR rats of 30 months age showed significantly higher pol β protein levels and activity when compared to control 30 month old rats. Yet, one-nucleotide gap repair in old control neurons and an improved efficiency in CR neurons could be visualized only after supplementation of the extracts with T4 DNA ligase indicating the lack of CR affect on ligase activity. No impressive primer extension activity is seen either in the CR or old control neurons. These results are taken to convey that extended CR through adult life leads to improved pol β activity and therefore, pol β dependent DNA gap repair activity.
Collapse
|
9
|
Bauer NC, Corbett AH, Doetsch PW. The current state of eukaryotic DNA base damage and repair. Nucleic Acids Res 2015; 43:10083-101. [PMID: 26519467 PMCID: PMC4666366 DOI: 10.1093/nar/gkv1136] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/16/2015] [Indexed: 12/15/2022] Open
Abstract
DNA damage is a natural hazard of life. The most common DNA lesions are base, sugar, and single-strand break damage resulting from oxidation, alkylation, deamination, and spontaneous hydrolysis. If left unrepaired, such lesions can become fixed in the genome as permanent mutations. Thus, evolution has led to the creation of several highly conserved, partially redundant pathways to repair or mitigate the effects of DNA base damage. The biochemical mechanisms of these pathways have been well characterized and the impact of this work was recently highlighted by the selection of Tomas Lindahl, Aziz Sancar and Paul Modrich as the recipients of the 2015 Nobel Prize in Chemistry for their seminal work in defining DNA repair pathways. However, how these repair pathways are regulated and interconnected is still being elucidated. This review focuses on the classical base excision repair and strand incision pathways in eukaryotes, considering both Saccharomyces cerevisiae and humans, and extends to some important questions and challenges facing the field of DNA base damage repair.
Collapse
Affiliation(s)
- Nicholas C Bauer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Paul W Doetsch
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| |
Collapse
|
10
|
DNA polymerases β and λ and their roles in cell. DNA Repair (Amst) 2015; 29:112-26. [DOI: 10.1016/j.dnarep.2015.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 01/29/2015] [Accepted: 02/02/2015] [Indexed: 10/24/2022]
|
11
|
Gridley CL, Rangarajan S, Firbank S, Dalal S, Sweasy JB, Jaeger J. Structural changes in the hydrophobic hinge region adversely affect the activity and fidelity of the I260Q mutator DNA polymerase β. Biochemistry 2013; 52:4422-32. [PMID: 23651085 DOI: 10.1021/bi301368f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The I260Q variant of DNA polymerase β is an efficient mutator polymerase with fairly indiscriminate misincorporation activities opposite all template bases. Previous modeling studies have suggested that I260Q harbors structural variations in its hinge region. Here, we present the crystal structures of wild type and I260Q rat polymerase β in the presence and absence of substrates. Both the I260Q apoenzyme structure and the closed ternary complex with double-stranded DNA and ddTTP show ordered water molecules in the hydrophobic hinge near Gln260, whereas this is not the case in the wild type polymerase. Compared to wild type polymerase β ternary complexes, there are subtle movements around residues 260, 272, 295, and 296 in the mutant. The rearrangements in this region, coupled with side chain movements in the immediate neighborhood of the dNTP-binding pocket, namely, residues 258 and 272, provide an explanation for the altered activity and fidelity profiles observed in the I260Q mutator polymerase.
Collapse
Affiliation(s)
- Chelsea L Gridley
- Division of Genetics, Wadsworth Center, New York State Department of Health, New Scotland Avenue, Albany, New York 12208, United States
| | | | | | | | | | | |
Collapse
|
12
|
Jonson I, Ougland R, Larsen E. DNA repair mechanisms in Huntington's disease. Mol Neurobiol 2013; 47:1093-102. [PMID: 23361256 DOI: 10.1007/s12035-013-8409-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 01/13/2013] [Indexed: 11/25/2022]
Abstract
The human genome is under continuous attack by a plethora of harmful agents. Without the development of several dedicated DNA repair pathways, the genome would have been destroyed and cell death, inevitable. However, while DNA repair enzymes generally maintain the integrity of the whole genome by properly repairing mutagenic and cytotoxic intermediates, there are cases in which the DNA repair machinery is implicated in causing disease rather than protecting against it. One case is the instability of gene-specific trinucleotides, the causative mutations of numerous disorders including Huntington's disease. The DNA repair proteins induce mutations that are different from the genome-wide mutations that arise in the absence of repair enzymes; they occur at definite loci, they occur in specific tissues during development, and they are age-dependent. These latter characteristics make pluripotent stem cells a suitable model system for triplet repeat expansion disorders. Pluripotent stem cells can be kept in culture for a prolonged period of time and can easily be differentiated into any tissue, e.g., cells along the neural lineage. Here, we review the role of DNA repair proteins in the process of triplet repeat instability in Huntington's disease and also the potential use of pluripotent stem cells to investigate neurodegenerative disorders.
Collapse
Affiliation(s)
- Ida Jonson
- Department of Microbiology, University of Oslo, Oslo University Hospital, Rikshospitalet, P. O. Box 4950 Nydalen, 0424 Oslo, Norway
| | | | | |
Collapse
|
13
|
Ramsden DA, Asagoshi K. DNA polymerases in nonhomologous end joining: are there any benefits to standing out from the crowd? ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2012; 53:741-751. [PMID: 22987211 DOI: 10.1002/em.21725] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 07/17/2012] [Accepted: 07/17/2012] [Indexed: 06/01/2023]
Abstract
Chromosome breaks, often with damaged or missing DNA flanking the break site, are an important threat to genome stability. They are repaired in vertebrates primarily by nonhomologous end joining (NHEJ). NHEJ is unique among the major DNA repair pathways in that a continuous template cannot be used by DNA polymerases to instruct replacement of damaged or lost DNA. Nevertheless, at least 3 out of the 17 mammalian DNA polymerases are specifically employed by NHEJ. Biochemical and structural studies are further revealing how each of the polymerases employed by NHEJ possesses distinct and sophisticated means to overcome the barriers this pathway presents to polymerase activity. Still unclear, though, is how the resulting network of overlapping and nonoverlapping polymerase activities contributes to repair in cells.
Collapse
Affiliation(s)
- Dale A Ramsden
- Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA.
| | | |
Collapse
|
14
|
Age-dependent decline of DNA base excision repair activity in rat cortical neurons. Mech Ageing Dev 2012; 133:186-94. [DOI: 10.1016/j.mad.2012.01.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Revised: 01/01/2012] [Accepted: 01/02/2012] [Indexed: 10/14/2022]
|
15
|
Kumar P, Bharti SK, Varshney U. Uracil excision repair in Mycobacterium tuberculosis cell-free extracts. Tuberculosis (Edinb) 2011; 91:212-8. [PMID: 21371942 DOI: 10.1016/j.tube.2011.02.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 01/27/2011] [Accepted: 02/01/2011] [Indexed: 11/28/2022]
Abstract
Uracil excision repair is ubiquitous in all domains of life and initiated by uracil DNA glycosylases (UDGs) which excise the promutagenic base, uracil, from DNA to leave behind an abasic site (AP-site). Repair of the resulting AP-sites requires an AP-endonuclease, a DNA polymerase, and a DNA ligase whose combined activities result in either short-patch or long-patch repair. Mycobacterium tuberculosis, the causative agent of tuberculosis, has an increased risk of accumulating uracils because of its G + C-rich genome, and its niche inside host macrophages where it is exposed to reactive nitrogen and oxygen species, two major causes of cytosine deamination (to uracil) in DNA. In vitro assays to study DNA repair in this important human pathogen are limited. To study uracil excision repair in mycobacteria, we have established assay conditions using cell-free extracts of M. tuberculosis and M. smegmatis (a fast-growing mycobacterium) and oligomer or plasmid DNA substrates. We show that in mycobacteria, uracil excision repair is completed primarily via long-patch repair. In addition, we show that M. tuberculosis UdgB, a newly characterized family 5 UDG, substitutes for the highly conserved family 1 UDG, Ung, thereby suggesting that UdgB might function as backup enzyme for uracil excision repair in mycobacteria.
Collapse
Affiliation(s)
- Pradeep Kumar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | | | | |
Collapse
|
16
|
Belousova EA, Lavrik OI. DNA polymerases β and λ and their roles in DNA replication and repair. Mol Biol 2010. [DOI: 10.1134/s0026893310060014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
17
|
Brown JA, Pack LR, Sanman LE, Suo Z. Efficiency and fidelity of human DNA polymerases λ and β during gap-filling DNA synthesis. DNA Repair (Amst) 2010; 10:24-33. [PMID: 20961817 DOI: 10.1016/j.dnarep.2010.09.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Revised: 09/14/2010] [Accepted: 09/16/2010] [Indexed: 12/31/2022]
Abstract
The base excision repair (BER) pathway coordinates the replacement of 1-10 nucleotides at sites of single-base lesions. This process generates DNA substrates with various gap sizes which can alter the catalytic efficiency and fidelity of a DNA polymerase during gap-filling DNA synthesis. Here, we quantitatively determined the substrate specificity and base substitution fidelity of human DNA polymerase λ (Pol λ), an enzyme proposed to support the known BER DNA polymerase β (Pol β), as it filled 1-10-nucleotide gaps at 1-nucleotide intervals. Pol λ incorporated a correct nucleotide with relatively high efficiency until the gap size exceeded 9 nucleotides. Unlike Pol λ, Pol β did not have an absolute threshold on gap size as the catalytic efficiency for a correct dNTP gradually decreased as the gap size increased from 2 to 10 nucleotides and then recovered for non-gapped DNA. Surprisingly, an increase in gap size resulted in lower polymerase fidelity for Pol λ, and this downregulation of fidelity was controlled by its non-enzymatic N-terminal domains. Overall, Pol λ was up to 160-fold more error-prone than Pol β, thereby suggesting Pol λ would be more mutagenic during long gap-filling DNA synthesis. In addition, dCTP was the preferred misincorporation for Pol λ and its N-terminal domain truncation mutants. This nucleotide preference was shown to be dependent upon the identity of the adjacent 5'-template base. Our results suggested that both Pol λ and Pol β would catalyze nucleotide incorporation with the highest combination of efficiency and accuracy when the DNA substrate contains a single-nucleotide gap. Thus, Pol λ, like Pol β, is better suited to catalyze gap-filling DNA synthesis during short-patch BER in vivo, although, Pol λ may play a role in long-patch BER.
Collapse
Affiliation(s)
- Jessica A Brown
- Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | | | | | | |
Collapse
|
18
|
Morita R, Nakane S, Shimada A, Inoue M, Iino H, Wakamatsu T, Fukui K, Nakagawa N, Masui R, Kuramitsu S. Molecular mechanisms of the whole DNA repair system: a comparison of bacterial and eukaryotic systems. J Nucleic Acids 2010; 2010:179594. [PMID: 20981145 PMCID: PMC2957137 DOI: 10.4061/2010/179594] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 07/27/2010] [Indexed: 11/20/2022] Open
Abstract
DNA is subjected to many endogenous and exogenous damages. All organisms have developed a complex network of DNA repair mechanisms. A variety of different DNA repair pathways have been reported: direct reversal, base excision repair, nucleotide excision repair, mismatch repair, and recombination repair pathways. Recent studies of the fundamental mechanisms for DNA repair processes have revealed a complexity beyond that initially expected, with inter- and intrapathway complementation as well as functional interactions between proteins involved in repair pathways. In this paper we give a broad overview of the whole DNA repair system and focus on the molecular basis of the repair machineries, particularly in Thermus thermophilus HB8.
Collapse
Affiliation(s)
- Rihito Morita
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Zhao SM, Chen XD, Zhang CJ, Zhao GQ, Dong ZM. DNA repair function of DNA polymerase β in human esophageal cancer. Shijie Huaren Xiaohua Zazhi 2010; 18:2460-2463. [DOI: 10.11569/wcjd.v18.i23.2460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To observe the variation in base excision repair (BER) function of mutant DNA polymerase β (polβ).
METHODS: The plasmids pcDNA4-C-polβ1 and pcDNA4-C-polβ2 were transfected into polβ-knockout EC9706 cells by lipotransfection. The stable transfectants were screened in the medium containing G418. The recombinant proteins were purified by nickel column chromatography. DNA substrate that contains a single-base deletion was synthesized to test the BER function of the purified recombinant proteins.
RESULTS: Cell strains stably transfected with pcDNA4-C-pol β1 and pcDNA4-C-pol β2 were successfully obtained. Purified proteins polβ1 and polβ2 were incubated with synthesized DNA substrate that contains a single-base deletion to test their BER function. Wild-type polβ could completely excise the DNA substrate while the mutant polβ could only partly excise the DNA substrate.
CONCLUSION: Wide-type polβ has stronger activity than mutant polβ in repairing DNA substrate that contains a single-base deletion.
Collapse
|
20
|
Theriot CA, Hegde ML, Hazra TK, Mitra S. RPA physically interacts with the human DNA glycosylase NEIL1 to regulate excision of oxidative DNA base damage in primer-template structures. DNA Repair (Amst) 2010; 9:643-52. [PMID: 20338831 DOI: 10.1016/j.dnarep.2010.02.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 02/19/2010] [Accepted: 02/23/2010] [Indexed: 12/11/2022]
Abstract
The human DNA glycosylase NEIL1, activated during the S-phase, has been shown to excise oxidized base lesions in single-strand DNA substrates. Furthermore, our previous work demonstrating functional interaction of NEIL1 with PCNA and flap endonuclease 1 (FEN1) suggested its involvement in replication-associated repair. Here we show interaction of NEIL1 with replication protein A (RPA), the heterotrimeric single-strand DNA binding protein that is essential for replication and other DNA transactions. The NEIL1 immunocomplex isolated from human cells contains RPA, and its abundance in the complex increases after exposure to oxidative stress. NEIL1 directly interacts with the large subunit of RPA (K(d) approximately 20 nM) via the common interacting interface (residues 312-349) in NEIL1's disordered C-terminal region. RPA inhibits the base excision activity of both wild-type NEIL1 (389 residues) and its C-terminal deletion CDelta78 mutant (lacking the interaction domain) for repairing 5-hydroxyuracil (5-OHU) in a primer-template structure mimicking the DNA replication fork. This inhibition is reduced when the damage is located near the primer-template junction. Contrarily, RPA moderately stimulates wild-type NEIL1 but not the CDelta78 mutant when 5-OHU is located within the duplex region. While NEIL1 is inhibited by both RPA and Escherichia coli single-strand DNA binding protein, only inhibition by RPA is relieved by PCNA. These results showing modulation of NEIL1's activity on single-stranded DNA substrate by RPA and PCNA support NEIL1's involvement in repairing the replicating genome.
Collapse
Affiliation(s)
- Corey A Theriot
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA.
| | | | | | | |
Collapse
|
21
|
Masaoka A, Horton JK, Beard WA, Wilson SH. DNA polymerase beta and PARP activities in base excision repair in living cells. DNA Repair (Amst) 2009; 8:1290-9. [PMID: 19748837 DOI: 10.1016/j.dnarep.2009.08.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 07/29/2009] [Accepted: 08/14/2009] [Indexed: 01/08/2023]
Abstract
To examine base excision repair (BER) capacity in the context of living cells, we developed and applied a plasmid-based reporter assay. Non-replicating plasmids containing unique DNA base lesions were designed to express luciferase only after lesion repair had occurred, and luciferase expression in transfected cells was measured continuously during a repair period of 14 h. Two types of DNA lesions were examined: uracil opposite T reflecting repair primarily by the single-nucleotide BER sub-pathway, and the abasic site analogue tetrahydrofuran (THF) opposite C reflecting repair by long-patch BER. We found that the repair capacity for uracil-DNA in wild type mouse fibroblasts was very strong, whereas the repair capacity for THF-DNA, although strong, was slightly weaker. Repair capacity in DNA polymerase beta (Pol beta) null cells for uracil-DNA and THF-DNA was reduced by approximately 15% and 20%, respectively, compared to that in wild type cells. In both cases, the repair deficiency was fully complemented in Pol beta null cells expressing recombinant Pol beta. The effect of inhibition of poly(ADP-ribose) polymerase (PARP) activity on repair capacity was examined by treatment of cells with the inhibitor 4-amino-1,8-naphthalimide (4-AN). PARP inhibition decreased the repair capacity for both lesions in wild type cells, and this reduction was to the same level as that seen in Pol beta null cells. In contrast, 4-AN had no effect on repair in Pol beta null cells. The results highlight that Pol beta and PARP function in the same repair pathway, but also suggest that there is repair independent of both Pol beta and PARP activities. Thus, before the BER capacity of a cell can be predicted or modulated, a better understanding of Pol beta and PARP activity-independent BER pathways is required.
Collapse
Affiliation(s)
- Aya Masaoka
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | | | | | | |
Collapse
|
22
|
Dalal S, Starcevic D, Jaeger J, Sweasy JB. The I260Q variant of DNA polymerase beta extends mispaired primer termini due to its increased affinity for deoxynucleotide triphosphate substrates. Biochemistry 2008; 47:12118-25. [PMID: 18937502 DOI: 10.1021/bi8011548] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA polymerase beta plays a key role in base excision repair. We have previously shown that the hydrophobic hinge region of polymerase beta, which is distant from its active site, plays a critical role in the fidelity of DNA synthesis by this enzyme. The I260Q hinge variant of polymerase beta misincorporates nucleotides with a significantly higher catalytic efficiency than the wild-type enzyme. In the study described here, we show that I260Q extends mispaired primer termini. The kinetic basis for extension of mispairs is defective discrimination by I260Q at the level of ground-state binding of the dNTP substrate. Our results suggest that the hydrophobic hinge region influences the geometry of the dNTP binding pocket exclusively. Because the DNA forms part of the binding pocket, our data are also consistent with the interpretation that the mispaired primer terminus affects the geometry of the dNTP binding pocket such that the I260Q variant has a higher affinity for the incoming dNTP than wild-type polymerase beta.
Collapse
Affiliation(s)
- Shibani Dalal
- Department of Therapeutic Radiology and Genetics, Yale University School of Medicine, New Haven, Connecticut 06250, USA
| | | | | | | |
Collapse
|
23
|
Sharma RA, Dianov GL. Targeting base excision repair to improve cancer therapies. Mol Aspects Med 2007; 28:345-74. [PMID: 17706275 DOI: 10.1016/j.mam.2007.06.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2007] [Revised: 05/30/2007] [Accepted: 06/05/2007] [Indexed: 01/05/2023]
Abstract
Most commonly used cancer therapies, particularly ionizing radiation and certain classes of cytotoxic chemotherapies, cause cell death by damaging DNA. Base excision repair (BER) is the major system responsible for the removal of corrupt DNA bases and repair of DNA single strand breaks generated spontaneously and induced by exogenous DNA damaging factors such as certain cancer therapies. In this review, the physico-chemical properties of the proteins involved in BER are discussed with particular emphasis on molecular mechanisms coordinating repair processes. The aim of this review is to apply extensive knowledge that currently exists regarding the biochemical mechanisms involved in human BER to the molecular biology of current therapies for cancer. It is anticipated that the application of this knowledge will translate into the development of novel effective therapies for improving existing treatments such as radiation therapy and oxaliplatin chemotherapy.
Collapse
Affiliation(s)
- Ricky A Sharma
- Radiation Oncology & Biology, University of Oxford, Churchill Hospital, Oxford OX3 7LJ, UK
| | | |
Collapse
|
24
|
Lin GC, Jaeger J, Sweasy JB. Loop II of DNA polymerase beta is important for polymerization activity and fidelity. Nucleic Acids Res 2007; 35:2924-35. [PMID: 17439962 PMCID: PMC1888816 DOI: 10.1093/nar/gkm126] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The accurate replication and transmission of genetic information is critical in the life of an organism. During its entire lifespan, the genetic information is constantly under attack from endogenous and exogenous sources of damage. To ensure that the content of its genetic information is faithfully preserved for synthesis and transmission, eukaryotic cells have developed a complex system of genomic quality control. Key players in this process are DNA polymerases, the enzymes responsible for synthesizing the DNA, because errors introduced into the genome by polymerase can result in mutations. We use DNA polymerase beta (pol β) as a model system to investigate mechanisms of preserving fidelity during nucleotide incorporation. In the study described here, we characterized the role that loop II of pol β plays in maintaining the activity and fidelity of pol β. We report here that the absence or shortening of loop II compromises the catalytic activity of pol β. Our data also show that loop variants of a specific length have a lower fidelity when compared to the wild-type polymerase. Taken together, our results indicate that loop II is important for the catalytic activity and fidelity of pol β.
Collapse
Affiliation(s)
- George C. Lin
- Department of Therapeutic Radiology and Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA and Center for Medical Sciences, Wadsworth Center, Albany, New York 12201, USA
| | - Joachim Jaeger
- Department of Therapeutic Radiology and Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA and Center for Medical Sciences, Wadsworth Center, Albany, New York 12201, USA
| | - Joann B. Sweasy
- Department of Therapeutic Radiology and Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA and Center for Medical Sciences, Wadsworth Center, Albany, New York 12201, USA
- *To whom correspondence should be addressed. 203-737-2626203-785-6309
| |
Collapse
|
25
|
Sukhanova M, Khodyreva S, Lavrik O. Suppression of base excision repair reactions by apoptotic 24kDa-fragment of poly(ADP-ribose) polymerase 1 in bovine testis nuclear extract. DNA Repair (Amst) 2007; 6:615-25. [PMID: 17236819 DOI: 10.1016/j.dnarep.2006.11.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2006] [Revised: 11/30/2006] [Accepted: 11/30/2006] [Indexed: 11/18/2022]
Abstract
In this study, we examined the interaction of PARP1 and its apoptotic 24kDa-fragment with DNA duplexes mimicking different stages/pathways of base excision repair (BER) using a photocross-linking technique combined to in vitro functional assay. We found that endogenous PARP1 was photocross-linked to the gapped, nicked and flap containing DNA structures and its apoptotic 24kDa-fragment (p24), like PARP1, can interact with the same BER DNA intermediates. Effects of exogenous p24 on the repair of DNA duplexes containing a one nucleotide gap with furan phosphate or phosphate group at the 5'-end of the downstream primer were studied in bovine testis nuclear extract. We showed that the interaction of p24 with DNA, as a whole, inhibited the BER reactions. However, gap filling and nick sealing catalyzed by the enzymes of the extract with DNA substrates characteristic for short patch (SP) BER pathway cannot be completely inhibited by p24. In contrast, binding of p24 to DNA duplex with a 5'-furan or a 5'-flap at the 5'-side of a nick inhibits strand-displacement DNA synthesis and activity of FEN1 in the repair of DNA via long patch (LP) BER pathway. Stimulation of the LP BER reactions induced by the addition of FEN1 or PCNA to the extract is suppressed by p24 thereby indicating that p24 can efficiently compete with these proteins of LP BER. Addition of pol beta to the extract can partially overcome the inhibitory effect of p24 and restore strand-displacement DNA synthesis. Thus, the apoptotic 24kDa-fragment of PARP1 may be considered as more efficient in inhibition of the LP than SP pathway and the effect may depend on the ratio of p24 to the repair enzymes catalyzing precise stages of BER.
Collapse
Affiliation(s)
- Maria Sukhanova
- Institute of Chemical Biology and Fundamental Medicine, Prospect Lavrentieva 8, 630090 Novosibirsk, Russia
| | | | | |
Collapse
|
26
|
Sweasy JB, Lauper JM, Eckert KA. DNA polymerases and human diseases. Radiat Res 2006; 166:693-714. [PMID: 17067213 DOI: 10.1667/rr0706.1] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2006] [Accepted: 07/12/2006] [Indexed: 11/03/2022]
Abstract
DNA polymerases function in DNA replication, repair, recombination and translesion synthesis. Currently, 15 DNA polymerase genes have been identified in human cells, belonging to four distinct families. In this review, we briefly describe the biochemical activities and known cellular roles of each DNA polymerase. Our major focus is on the phenotypic consequences of mutation or ablation of individual DNA polymerase genes. We discuss phenotypes of current mouse models and altered polymerase functions and the relationship of DNA polymerase gene mutations to human cell phenotypes. Interestingly, over 120 single nucleotide polymorphisms (SNPs) have been identified in human populations that are predicted to result in nonsynonymous amino acid substitutions of DNA polymerases. We discuss the putative functional consequences of these SNPs in relation to human disease.
Collapse
Affiliation(s)
- Joann B Sweasy
- Department of Therapeutic Radiology, Yale University School of Medicine, 15 York Street, HRT 313D, P.O. Box 208040, New Haven, CT 06520-8040, USA.
| | | | | |
Collapse
|
27
|
Grin IR, Khodyreva SN, Nevinsky GA, Zharkov DO. Deoxyribophosphate lyase activity of mammalian endonuclease VIII-like proteins. FEBS Lett 2006; 580:4916-22. [PMID: 16920106 DOI: 10.1016/j.febslet.2006.08.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2006] [Revised: 08/04/2006] [Accepted: 08/07/2006] [Indexed: 11/28/2022]
Abstract
Base excision repair (BER) protects cells from nucleobase DNA damage. In eukaryotic BER, DNA glycosylases generate abasic sites, which are then converted to deoxyribo-5'-phosphate (dRP) and excised by a dRP lyase (dRPase) activity of DNA polymerase beta (Polbeta). Here, we demonstrate that NEIL1 and NEIL2, mammalian homologs of bacterial endonuclease VIII, excise dRP by beta-elimination with the efficiency similar to Polbeta. DNA duplexes imitating BER intermediates after insertion of a single nucleotide were better substrates. NEIL1 and NEIL2 supplied dRPase activity in BER reconstituted with dRPase-null Polbeta. Our results suggest a role for NEILs as backup dRPases in mammalian cells.
Collapse
Affiliation(s)
- Inga R Grin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | | | | | | |
Collapse
|
28
|
El-Andaloussi N, Valovka T, Toueille M, Steinacher R, Focke F, Gehrig P, Covic M, Hassa PO, Schär P, Hübscher U, Hottiger MO. Arginine methylation regulates DNA polymerase beta. Mol Cell 2006; 22:51-62. [PMID: 16600869 DOI: 10.1016/j.molcel.2006.02.013] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2005] [Revised: 12/07/2005] [Accepted: 02/10/2006] [Indexed: 11/24/2022]
Abstract
Alterations in DNA repair lead to genomic instability and higher risk of cancer. DNA base excision repair (BER) corrects damaged bases, apurinic sites, and single-strand DNA breaks. Here, a regulatory mechanism for DNA polymerase beta (Pol beta) is described. Pol beta was found to form a complex with the protein arginine methyltransferase 6 (PRMT6) and was specifically methylated in vitro and in vivo. Methylation of Pol beta by PRMT6 strongly stimulated DNA polymerase activity by enhancing DNA binding and processivity, while single nucleotide insertion and dRP-lyase activity were not affected. Two residues, R83 and R152, were identified in Pol beta as the sites of methylation by PRMT6. Genetic complementation of Pol beta knockout cells with R83/152K mutant revealed the importance of these residues for the cellular resistance to DNA alkylating agent. Based on our findings, we propose that PRMT6 plays a role as a regulator of BER.
Collapse
Affiliation(s)
- Nazim El-Andaloussi
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
|
30
|
Alonso A, Terrados G, Picher AJ, Giraldo R, Blanco L, Larraga V. An intrinsic 5′-deoxyribose-5-phosphate lyase activity in DNA polymerase beta from Leishmania infantum supports a role in DNA repair. DNA Repair (Amst) 2006; 5:89-101. [PMID: 16174567 DOI: 10.1016/j.dnarep.2005.08.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2005] [Revised: 08/08/2005] [Accepted: 08/08/2005] [Indexed: 11/20/2022]
Abstract
Leishmania infantum is a parasitic protozoan which infects humans. This paper reports the expression in Escherichia coli and purification of the L. infantum gene product (AF182167), as well as its characterization as a DNA polymerase beta (Polbeta)-like, template-dependent DNA repair enzyme, with a metal preference for Mn2+ over Mg2+. As is the case with mammalian Polbeta and DNA polymerase lambda (Pollambda), L. infantum DNA polymerase beta (Li Polbeta) prefers gapped-DNA substrates having a 5'-phosphate end, in agreement with its role in DNA repair reactions. Purified Li Polbeta also displayed a 5'-deoxyribose-5-phosphate (dRP) lyase activity, consistent with a beta-elimination mechanism. The concerted action of dRP lyase and DNA polymerization activities of Li Polbeta on a uracil-containing DNA suggests its participation in "single-nucleotide" base excision repair (BER). Analysis of Li Polbeta DNA polymerization activity at different stages of the L. infantum infective cycle supports a role for Li Polbeta in nuclear DNA repair after the oxidative damage occurring inside the macrophage.
Collapse
Affiliation(s)
- Ana Alonso
- Centro de Investigaciones Biológicas, CSIC, c/Ramiro de Maeztu 9, 28040 Madrid, Spain
| | | | | | | | | | | |
Collapse
|
31
|
Parsons JL, Dianova II, Boswell E, Weinfeld M, Dianov GL. End-damage-specific proteins facilitate recruitment or stability of X-ray cross-complementing protein 1 at the sites of DNA single-strand break repair. FEBS J 2005; 272:5753-63. [PMID: 16279940 DOI: 10.1111/j.1742-4658.2005.04962.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ionizing radiation, oxidative stress and endogenous DNA-damage processing can result in a variety of single-strand breaks with modified 5' and/or 3' ends. These are thought to be one of the most persistent forms of DNA damage and may threaten cell survival. This study addresses the mechanism involved in recognition and processing of DNA strand breaks containing modified 3' ends. Using a DNA-protein cross-linking assay, we followed the proteins involved in the repair of oligonucleotide duplexes containing strand breaks with a phosphate or phosphoglycolate group at the 3' end. We found that, in human whole cell extracts, end-damage-specific proteins (apurinic/apyrimidinic endonuclease 1 and polynucleotide kinase in the case of 3' ends containing phosphoglycolate and phosphate, respectively) which recognize and process 3'-end-modified DNA strand breaks are required for efficient recruitment of X-ray cross-complementing protein 1-DNA ligase IIIalpha heterodimer to the sites of DNA repair.
Collapse
|
32
|
Shen X, Woodgate R, Goodman MF. Lyase activities intrinsic to Escherichia coli polymerases IV and V. DNA Repair (Amst) 2005; 4:1368-73. [PMID: 16202661 DOI: 10.1016/j.dnarep.2005.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Escherichia coli DNA polymerase IV and V (pol IV and pol V) are error-prone DNA polymerases that are induced as part of the SOS regulon in response to DNA damage. Both are members of the Y-family of DNA polymerases. Their principal biological roles appear to involve translesion synthesis (TLS) and the generation of mutational diversity to cope with stress. Although neither enzyme is known to be involved in base excision repair (BER), we have nevertheless observed apurinic/apyrimidinic 5'-deoxyribose phosphate (AP/5'-dRP) lyase activities intrinsic to each polymerase. Pols IV and V catalyze cleavage of the phosphodiester backbone at the 3'-side of an apurinic/apyrimidinic (AP) site as well as the removal of a 5'-deoxyribose phosphate (dRP) at a preincised AP site. The specific activities of the two error-prone polymerase-associated lyases are approximately 80-fold less than the associated lyase activity of human DNA polymerase beta, which is a key enzyme used in short patch BER. Pol IV forms a covalent Schiff's base intermediate with substrate DNA that is trapped by sodium borohydride, as proscribed by a beta-elimination mechanism. In contrast, a NaBH(4) trapped intermediate is not observed for pol V, even though the lyase specific activity of pol V is slightly higher than that of pol IV. Incubation of pol V (UmuD'(2)C) with a molar excess of UmuD drives an exchange of subunits to form UmuD'D+insoluble UmuC causing inactivation of polymerase and lyase activities. The concomitant loss of both activities is strong evidence that pol V contains a bona fide lyase activity.
Collapse
Affiliation(s)
- Xuan Shen
- Department of Biological Sciences and Chemistry, Hedco Molecular Biology Laboratories, University of Southern California, University Park, Los Angeles, 90089-1340, USA
| | | | | |
Collapse
|
33
|
Rosales AL, Cunningham JM, Bone AJ, Green IC, Green MHL. Repair of cytokine-induced DNA damage in cultured rat islets of Langerhans. Free Radic Res 2005; 38:665-74. [PMID: 15453631 DOI: 10.1080/10715760410001697609] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Treatment of cultured rat pancreatic islets of Langerhans with the combined cytokines interleukin-1beta (IL-1beta), interferon gamma (IFN gamma) and tumour necrosis factor alpha (TNF alpha) leads to DNA damage including strand breakage. We have investigated the nature of this damage and its repairability. When islets are further incubated for 4 h in fresh medium, the level of cytokine-induced strand breakage remains constant. If the nitric oxide synthase inhibitor N(G)-monomethyl-L-arginine (NMMA) is present during cytokine treatment, then strand breakage is prevented. If NMMA is added following, rather than during,the cytokine treatment and islets are incubated for 4 h, further nitric oxide synthesis is prevented and most cytokine-induced strand breaks are no longer seen. To investigate DNA repair following cytokine treatment, cells were transferred to fresh medium and incubated for 4 h in the presence of hydroxyurea (HU) and 1-beta-D-arabinosyl cytosine (AraC), as inhibitors of strand rejoining. In the presence of these inhibitors there was an accumulation of strand breaks that would otherwise have been repaired. However, when further nitric oxide synthesis was inhibited by NMMA, significantly less additional strand breakage was seen in the presence of HU and AraC. We interpret this, as indicating that excision repair of previously induced base damage did not contribute significantly to strand breakage. Levels of oxidised purines, as indicated by formamidopyrimidine glycosylase (Fpg) sensitive sites, were not increased in cytokine-treated islets. We conclude that in these primary insulin-secreting cells: (a) the DNA damage induced by an 18h cytokine treatment is prevented by an inhibitor of nitric oxide synthase, (b) much of the damage is in the form of apparent strand breaks rather than altered bases such as oxidised purines, (c) substantial repair is ongoing during the cytokine treatment and this repair is not inhibited in the presence of nitric oxide.
Collapse
Affiliation(s)
- Alma L Rosales
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Cockcroft Building, Lewes Road, Brighton BN2 4GJ, UK
| | | | | | | | | |
Collapse
|
34
|
Feng X, Gao Z, Li S, Jones SH, Hecht SM. DNA polymerase beta lyase inhibitors from Maytenus putterlickoides. JOURNAL OF NATURAL PRODUCTS 2004; 67:1744-1747. [PMID: 15497954 DOI: 10.1021/np040057p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
During a survey of plant secondary metabolites for DNA polymerase beta lyase inhibitors, we found that a crude methyl ethyl ketone extract prepared from Maytenus putterlickoides showed strong inhibition of the lyase activity of DNA polymerase beta in an in vitro assay. Bioassay-guided fractionation of the extract, using an in vitro assay, resulted in the discovery of a new active principle, 30-(4'-hydroxybenzoyloxy)-11alpha-hydroxylupane-20(29)-en-3-one (1), as well as a known compound, (-)-epicatechin (2). Compounds 1 and 2 exhibited DNA polymerase beta lyase inhibitory activity with IC50 values of 62.8 and 18.5 microM, respectively. Compound 2 was capable of potentiating the action of the monofunctional methylating agent methyl methanesulfonate in cultured human cancer cells, consistent with the possible utility of inhibitors of this type in vivo.
Collapse
Affiliation(s)
- Xizhi Feng
- Department of Chemistry, University of Virginia, Charlottesville 22901, USA
| | | | | | | | | |
Collapse
|
35
|
Li SS, Gao Z, Feng X, Hecht SM. Biscoumarin derivatives from Edgeworthia gardneri that inhibit the lyase activity of DNA polymerase beta. JOURNAL OF NATURAL PRODUCTS 2004; 67:1608-1610. [PMID: 15387673 DOI: 10.1021/np040127s] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Bioassay-guided fractionation of an active methyl ethyl ketone extract of Edgeworthia gardneri, using an assay to monitor DNA polymerase beta lyase inhibition, resulted in the isolation of three known biscoumarin derivatives, 7-hydroxy-3,7'-dicoumaryl ether (edgeworin, 1), 7-hydroxy-6-methoxy-3,7'-dicoumaryl ether (daphnoretin, 2), and 6,7-dihydroxy-3,7'-dicoumaryl ether (edgeworthin, 3). Compounds 1-3 inhibited the lyase activity of DNA polymerase beta with IC(50) values of 7.3 microg/mL (22.5 microM), 43.0 microg/mL (122.3 microM), and 32.1 microg/mL (94.8 microM), respectively.
Collapse
Affiliation(s)
- Shi-Sheng Li
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, USA
| | | | | | | |
Collapse
|
36
|
Sarkar SN, Bakshi S, Mokkapati SK, Roy S, Sengupta DN. Dideoxynucleoside triphosphate-sensitive DNA polymerase from rice is involved in base excision repair and immunologically similar to mammalian DNA pol beta. Biochem Biophys Res Commun 2004; 320:145-55. [PMID: 15207714 DOI: 10.1016/j.bbrc.2004.05.152] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2004] [Indexed: 11/24/2022]
Abstract
A single polypeptide with ddNTP-sensitive DNA polymerase activity was purified to near homogeneity from the shoot tips of rice seedlings and analysis of the preparations by SDS-PAGE followed by silver staining showed a polypeptide of 67 kDa size. The DNA polymerase activity was found to be inhibitory by ddNTP in both in vitro DNA polymerase activity assay and activity gel analysis. Aphidicolin, an inhibitor of other types of DNA polymerases, had no effect on plant enzyme. The 67 kDa rice DNA polymerase was found to be recognized by the polyclonal antibody (purified IgG) made against rat DNA polymerase beta (pol beta) both in solution and also on Western blot. The recognition was found to be very specific as the activity of Klenow enzyme was unaffected by the antibody. The ability of rice nuclear extract to correct G:U mismatch of oligo-duplex was observed when oligo-duplex with 32P-labeled lower strand containing U (at 22nd position) was used as substrate. Differential appearance of bands at 21-mer, 22-mer, and 51-mer position in presence of dCTP was visible only with G:U mismatch oligo-duplex, but not with G:C oligo-duplex. While ddCTP or polyclonal antibody against rat-DNA pol beta inhibits base excision repair (BER), aphidicolin had no effect. These results for the first time clearly demonstrate the ability of rice nuclear extract to run BER and the involvement of ddNTP-sensitive pol beta type DNA polymerase. Immunological similarity of the ddNTP-sensitive DNA polymerase beta of rice and rat and its involvement in BER revealed the conservation of structure and function of ddNTP-sensitive DNA pol beta in plant and animal.
Collapse
Affiliation(s)
- Sailendra Nath Sarkar
- Department of Botany, Bose Institute, 93/1, Acharya Prafulla Chandra Road, Kolkata-700 009, India
| | | | | | | | | |
Collapse
|
37
|
Oehlers LP, Heater SJ, Rains JD, Wells MC, David WM, Walter RB. Gene structure, purification and characterization of DNA polymerase beta from Xiphophorus maculatus. Comp Biochem Physiol C Toxicol Pharmacol 2004; 138:311-24. [PMID: 15533789 DOI: 10.1016/j.cca.2004.06.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2004] [Revised: 06/23/2004] [Accepted: 06/30/2004] [Indexed: 11/28/2022]
Abstract
Cloning of the Xiphophorus maculatus Polbeta gene and overexpression of the recombinant Polbeta protein has been performed. The organization of the XiphPolbeta introns and exons, including intron-exon boundaries, have been assigned and were found to be similar to that for human Polbeta with identical exon sizes except for exon XII coding for an additional two amino acid residues in Xiphophorus. The cDNA sequence encoding the 337-amino acid X. maculatus DNA polymerase beta (Polbeta) protein was subcloned into the Escherichia coli expression plasmid pET. Induction of transformed E. coli cells resulted in the high-level expression of soluble recombinant Polbeta, which catalyzed DNA synthesis on template-primer substrates. The steady-state Michaelis constants (Km) and catalytic efficiencies (kcat/Km) of the recombinant XiphPolbeta for nucleotide insertion opposite single-nucleotide gap DNA substrates were measured and compared with previously published values for recombinant human Polbeta. Steady-state in vitro Km and kcat/Km values for correct nucleotide insertion by XiphPolbeta and human Polbeta were similar, although the recombinant Xiphophorus protein exhibited 2.5-7-fold higher catalytic efficiencies for dGTP and dCTP insertion versus human Polbeta. In contrast, the recombinant XiphPolbeta displayed significantly lower fidelities than human Polbeta for dNTP insertion opposite a single-nucleotide gap at 37 degrees C.
Collapse
Affiliation(s)
- Leon P Oehlers
- Molecular Biosciences Research Group, Department of Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | | | | | | | | | | |
Collapse
|
38
|
Lang T, Maitra M, Starcevic D, Li SX, Sweasy JB. A DNA polymerase beta mutant from colon cancer cells induces mutations. Proc Natl Acad Sci U S A 2004; 101:6074-9. [PMID: 15075389 PMCID: PMC395925 DOI: 10.1073/pnas.0308571101] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Previous investigations have shown that approximately 35% of the 90 tumors analyzed to date contain mutations within the DNA polymerasebeta (pol beta) gene. The existence of pol beta mutations in a substantial fraction of human tumors studied suggests a link between DNA pol beta and cancer. A DNA pol beta variant, in which Lys-289 has been altered to Met, was identified previously in a colorectal carcinoma. The K289M protein was expressed in mouse L cells containing the lambda cII mutational target. The lambda DNA was packaged and used to infect bacterial cells to obtain the spontaneous mutation frequency. We found that expression of K289M in the mouse cells resulted in a 2.5-fold increase in the mutation frequency. What was most interesting was that expression of K289M in these cells resulted in a 16-fold increase in the frequency of C to G or G to C base substitutions at a specific site within the cII target. By using this cII target sequence, kinetic analysis of the purified K289M protein revealed that it was able to misincorporate dCTP opposite template C and dGTP opposite template G with significantly higher efficiency than the wild-type pol beta protein. We provide evidence that misincorporation of nucleotides by K289M results from altered positioning of the DNA within the active site of the enzyme. Our data are consistent with the interpretation that misincorporation of nucleotides resulting from altered DNA positioning by the K289M protein has the potential to result in tumorigenesis or neoplastic progression.
Collapse
Affiliation(s)
- Tieming Lang
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | | | | | | | | |
Collapse
|
39
|
Sweasy JB. Fidelity mechanisms of DNA polymerase beta. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2004; 73:137-69. [PMID: 12882517 DOI: 10.1016/s0079-6603(03)01005-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
DNA polymerase 3 (Pol beta) is one of the best characterized eukaryotic DNA polymerases. Pol beta is a member of the X family of DNA polymerases. The Pol beta protein has two catalytic activities: DNA polymerase activity and dRP lyase activity. Pol beta has no known proofreading activity, so its accuracy in vitro results exclusively from the nucleotide selectivity of this enzyme. Presteady-state kinetic analysis has shown that Pol beta functions in nucleotide selectivity predominantly during phosphodiester bond formation, although this enzyme also possesses some ability to discriminate the correct from the incorrect deoxynucleoside triphosphate (dNTP) substrate during ground state binding. Recent results strongly suggest that Pol beta does not employ an induced fit mechanism of nucleotide discrimination. The fidelity of Pol beta appears to be determined through steric exclusion against the incorrect substrate and by the precise positioning of the catalytic residues, DNA, and substrate within the active site of the enzyme. Imprecise positioning of active site residues or DNA can result in the incorporation of the incorrect substrate into DNA. Amino acid residues both distant and near to the active site of Pol beta influence its geometry, suggesting that the movements and positioning of subdomains of Pol beta have a significant impact upon its fidelity.
Collapse
Affiliation(s)
- Joann B Sweasy
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| |
Collapse
|
40
|
Abstract
The human genome, comprising three billion base pairs coding for 30000-40000 genes, is constantly attacked by endogenous reactive metabolites, therapeutic drugs and a plethora of environmental mutagens that impact its integrity. Thus it is obvious that the stability of the genome must be under continuous surveillance. This is accomplished by DNA repair mechanisms, which have evolved to remove or to tolerate pre-cytotoxic, pre-mutagenic and pre-clastogenic DNA lesions in an error-free, or in some cases, error-prone way. Defects in DNA repair give rise to hypersensitivity to DNA-damaging agents, accumulation of mutations in the genome and finally to the development of cancer and various metabolic disorders. The importance of DNA repair is illustrated by DNA repair deficiency and genomic instability syndromes, which are characterised by increased cancer incidence and multiple metabolic alterations. Up to 130 genes have been identified in humans that are associated with DNA repair. This review is aimed at updating our current knowledge of the various repair pathways by providing an overview of DNA-repair genes and the corresponding proteins, participating either directly in DNA repair, or in checkpoint control and signaling of DNA damage.
Collapse
Affiliation(s)
- Markus Christmann
- Division of Applied Toxicology, Institute of Toxicology, University of Mainz, Obere Zahlbacher Str. 67, D-55131 Mainz, Germany
| | | | | | | |
Collapse
|
41
|
Marenstein DR, Chan MK, Altamirano A, Basu AK, Boorstein RJ, Cunningham RP, Teebor GW. Substrate specificity of human endonuclease III (hNTH1). Effect of human APE1 on hNTH1 activity. J Biol Chem 2003; 278:9005-12. [PMID: 12519758 DOI: 10.1074/jbc.m212168200] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Base excision repair of oxidized pyrimidines in human DNA is initiated by the DNA N-glycosylase/apurinic/apyrimidinic (AP) lyase, human NTH1 (hNTH1), the homolog of Escherichia coli endonuclease III (Nth). In contrast to Nth, the DNA N-glycosylase activity of hNTH1 is 7-fold greater than its AP lyase activity when the DNA substrate contains a thymine glycol (Tg) opposite adenine (Tg:A) (Marenstein, D. R., Ocampo, M. T. A., Chan, M. K., Altamirano, A., Basu, A. K., Boorstein, R. J., Cunningham, R. P., and Teebor, G. W. (2001) J. Biol. Chem. 276, 21242-21249). When Tg is opposite guanine (Tg:G), the two activities are of the same specific activity as the AP lyase activity of hNTH1 against Tg:A (Ocampo, M. T. A., Chaung, W., Marenstein, D. R., Chan, M. K., Altamirano, A., Basu, A. K., Boorstein, R. J., Cunningham, R. P., and Teebor, G. W. (2002) Mol. Cell. Biol. 22, 6111-6121). We demonstrate here that hNTH1 was inhibited by the product of its DNA N-glycosylase activity directed against Tg:G, the AP:G site. In contrast, hNTH1 was not as inhibited by the AP:A site arising from release of Tg from Tg:A. Addition of human APE1 (AP endonuclease-1) increased dissociation of hNTH1 from the DNA N-glycosylase-generated AP:A site, resulting in abrogation of AP lyase activity and an increase in turnover of the DNA N-glycosylase activity of hNTH1. Addition of APE1 did not abrogate hNTH1 AP lyase activity against Tg:G. The stimulatory protein YB-1 (Marenstein et al.), added to APE1, resulted in an additive increase in both activities of hNTH1 regardless of base pairing. Tg:A is formed by oxidative attack on thymine opposite adenine. Tg:G is formed by oxidative attack on 5-methylcytosine opposite guanine (Zuo, S., Boorstein, R. J., and Teebor, G. W. (1995) Nucleic Acids Res. 23, 3239-3243). It is possible that the in vitro substrate selectivity of mammalian NTH1 and the concomitant selective stimulation of activity by APE1 are indicative of selective repair of oxidative damage in different regions of the genome.
Collapse
Affiliation(s)
- Dina R Marenstein
- Department of Pathology and the Kaplan Comprehensive Cancer Center, New York University School of Medicine, New York, New York 10016, USA
| | | | | | | | | | | | | |
Collapse
|
42
|
Vens C, Dahmen-Mooren E, Verwijs-Janssen M, Blyweert W, Graversen L, Bartelink H, Begg AC. The role of DNA polymerase beta in determining sensitivity to ionizing radiation in human tumor cells. Nucleic Acids Res 2002; 30:2995-3004. [PMID: 12087186 PMCID: PMC117058 DOI: 10.1093/nar/gkf403] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Lethal lesions after ionizing radiation are thought to be mainly unrepaired or misrepaired DNA double-strand breaks, ultimately leading to lethal chromosome aberrations. However, studies with radioprotectors and repair inhibitors indicate that single-strand breaks, damaged nucleotides or abasic sites can also influence cell survival. This paper reports on studies to further define the role of base damage and base excision repair on the radiosensitivity of human cells. We retrovirally transduced human tumor cells with a dominant negative form of DNA polymerase beta, comprising the 14 kDa DNA-binding domain of DNA polymerase beta but lacking polymerase function. Radiosensitization of two human carcinoma cell lines, A549 and SQD9, was observed, achieving dose enhancement factors of 1.5-1.7. Sensitization was dependent on expression level of the dominant negative and was seen in both single cell clones and in unselected virally transduced populations. Sensitization was not due to changes in cell cycle distribution. Little or no sensitization was seen in G(1)-enriched populations, indicating cell cycle specificity for the observed sensitization. These results contrast with the lack of effect seen in DNA polymerase beta knockout cells, suggesting that polDN also inhibits the long patch, DNA polymerase beta-independent repair pathway. These data demonstrate an important role for BER in determining sensitivity to ionizing radiation and might help identify targets for radiosensitizing tumor cells.
Collapse
Affiliation(s)
- Conchita Vens
- Division of Experimental Therapy and Department of Radiotherapy, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
43
|
Ranalli TA, DeMott MS, Bambara RA. Mechanism underlying replication protein a stimulation of DNA ligase I. J Biol Chem 2002; 277:1719-27. [PMID: 11698410 DOI: 10.1074/jbc.m109053200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Replication protein A (RPA) is a heterotrimeric single-stranded DNA-binding protein that participates in multiple DNA transactions that include replication and repair. Base excision repair is a central DNA repair pathway, responsible for the removal of damaged bases. We have shown previously that RPA was able to stimulate long patch base excision repair reconstituted in vitro. Herein we show that human RPA stimulates the activity of the base excision repair component human DNA ligase I by approximately 15-fold. Other analyzed single-stranded binding proteins would not substitute, attesting to the specificity of the stimulation. Conversely, RPA was unable to stimulate the functionally homologous ATP-dependent ligase from T4 bacteriophage. Kinetic analyses suggest that catalysis of ligation is enhanced by RPA, as a 4-fold increase in k(cat) is observed, whereas K(m) is not significantly changed. Substrate competition experiments further support the conclusion that RPA does not alter the specificity or rate of substrate binding by DNA ligase I. Additionally, RPA is unable to significantly enhance ligation on substrates containing an unannealed 3'-upstream primer terminus, suggesting that RPA does not stabilize the nick site to enhance ligase recognition. Furthermore when DNA ligase I is pre-bound to the substrate and limited to a single turnover, RPA is still able to stimulate ligation. Overall, the results support a mechanism of stimulation that involves increasing the rate of catalysis of ligation.
Collapse
Affiliation(s)
- Tamara A Ranalli
- Department of Biochemistry, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | | | | |
Collapse
|
44
|
Tom S, Ranalli TA, Podust VN, Bambara RA. Regulatory roles of p21 and apurinic/apyrimidinic endonuclease 1 in base excision repair. J Biol Chem 2001; 276:48781-9. [PMID: 11641413 DOI: 10.1074/jbc.m109626200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Many types of DNA damage induce a cellular response that inhibits replication but allows repair by up-regulating the p53 pathway and inducing p21(Cip1, Waf1, Sdi1). The p21 regulatory protein can bind proliferating cell nuclear antigen (PCNA) and prohibit DNA replication. We show here that p21 also inhibits PCNA stimulation of long patch base excision repair (BER) in vitro. p21 disrupts PCNA-directed stimulation of flap endonuclease 1 (FEN1), DNA ligase I, and DNA polymerase delta. The dilemma is to understand how p21 prevents DNA replication but allows BER in vivo. Differential regulation by p21 is likely to relate to the utilization of DNA polymerase beta, which is not sensitive to p21, in the repair pathway. We have also found that apurinic/apyrimidinic endonuclease 1 (APE1) stimulates long patch BER. Furthermore, neither APE1 activity nor its ability to stimulate long patch BER is significantly affected by p21 in vitro. We propose that APE1 serves as an assembly and coordination factor for long patch BER proteins. APE1 initially cleaves the DNA and then facilitates the sequential binding and catalysis by DNA polymerase beta, DNA polymerase delta, FEN1, and DNA ligase I. This model implies that BER can be regulated differentially, based upon the assembly of relevant proteins around APE1 in the presence or absence of PCNA.
Collapse
Affiliation(s)
- S Tom
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | | | | | | |
Collapse
|
45
|
García-Díaz M, Bebenek K, Kunkel TA, Blanco L. Identification of an intrinsic 5'-deoxyribose-5-phosphate lyase activity in human DNA polymerase lambda: a possible role in base excision repair. J Biol Chem 2001; 276:34659-63. [PMID: 11457865 DOI: 10.1074/jbc.m106336200] [Citation(s) in RCA: 185] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Base excision repair (BER) is a major repair pathway in eukaryotic cells responsible for repair of lesions that give rise to abasic (AP) sites in DNA. Pivotal to this process is the 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity of DNA polymerase beta (Pol beta). DNA polymerase lambda (Pol lambda) is a recently identified eukaryotic DNA polymerase that is homologous to Pol beta. We show here that human Pol lambda exhibits dRP lyase, but not AP lyase, activity in vitro and that this activity is consistent with a beta-elimination mechanism. Accordingly, a single amino acid substitution (K310A) eliminated more than 90% of the wild-type dRP lyase activity, thus suggesting that Lys(310) of Pol lambda is the main nucleophile involved in the reaction. The dRP lyase activity of Pol lambda, in coordination with its polymerization activity, efficiently repaired uracil-containing DNA in an in vitro reconstituted BER reaction. These results suggest that Pol lambda may participate in "single-nucleotide" base excision repair in mammalian cells.
Collapse
Affiliation(s)
- M García-Díaz
- Centro de Biologia Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma, 28049 Madrid, Spain
| | | | | | | |
Collapse
|