1
|
Greenwood SN, Kulkarni RS, Mikhail M, Weiser BP. Replication Protein A Enhances Kinetics of Uracil DNA Glycosylase on ssDNA and Across DNA Junctions: Explored with a DNA Repair Complex Produced with SpyCatcher/SpyTag Ligation. Chembiochem 2023; 24:e202200765. [PMID: 36883884 PMCID: PMC10267839 DOI: 10.1002/cbic.202200765] [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: 12/22/2022] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/09/2023]
Abstract
DNA repair proteins participate in extensive protein-protein interactions that promote the formation of DNA repair complexes. To understand how complex formation affects protein function during base excision repair, we used SpyCatcher/SpyTag ligation to produce a covalent complex between human uracil DNA glycosylase (UNG2) and replication protein A (RPA). Our covalent "RPA-Spy-UNG2" complex could identify and excise uracil bases in duplex areas next to ssDNA-dsDNA junctions slightly faster than the wild-type proteins, but this was highly dependent on DNA structure, as the turnover of the RPA-Spy-UNG2 complex slowed at DNA junctions where RPA tightly engaged long ssDNA sections. Conversely, the enzymes preferred uracil sites in ssDNA where RPA strongly enhanced uracil excision by UNG2 regardless of ssDNA length. Finally, RPA was found to promote UNG2 excision of two uracil sites positioned across a ssDNA-dsDNA junction, and dissociation of UNG2 from RPA enhanced this process. Our approach of ligating together RPA and UNG2 to reveal how complex formation affects enzyme function could be applied to examine other assemblies of DNA repair proteins.
Collapse
Affiliation(s)
- Sharon N Greenwood
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Rashmi S Kulkarni
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Michel Mikhail
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
- Department of Internal Medicine, Newark Beth Israel Medical Center, Newark, NJ 07112, USA
| | - Brian P Weiser
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
| |
Collapse
|
2
|
Blair K, Tehseen M, Raducanu VS, Shahid T, Lancey C, Rashid F, Crehuet R, Hamdan SM, De Biasio A. Mechanism of human Lig1 regulation by PCNA in Okazaki fragment sealing. Nat Commun 2022; 13:7833. [PMID: 36539424 PMCID: PMC9767926 DOI: 10.1038/s41467-022-35475-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
During lagging strand synthesis, DNA Ligase 1 (Lig1) cooperates with the sliding clamp PCNA to seal the nicks between Okazaki fragments generated by Pol δ and Flap endonuclease 1 (FEN1). We present several cryo-EM structures combined with functional assays, showing that human Lig1 recruits PCNA to nicked DNA using two PCNA-interacting motifs (PIPs) located at its disordered N-terminus (PIPN-term) and DNA binding domain (PIPDBD). Once Lig1 and PCNA assemble as two-stack rings encircling DNA, PIPN-term is released from PCNA and only PIPDBD is required for ligation to facilitate the substrate handoff from FEN1. Consistently, we observed that PCNA forms a defined complex with FEN1 and nicked DNA, and it recruits Lig1 to an unoccupied monomer creating a toolbelt that drives the transfer of DNA to Lig1. Collectively, our results provide a structural model on how PCNA regulates FEN1 and Lig1 during Okazaki fragments maturation.
Collapse
Affiliation(s)
- Kerry Blair
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester, LE1 7HB, UK
| | - Muhammad Tehseen
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Vlad-Stefan Raducanu
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Taha Shahid
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester, LE1 7HB, UK
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Claudia Lancey
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester, LE1 7HB, UK
| | - Fahad Rashid
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Ramon Crehuet
- CSIC-Institute for Advanced Chemistry of Catalonia (IQAC) C/ Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Samir M Hamdan
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
| | - Alfredo De Biasio
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester, LE1 7HB, UK.
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
| |
Collapse
|
3
|
Influence of pork liver drying on ferrochelatase activity for zinc protoporphyrin formation. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.114128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
4
|
Tarantino ME, Delaney S. Kinetic Analysis of the Effect of N-Terminal Acetylation on Thymine DNA Glycosylase. Biochemistry 2022; 61:895-908. [PMID: 35436101 PMCID: PMC9117521 DOI: 10.1021/acs.biochem.1c00823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Thymine DNA glycosylase (TDG) is tasked with initiating DNA base excision repair by recognizing and removing T, U, the chemotherapeutic 5-fluorouracil (5-FU), and many other oxidized and halogenated pyrimidine bases. TDG contains a long, unstructured N-terminus that contains four known sites of acetylation: lysine (K) residues 59, 83, 84, and 87. Here, K to glutamine (Q) mutants are used as acetyl-lysine (AcK) analogues to probe the effect of N-terminal acetylation on the kinetics of TDG. We find that mimicking acetylation affects neither the maximal single-turnover rate kmax nor the turnover rate kTO, indicating that the steps after initial binding, through chemistry and product release, are not affected. Under subsaturating conditions, however, acetylation changes the processing of U substrates. Subtle differences among AcK analogues are revealed with 5-FU in single-stranded DNA. We propose that the subtleties observed among the AcK analogues may be amplified on the genomic scale, leading to regulation of TDG activity. N-terminal acetylation, though, may also play a structural, rather than kinetic role in vivo.
Collapse
Affiliation(s)
- Mary E. Tarantino
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, United States
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, RI 02912, United States
| |
Collapse
|
5
|
Abril B, Sanchez-Torres EA, Bou R, Garcia-Perez JV, Benedito J. Ultrasound intensification of Ferrochelatase extraction from pork liver as a strategy to improve ZINC-protoporphyrin formation. ULTRASONICS SONOCHEMISTRY 2021; 78:105703. [PMID: 34388654 PMCID: PMC8363878 DOI: 10.1016/j.ultsonch.2021.105703] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 07/15/2021] [Accepted: 07/29/2021] [Indexed: 05/06/2023]
Abstract
The enzyme Ferrochelatase (FeCH), which is naturally present in pork liver, catalyses the formation of Zinc-protoporphyrin (ZnPP), a natural pigment responsible for the typical color of dry-cured Italian Parma ham. The aim of this study was to evaluate the feasibility of using high power ultrasound in continuous and pulsed modes to intensify the extraction of the enzyme FeCH from pork liver. US application during FeCH extraction led to an improved enzymatic activity and further increase in the formation of ZnPP. The optimal condition tested was that of 1 min in continuous US application, in which time the enzymatic activity increased by 33.3 % compared to conventional extraction (30 min). Pulsed US application required 5 min treatments to observe a significant intensification effect. Therefore, ultrasound is a potentially feasible technique as it increases the catalytic activity of FeCH and saves time compared to the conventional extraction method.
Collapse
Affiliation(s)
- B Abril
- Department of Food Technology, Universitat Politècnica de València, Camí de Vera, s/n, Valencia 46022, Spain
| | - E A Sanchez-Torres
- IRTA, XaRTA, Food Technology, Finca Camps i Armet, Monells, Girona E-17121, Spain
| | - R Bou
- IRTA, XaRTA, Food Technology, Finca Camps i Armet, Monells, Girona E-17121, Spain
| | - J V Garcia-Perez
- Department of Food Technology, Universitat Politècnica de València, Camí de Vera, s/n, Valencia 46022, Spain
| | - J Benedito
- Department of Food Technology, Universitat Politècnica de València, Camí de Vera, s/n, Valencia 46022, Spain.
| |
Collapse
|
6
|
Sassa A, Odagiri M. Understanding the sequence and structural context effects in oxidative DNA damage repair. DNA Repair (Amst) 2021; 93:102906. [PMID: 33087272 DOI: 10.1016/j.dnarep.2020.102906] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
8-Oxo-7,8-dihydroguanine (8-oxoG) is the major base damage in the genomic DNA by exposure to reactive oxygen species. Organisms have evolved various DNA repair mechanisms, such as base excision repair (BER) and nucleotide excision repair (NER), to protect the cellular genome from these mutagenic DNA lesions. The efficiency and capacity of BER and NER mechanisms can be modulated by the local sequence and structural contexts in which 8-oxoG is located. This graphical review summarizes the biochemical and structural studies that have provided insights into the impact of the microenvironment around the site of the lesion on oxidative DNA damage repair.
Collapse
Affiliation(s)
- Akira Sassa
- Department of Biology, Graduate School of Science, Chiba University, Chiba 263-8522, Japan.
| | - Mizuki Odagiri
- Department of Biology, Graduate School of Science, Chiba University, Chiba 263-8522, Japan
| |
Collapse
|
7
|
Laverty DJ, Greenberg MM. Expanded Substrate Scope of DNA Polymerase θ and DNA Polymerase β: Lyase Activity on 5'-Overhangs and Clustered Lesions. Biochemistry 2018; 57:6119-6127. [PMID: 30299084 PMCID: PMC6200648 DOI: 10.1021/acs.biochem.8b00911] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
DNA polymerase θ (Pol θ) is a multifunctional enzyme with double-strand break (DSB) repair, translesion synthesis, and lyase activities. Pol θ lyase activity on ternary substrates containing a 5'-dRP that are produced during base excision repair of abasic sites (AP) is weak compared to that of DNA polymerase β (Pol β), a polymerase integrally involved in base excision repair. This led us to explore whether Pol θ utilizes its lyase activity to remove 5'-dRP and incise abasic sites from alternative substrates that might be produced during DNA damage and repair. We found that Pol θ exhibited lyase activity on abasic lesions near DSB termini and on clustered lesions. To calibrate the Pol θ activity, Pol β reactivity was examined with the same substrates. Pol β excised 5'-dRP from within a 5'-overhang 80 times faster than did Pol θ. Pol θ and Pol β also incised AP within clustered lesions but showed opposite preferences with respect to the polarity of the lesions. AP lesions in 5'-overhangs were typically excised by Pol β 35-50 times faster than those in a duplex substrate but 15-20-fold more slowly than 5'-dRP in a ternary complex. This is the first report of Pol θ exhibiting lyase activity within an unincised strand. These results suggest that bifunctional polymerases may exhibit lyase activity on a greater variety of substrates than previously recognized. A role in DSB repair could potentially be beneficial, while the aberrant activity exhibited on clustered lesions may be deleterious because of their conversion to DSBs.
Collapse
Affiliation(s)
- Daniel J. Laverty
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
| | - Marc M. Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
| |
Collapse
|
8
|
Mittal C, Culbertson SJ, Shogren-Knaak MA. Distinct requirements of linker DNA and transcriptional activators in promoting SAGA-mediated nucleosome acetylation. J Biol Chem 2018; 293:13736-13749. [PMID: 30054274 DOI: 10.1074/jbc.ra118.004487] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 07/20/2018] [Indexed: 01/08/2023] Open
Abstract
The Spt-Ada-Gcn5 acetyltransferase (SAGA) family of transcriptional coactivators are prototypical nucleosome acetyltransferase complexes that regulate multiple steps in gene transcription. The size and complexity of both the SAGA enzyme and the chromatin substrate provide numerous opportunities for regulating the acetylation process. To better probe this regulation, here we developed a bead-based nucleosome acetylation assay to characterize the binding interactions and kinetics of acetylation with different nucleosomal substrates and the full SAGA complex purified from budding yeast (Saccharomyces cerevisiae). We found that SAGA-mediated nucleosome acetylation is stimulated up to 9-fold by DNA flanking the nucleosome, both by facilitating the binding of SAGA and by accelerating acetylation turnover. This stimulation required that flanking DNA is present on both sides of the nucleosome and that one side is >15 bp long. The Gal4-VP16 transcriptional activator fusion protein could also augment nucleosome acetylation up to 5-fold. However, contrary to our expectations, this stimulation did not appear to occur by stabilizing the binding of SAGA toward nucleosomes containing an activator-binding site. Instead, increased acetylation turnover by SAGA stimulated nucleosome acetylation. These results suggest that the Gal4-VP16 transcriptional activator directly stimulates acetylation via a dual interaction with both flanking DNA and SAGA. Altogether, these findings uncover several critical mechanisms of SAGA regulation by chromatin substrates.
Collapse
Affiliation(s)
- Chitvan Mittal
- From the Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011
| | - Sannie J Culbertson
- From the Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011
| | - Michael A Shogren-Knaak
- From the Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011
| |
Collapse
|
9
|
Khrenova MG, Nemukhin AV. Modeling the Transient Kinetics of the L1 Metallo-β-Lactamase. J Phys Chem B 2018; 122:1378-1386. [DOI: 10.1021/acs.jpcb.7b10188] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Maria G. Khrenova
- Department
of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Alexander V. Nemukhin
- Department
of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
- Emanuel
Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
| |
Collapse
|
10
|
Cross M, Rajan S, Chekaiban J, Saunders J, Hamilton C, Kim JS, Coster MJ, Gasser RB, Hofmann A. Enzyme characteristics of pathogen-specific trehalose-6-phosphate phosphatases. Sci Rep 2017; 7:2015. [PMID: 28515463 PMCID: PMC5435700 DOI: 10.1038/s41598-017-02220-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 04/07/2017] [Indexed: 12/21/2022] Open
Abstract
Owing to the key role of trehalose in pathogenic organisms, there has recently been growing interest in trehalose metabolism for therapeutic purposes. Trehalose-6-phosphate phosphatase (TPP) is a pivotal enzyme in the most prominent biosynthesis pathway (OtsAB). Here, we compare the enzyme characteristics of recombinant TPPs from five important nematode and bacterial pathogens, including three novel members of this protein family. Analysis of the kinetics of trehalose-6-phosphate hydrolysis reveals that all five enzymes display a burst-like kinetic behaviour which is characterised by a decrease of the enzymatic rate after the pre-steady state. The observed super-stoichiometric burst amplitudes can be explained by multiple global conformational changes in members of this enzyme family during substrate processing. In the search for specific TPP inhibitors, the trapping of the complex conformational transitions in TPPs during the catalytic cycle may present a worthwhile strategy to explore.
Collapse
Affiliation(s)
- Megan Cross
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, 4111, Australia
| | - Siji Rajan
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, 4111, Australia
| | - Janine Chekaiban
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, 4111, Australia
| | - Jake Saunders
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, 4111, Australia
| | - Chloe Hamilton
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, 4111, Australia
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Mark J Coster
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, 4111, Australia
| | - Robin B Gasser
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Andreas Hofmann
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, 4111, Australia.
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.
- Queensland Tropical Health Alliance, Smithfield, Queensland, 4878, Australia.
| |
Collapse
|
11
|
Müller TA, Tobar MA, Perian MN, Hausinger RP. Biochemical Characterization of AP Lyase and m 6A Demethylase Activities of Human AlkB Homologue 1 (ALKBH1). Biochemistry 2017; 56:1899-1910. [PMID: 28290676 DOI: 10.1021/acs.biochem.7b00060] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Alkbh1 is one of nine mammalian homologues of Escherichia coli AlkB, a 2-oxoglutarate-dependent dioxygenase that catalyzes direct DNA repair by removing alkyl lesions from DNA. Six distinct enzymatic activities have been reported for Alkbh1, including hydroxylation of variously methylated DNA, mRNA, tRNA, or histone substrates along with the cleavage of DNA at apurinic/apyrimidinic (AP) sites followed by covalent attachment to the 5'-product. The studies described here extend the biochemical characterization of two of these enzymatic activities using human ALKBH1: the AP lyase and 6-methyl adenine DNA demethylase activities. The steady-state and single-turnover kinetic parameters for ALKBH1 cleavage of AP sites in DNA were determined and shown to be comparable to those of other AP lyases. The α,β-unsaturated aldehyde of the 5'-product arising from DNA cleavage reacts predominantly with C129 of ALKBH1, but secondary sites also generate covalent adducts. The 6-methyl adenine demethylase activity was examined with a newly developed assay using a methylation-sensitive restriction endonuclease, and the enzymatic rate was found to be very low. Indeed, the demethylase activity was less than half that of the AP lyase activity when ALKBH1 samples were assayed using identical buffer conditions. The two enzymatic activities were examined using a series of site-directed variant proteins, revealing the presence of distinct but partially overlapping active sites for the two reactions. We postulate that the very low 6-methyl adenine oxygenase activity associated with ALKBH1 is unlikely to represent the major function of the enzyme in the cell, while the cellular role of the lyase activity (including its subsequent covalent attachment to DNA) remains uncertain.
Collapse
Affiliation(s)
- Tina A Müller
- Department of Microbiology and Molecular Genetics, Michigan State University , East Lansing, Michigan 48824, United States
| | - Michael A Tobar
- Department of Microbiology and Molecular Genetics, Michigan State University , East Lansing, Michigan 48824, United States
| | - Madison N Perian
- Biology Department, Kalamazoo College , Kalamazoo, Michigan 49006, United States
| | - Robert P Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University , East Lansing, Michigan 48824, United States.,Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824, United States
| |
Collapse
|
12
|
Sassa A, Çağlayan M, Rodriguez Y, Beard WA, Wilson SH, Nohmi T, Honma M, Yasui M. Impact of Ribonucleotide Backbone on Translesion Synthesis and Repair of 7,8-Dihydro-8-oxoguanine. J Biol Chem 2016; 291:24314-24323. [PMID: 27660390 DOI: 10.1074/jbc.m116.738732] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 08/28/2016] [Indexed: 12/21/2022] Open
Abstract
Numerous ribonucleotides are incorporated into the genome during DNA replication. Oxidized ribonucleotides can also be erroneously incorporated into DNA. Embedded ribonucleotides destabilize the structure of DNA and retard DNA synthesis by DNA polymerases (pols), leading to genomic instability. Mammalian cells possess translesion DNA synthesis (TLS) pols that bypass DNA damage. The mechanism of TLS and repair of oxidized ribonucleotides remains to be elucidated. To address this, we analyzed the miscoding properties of the ribonucleotides riboguanosine (rG) and 7,8-dihydro-8-oxo-riboguanosine (8-oxo-rG) during TLS catalyzed by the human TLS pols κ and η in vitro The primer extension reaction catalyzed by human replicative pol α was strongly blocked by 8-oxo-rG. pol κ inefficiently bypassed rG and 8-oxo-rG compared with dG and 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-oxo-dG), whereas pol η easily bypassed the ribonucleotides. pol α exclusively inserted dAMP opposite 8-oxo-rG. Interestingly, pol κ preferentially inserted dCMP opposite 8-oxo-rG, whereas the insertion of dAMP was favored opposite 8-oxo-dG. In addition, pol η accurately bypassed 8-oxo-rG. Furthermore, we examined the activity of the base excision repair (BER) enzymes 8-oxoguanine DNA glycosylase (OGG1) and apurinic/apyrimidinic endonuclease 1 on the substrates, including rG and 8-oxo-rG. Both BER enzymes were completely inactive against 8-oxo-rG in DNA. However, OGG1 suppressed 8-oxo-rG excision by RNase H2, which is involved in the removal of ribonucleotides from DNA. These results suggest that the different sugar backbones between 8-oxo-rG and 8-oxo-dG alter the capacity of TLS and repair of 8-oxoguanine.
Collapse
Affiliation(s)
- Akira Sassa
- From the Division of Genetics and Mutagenesis, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan and
| | - Melike Çağlayan
- the Genome Integrity and Structural Biology Laboratory, National Institutes of Health, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Yesenia Rodriguez
- the Genome Integrity and Structural Biology Laboratory, National Institutes of Health, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - William A Beard
- the Genome Integrity and Structural Biology Laboratory, National Institutes of Health, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Samuel H Wilson
- the Genome Integrity and Structural Biology Laboratory, National Institutes of Health, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Takehiko Nohmi
- From the Division of Genetics and Mutagenesis, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan and
| | - Masamitsu Honma
- From the Division of Genetics and Mutagenesis, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan and
| | - Manabu Yasui
- From the Division of Genetics and Mutagenesis, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan and
| |
Collapse
|
13
|
Su Y, Peter Guengerich F. Pre-Steady-State Kinetic Analysis of Single-Nucleotide Incorporation by DNA Polymerases. ACTA ACUST UNITED AC 2016; 65:7.23.1-7.23.10. [PMID: 27248785 DOI: 10.1002/cpnc.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Pre-steady-state kinetic analysis is a powerful and widely used method to obtain multiple kinetic parameters. This protocol provides a step-by-step procedure for pre-steady-state kinetic analysis of single-nucleotide incorporation by a DNA polymerase. It describes the experimental details of DNA substrate annealing, reaction mixture preparation, handling of the RQF-3 rapid quench-flow instrument, denaturing polyacrylamide DNA gel preparation, electrophoresis, quantitation, and data analysis. The core and unique part of this protocol is the rationale for preparation of the reaction mixture (the ratio of the polymerase to the DNA substrate) and methods for conducting pre-steady-state assays on an RQF-3 rapid quench-flow instrument, as well as data interpretation after analysis. In addition, the methods for the DNA substrate annealing and DNA polyacrylamide gel preparation, electrophoresis, quantitation and analysis are suitable for use in other studies. © 2016 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- Yan Su
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
| |
Collapse
|
14
|
Prasad R, Dyrkheeva N, Williams J, Wilson SH. Mammalian Base Excision Repair: Functional Partnership between PARP-1 and APE1 in AP-Site Repair. PLoS One 2015; 10:e0124269. [PMID: 26020771 PMCID: PMC4447435 DOI: 10.1371/journal.pone.0124269] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 03/11/2015] [Indexed: 01/09/2023] Open
Abstract
The apurinic/apyrimidinic- (AP-) site in genomic DNA arises through spontaneous base loss and base removal by DNA glycosylases and is considered an abundant DNA lesion in mammalian cells. The base excision repair (BER) pathway repairs the AP-site lesion by excising and replacing the site with a normal nucleotide via template directed gap-filling DNA synthesis. The BER pathway is mediated by a specialized group of proteins, some of which can be found in multiprotein complexes in cultured mouse fibroblasts. Using a DNA polymerase (pol) β immunoaffinity-capture technique to isolate such a complex, we identified five tightly associated and abundant BER factors in the complex: PARP-1, XRCC1, DNA ligase III, PNKP, and Tdp1. AP endonuclease 1 (APE1), however, was not present. Nevertheless, the complex was capable of BER activity, since repair was initiated by PARP-1’s AP lyase strand incision activity. Addition of purified APE1 increased the BER activity of the pol β complex. Surprisingly, the pol β complex stimulated the strand incision activity of APE1. Our results suggested that PARP-1 was responsible for this effect, whereas other proteins in the complex had no effect on APE1 strand incision activity. Studies of purified PARP-1 and APE1 revealed that PARP-1 was able to stimulate APE1 strand incision activity. These results illustrate roles of PARP-1 in BER including a functional partnership with APE1.
Collapse
Affiliation(s)
- Rajendra Prasad
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Nadezhda Dyrkheeva
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Jason Williams
- Epigenetics and Stem Cell Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Samuel H. Wilson
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
- * E-mail:
| |
Collapse
|
15
|
Su Y, Patra A, Harp JM, Egli M, Guengerich FP. Roles of Residues Arg-61 and Gln-38 of Human DNA Polymerase η in Bypass of Deoxyguanosine and 7,8-Dihydro-8-oxo-2'-deoxyguanosine. J Biol Chem 2015; 290:15921-33. [PMID: 25947374 DOI: 10.1074/jbc.m115.653691] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Indexed: 11/06/2022] Open
Abstract
Like the other Y-family DNA polymerases, human DNA polymerase η (hpol η) has relatively low fidelity and is able to tolerate damage during DNA synthesis, including 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-oxoG), one of the most abundant DNA lesions in the genome. Crystal structures show that Arg-61 and Gln-38 are located near the active site and may play important roles in the fidelity and efficiency of hpol η. Site-directed mutagenesis was used to replace these side chains either alone or together, and the wild type or mutant proteins were purified and tested by replicating DNA past deoxyguanosine (G) or 8-oxoG. The catalytic activity of hpol η was dramatically disrupted by the R61M and Q38A/R61A mutations, as opposed to the R61A and Q38A single mutants. Crystal structures of hpol η mutant ternary complexes reveal that polarized water molecules can mimic and partially compensate for the missing side chains of Arg-61 and Gln-38 in the Q38A/R61A mutant. The combined data indicate that the positioning and positive charge of Arg-61 synergistically contribute to the nucleotidyl transfer reaction, with additional influence exerted by Gln-38. In addition, gel filtration chromatography separated multimeric and monomeric forms of wild type and mutant hpol η, indicating the possibility that hpol η forms multimers in vivo.
Collapse
Affiliation(s)
- Yan Su
- From the Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Amritraj Patra
- From the Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Joel M Harp
- From the Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Martin Egli
- From the Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - F Peter Guengerich
- From the Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| |
Collapse
|
16
|
Sassa A, Çağlayan M, Dyrkheeva NS, Beard WA, Wilson SH. Base excision repair of tandem modifications in a methylated CpG dinucleotide. J Biol Chem 2014; 289:13996-4008. [PMID: 24695738 DOI: 10.1074/jbc.m114.557769] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cytosine methylation and demethylation in tracks of CpG dinucleotides is an epigenetic mechanism for control of gene expression. The initial step in the demethylation process can be deamination of 5-methylcytosine producing the TpG alteration and T:G mispair, and this step is followed by thymine DNA glycosylase (TDG) initiated base excision repair (BER). A further consideration is that guanine in the CpG dinucleotide may become oxidized to 7,8-dihydro-8-oxoguanine (8-oxoG), and this could affect the demethylation process involving TDG-initiated BER. However, little is known about the enzymology of BER of altered in-tandem CpG dinucleotides; e.g. Tp8-oxoG. Here, we investigated interactions between this altered dinucleotide and purified BER enzymes, the DNA glycosylases TDG and 8-oxoG DNA glycosylase 1 (OGG1), apurinic/apyrimidinic (AP) endonuclease 1, DNA polymerase β, and DNA ligases. The overall TDG-initiated BER of the Tp8-oxoG dinucleotide is significantly reduced. Specifically, TDG and DNA ligase activities are reduced by a 3'-flanking 8-oxoG. In contrast, the OGG1-initiated BER pathway is blocked due to the 5'-flanking T:G mispair; this reduces OGG1, AP endonuclease 1, and DNA polymerase β activities. Furthermore, in TDG-initiated BER, TDG remains bound to its product AP site blocking OGG1 access to the adjacent 8-oxoG. These results reveal BER enzyme specificities enabling suppression of OGG1-initiated BER and coordination of TDG-initiated BER at this tandem alteration in the CpG dinucleotide.
Collapse
Affiliation(s)
- Akira Sassa
- From the Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709 and
| | - Melike Çağlayan
- From the Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709 and
| | - Nadezhda S Dyrkheeva
- From the Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709 and Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, 630090 Novosibirsk, Russia
| | - William A Beard
- From the Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709 and
| | - Samuel H Wilson
- From the Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709 and
| |
Collapse
|