1
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Almohdar D, Murcia D, Tang Q, Ortiz A, Martinez E, Parwal T, Kamble P, Çağlayan M. Impact of DNA ligase 1 and IIIα interactions with APE1 and polβ on the efficiency of base excision repair pathway at the downstream steps. J Biol Chem 2024; 300:107355. [PMID: 38718860 PMCID: PMC11176775 DOI: 10.1016/j.jbc.2024.107355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 06/03/2024] Open
Abstract
Base excision repair (BER) requires a tight coordination between the repair enzymes through protein-protein interactions and involves gap filling by DNA polymerase (pol) β and subsequent nick sealing by DNA ligase (LIG) 1 or LIGIIIα at the downstream steps. Apurinic/apyrimidinic-endonuclease 1 (APE1), by its exonuclease activity, proofreads 3' mismatches incorporated by polβ during BER. We previously reported that the interruptions in the functional interplay between polβ and the BER ligases result in faulty repair events. Yet, how the protein interactions of LIG1 and LIGIIIα could affect the repair pathway coordination during nick sealing at the final steps remains unknown. Here, we demonstrate that LIGIIIα interacts more tightly with polβ and APE1 than LIG1, and the N-terminal noncatalytic region of LIG1 as well as the catalytic core and BRCT domain of LIGIIIα mediate interactions with both proteins. Our results demonstrated less efficient nick sealing of polβ nucleotide insertion products in the absence of LIGIIIα zinc-finger domain and LIG1 N-terminal region. Furthermore, we showed a coordination between APE1 and LIG1/LIGIIIα during the removal of 3' mismatches from the nick repair intermediate on which both BER ligases can seal noncanonical ends or gap repair intermediate leading to products of single deletion mutagenesis. Overall results demonstrate the importance of functional coordination from gap filling by polβ coupled to nick sealing by LIG1/LIGIIIα in the presence of proofreading by APE1, which is mainly governed by protein-protein interactions and protein-DNA intermediate communications, to maintain repair efficiency at the downstream steps of the BER pathway.
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Affiliation(s)
- Danah Almohdar
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - David Murcia
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Qun Tang
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Abigail Ortiz
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Ernesto Martinez
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Tanay Parwal
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Pradnya Kamble
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Melike Çağlayan
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA.
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2
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Balu KE, Gulkis M, Almohdar D, Çağlayan M. Structures of LIG1 provide a mechanistic basis for understanding a lack of sugar discrimination against a ribonucleotide at the 3'-end of nick DNA. J Biol Chem 2024; 300:107216. [PMID: 38522520 PMCID: PMC11035063 DOI: 10.1016/j.jbc.2024.107216] [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: 12/28/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 03/26/2024] Open
Abstract
Human DNA ligase 1 (LIG1) is the main replicative ligase that seals Okazaki fragments during nuclear replication and finalizes DNA repair pathways by joining DNA ends of the broken strand breaks in the three steps of the ligation reaction. LIG1 can tolerate the RNA strand upstream of the nick, yet an atomic insight into the sugar discrimination mechanism by LIG1 against a ribonucleotide at the 3'-terminus of nick DNA is unknown. Here, we determined X-ray structures of LIG1/3'-RNA-DNA hybrids and captured the ligase during pre- and post-step 3 the ligation reaction. Furthermore, the overlays of 3'-rA:T and 3'-rG:C step 3 structures with step 2 structures of canonical 3'-dA:T and 3'-dG:C uncover a network of LIG1/DNA interactions through Asp570 and Arg871 side chains with 2'-OH of the ribose at nick showing a final phosphodiester bond formation and the other ligase active site residues surrounding the AMP site. Finally, we demonstrated that LIG1 can ligate the nick DNA substrates with pre-inserted 3'-ribonucleotides as efficiently as Watson-Crick base-paired ends in vitro. Together, our findings uncover a novel atomic insight into a lack of sugar discrimination by LIG1 and the impact of improper sugar on the nick sealing of ribonucleotides at the last step of DNA replication and repair.
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Affiliation(s)
- Kanal Elamparithi Balu
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Mitchell Gulkis
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Danah Almohdar
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Melike Çağlayan
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA.
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3
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Chatterjee S, Chaubet L, van den Berg A, Mukhortava A, Gulkis M, Çağlayan M. Uncovering nick DNA binding by LIG1 at the single-molecule level. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.28.587287. [PMID: 38586032 PMCID: PMC10996606 DOI: 10.1101/2024.03.28.587287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
DNA ligases repair the strand breaks are made continually and naturally throughout the genome, if left unrepaired and allowed to persist, they can lead to genome instability in the forms of lethal double-strand (ds) breaks, deletions, and duplications. DNA ligase 1 (LIG1) joins Okazaki fragments during the replication machinery and seals nicks at the end of most DNA repair pathways. Yet, how LIG1 recognizes its target substrate is entirely missing. Here, we uncover the dynamics of nick DNA binding by LIG1 at the single-molecule level. Our findings reveal that LIG1 binds to dsDNA both specifically and non-specifically and exhibits diffusive behavior to form a stable complex at the nick. Furthermore, by comparing with the LIG1 C-terminal protein, we demonstrate that the N-terminal non-catalytic region promotes binding enriched at nick sites and facilitates an efficient nick search process by promoting 1D diffusion along the DNA. Our findings provide a novel single-molecule insight into the nick binding by LIG1, which is critical to repair broken phosphodiester bonds in the DNA backbone to maintain genome integrity.
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4
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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.
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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.
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5
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Mechanistic investigation of human maturation of Okazaki fragments reveals slow kinetics. Nat Commun 2022; 13:6973. [PMID: 36379932 PMCID: PMC9666535 DOI: 10.1038/s41467-022-34751-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 11/04/2022] [Indexed: 11/16/2022] Open
Abstract
The final steps of lagging strand synthesis induce maturation of Okazaki fragments via removal of the RNA primers and ligation. Iterative cycles between Polymerase δ (Polδ) and Flap endonuclease-1 (FEN1) remove the primer, with an intermediary nick structure generated for each cycle. Here, we show that human Polδ is inefficient in releasing the nick product from FEN1, resulting in non-processive and remarkably slow RNA removal. Ligase 1 (Lig1) can release the nick from FEN1 and actively drive the reaction toward ligation. These mechanisms are coordinated by PCNA, which encircles DNA, and dynamically recruits Polδ, FEN1, and Lig1 to compete for their substrates. Our findings call for investigating additional pathways that may accelerate RNA removal in human cells, such as RNA pre-removal by RNase Hs, which, as demonstrated herein, enhances the maturation rate ~10-fold. They also suggest that FEN1 may attenuate the various activities of Polδ during DNA repair and recombination.
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6
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Sverzhinsky A, Tomkinson AE, Pascal JM. Cryo-EM structures and biochemical insights into heterotrimeric PCNA regulation of DNA ligase. Structure 2022; 30:371-385.e5. [PMID: 34838188 PMCID: PMC8897274 DOI: 10.1016/j.str.2021.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/04/2021] [Accepted: 11/03/2021] [Indexed: 12/15/2022]
Abstract
DNA ligases act in the final step of many DNA repair pathways and are commonly regulated by the DNA sliding clamp proliferating cell nuclear antigen (PCNA), but there are limited insights into the physical basis for this regulation. Here, we use single-particle cryoelectron microscopy (cryo-EM) to analyze an archaeal DNA ligase and heterotrimeric PCNA in complex with a single-strand DNA break. The cryo-EM structures highlight a continuous DNA-binding surface formed between DNA ligase and PCNA that supports the distorted conformation of the DNA break undergoing repair and contributes to PCNA stimulation of DNA ligation. DNA ligase is conformationally flexible within the complex, with its domains fully ordered only when encircling the repaired DNA to form a stacked ring structure with PCNA. The structures highlight DNA ligase structural transitions while docked on PCNA, changes in DNA conformation during ligation, and the potential for DNA ligase domains to regulate PCNA accessibility to other repair factors.
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Affiliation(s)
- Aleksandr Sverzhinsky
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Québec H3T 1J4, Canada
| | - Alan E Tomkinson
- Departments of Internal Medicine, Molecular Genetics and Microbiology, and University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Québec H3T 1J4, Canada.
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7
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Matsumoto Y, Brooks RC, Sverzhinsky A, Pascal JM, Tomkinson AE. Dynamic DNA-bound PCNA complexes co-ordinate Okazaki fragment synthesis, processing and ligation. J Mol Biol 2020; 432:166698. [PMID: 33157085 DOI: 10.1016/j.jmb.2020.10.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 10/07/2020] [Accepted: 10/27/2020] [Indexed: 11/28/2022]
Abstract
More than a million Okazaki fragments are synthesized, processed and joined during replication of the human genome. After synthesis of an RNA-DNA oligonucleotide by DNA polymerase α holoenzyme, proliferating cell nuclear antigen (PCNA), a homotrimeric DNA sliding clamp and polymerase processivity factor, is loaded onto the primer-template junction by replication factor C (RFC). Although PCNA interacts with the enzymes DNA polymerase δ (Pol δ), flap endonuclease 1 (FEN1) and DNA ligase I (LigI) that complete Okazaki fragment processing and joining, it is not known how the activities of these enzymes are coordinated. Here we describe a novel interaction between Pol δ and LigI that is critical for Okazaki fragment joining in vitro. Both LigI and FEN1 associate with PCNA-Pol δ during gap-filling synthesis, suggesting that gap-filling synthesis is carried out by a complex of PCNA, Pol δ, FEN1 and LigI. Following ligation, PCNA and LigI remain on the DNA, indicating that Pol δ and FEN1 dissociate during 5' end processing and that LigI engages PCNA at the DNA nick generated by FEN1 and Pol δ. Thus, dynamic PCNA complexes coordinate Okazaki fragment synthesis and processing with PCNA and LigI forming a terminal structure of two linked protein rings encircling the ligated DNA.
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Affiliation(s)
- Yoshihiro Matsumoto
- Departments of Internal Medicine, Molecular Genetics and Microbiology and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, United States
| | - Rhys C Brooks
- Departments of Internal Medicine, Molecular Genetics and Microbiology and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, United States
| | - Aleksandr Sverzhinsky
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Alan E Tomkinson
- Departments of Internal Medicine, Molecular Genetics and Microbiology and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, United States.
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8
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Kowalska E, Bartnicki F, Fujisawa R, Bonarek P, Hermanowicz P, Tsurimoto T, Muszynska K, Strzalka W. Inhibition of DNA replication by an anti-PCNA aptamer/PCNA complex. Nucleic Acids Res 2019; 46:25-41. [PMID: 29186524 PMCID: PMC5758903 DOI: 10.1093/nar/gkx1184] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 11/13/2017] [Indexed: 12/29/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is a multifunctional protein present in the nuclei of eukaryotic cells that plays an important role as a component of the DNA replication machinery, as well as DNA repair systems. PCNA was recently proposed as a potential non-oncogenic target for anti-cancer therapy. In this study, using the Systematic Evolution of Ligands by EXponential enrichment (SELEX) method, we developed a short DNA aptamer that binds human PCNA. In the presence of PCNA, the anti-PCNA aptamer inhibited the activity of human DNA polymerase δ and ϵ at nM concentrations. Moreover, PCNA protected the anti-PCNA aptamer against the exonucleolytic activity of these DNA polymerases. Investigation of the mechanism of anti-PCNA aptamer-dependent inhibition of DNA replication revealed that the aptamer did not block formation, but was a component of PCNA/DNA polymerase δ or ϵ complexes. Additionally, the anti-PCNA aptamer competed with the primer-template DNA for binding to the PCNA/DNA polymerase δ or ϵ complex. Based on the observations, a model of anti-PCNA aptamer/PCNA complex-dependent inhibition of DNA replication was proposed.
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Affiliation(s)
- Ewa Kowalska
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow 30-387, Poland
| | - Filip Bartnicki
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow 30-387, Poland
| | - Ryo Fujisawa
- Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Piotr Bonarek
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow 30-387, Poland
| | - Pawel Hermanowicz
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow 30-387, Poland.,Laboratory of Photobiology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, Krakow 30-387, Poland
| | - Toshiki Tsurimoto
- Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Klaudia Muszynska
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow 30-387, Poland
| | - Wojciech Strzalka
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow 30-387, Poland
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9
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Çağlayan M. Interplay between DNA Polymerases and DNA Ligases: Influence on Substrate Channeling and the Fidelity of DNA Ligation. J Mol Biol 2019; 431:2068-2081. [PMID: 31034893 DOI: 10.1016/j.jmb.2019.04.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/18/2019] [Accepted: 04/18/2019] [Indexed: 02/06/2023]
Abstract
DNA ligases are a highly conserved group of nucleic acid enzymes that play an essential role in DNA repair, replication, and recombination. This review focuses on functional interaction between DNA polymerases and DNA ligases in the repair of single- and double-strand DNA breaks, and discusses the notion that the substrate channeling during DNA polymerase-mediated nucleotide insertion coupled to DNA ligation could be a mechanism to minimize the release of potentially mutagenic repair intermediates. Evidence suggesting that DNA ligases are essential for cell viability includes the fact that defects or insufficiency in DNA ligase are casually linked to genome instability. In the future, it may be possible to develop small molecule inhibitors of mammalian DNA ligases and/or their functional protein partners that potentiate the effects of chemotherapeutic compounds and improve cancer treatment outcomes.
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Affiliation(s)
- Melike Çağlayan
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA.
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10
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Shi K, Bohl TE, Park J, Zasada A, Malik S, Banerjee S, Tran V, Li N, Yin Z, Kurniawan F, Orellana K, Aihara H. T4 DNA ligase structure reveals a prototypical ATP-dependent ligase with a unique mode of sliding clamp interaction. Nucleic Acids Res 2018; 46:10474-10488. [PMID: 30169742 PMCID: PMC6212786 DOI: 10.1093/nar/gky776] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 08/18/2018] [Indexed: 01/07/2023] Open
Abstract
DNA ligases play essential roles in DNA replication and repair. Bacteriophage T4 DNA ligase is the first ATP-dependent ligase enzyme to be discovered and is widely used in molecular biology, but its structure remained unknown. Our crystal structure of T4 DNA ligase bound to DNA shows a compact α-helical DNA-binding domain (DBD), nucleotidyl-transferase (NTase) domain, and OB-fold domain, which together fully encircle DNA. The DBD of T4 DNA ligase exhibits remarkable structural homology to the core DNA-binding helices of the larger DBDs from eukaryotic and archaeal DNA ligases, but it lacks additional structural components required for protein interactions. T4 DNA ligase instead has a flexible loop insertion within the NTase domain, which binds tightly to the T4 sliding clamp gp45 in a novel α-helical PIP-box conformation. Thus, T4 DNA ligase represents a prototype of the larger eukaryotic and archaeal DNA ligases, with a uniquely evolved mode of protein interaction that may be important for efficient DNA replication.
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Affiliation(s)
- Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street S.E. Minneapolis, MN 55455, USA
| | - Thomas E Bohl
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street S.E. Minneapolis, MN 55455, USA
| | - Jeonghyun Park
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street S.E. Minneapolis, MN 55455, USA
| | - Andrew Zasada
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street S.E. Minneapolis, MN 55455, USA
| | - Shray Malik
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street S.E. Minneapolis, MN 55455, USA
| | - Surajit Banerjee
- Northeastern Collaborative Access Team, Cornell University, Advanced Photon Source, Lemont, Illinois, 60439, USA
| | - Vincent Tran
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street S.E. Minneapolis, MN 55455, USA
| | - Na Li
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street S.E. Minneapolis, MN 55455, USA
| | - Zhiqi Yin
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street S.E. Minneapolis, MN 55455, USA
| | - Fredy Kurniawan
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street S.E. Minneapolis, MN 55455, USA
| | - Kayo Orellana
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street S.E. Minneapolis, MN 55455, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street S.E. Minneapolis, MN 55455, USA,To whom correspondence should be addressed. Tel: +1 612 624 1491;
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11
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Stodola JL, Burgers PM. Mechanism of Lagging-Strand DNA Replication in Eukaryotes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1042:117-133. [PMID: 29357056 DOI: 10.1007/978-981-10-6955-0_6] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This chapter focuses on the enzymes and mechanisms involved in lagging-strand DNA replication in eukaryotic cells. Recent structural and biochemical progress with DNA polymerase α-primase (Pol α) provides insights how each of the millions of Okazaki fragments in a mammalian cell is primed by the primase subunit and further extended by its polymerase subunit. Rapid kinetic studies of Okazaki fragment elongation by Pol δ illuminate events when the polymerase encounters the double-stranded RNA-DNA block of the preceding Okazaki fragment. This block acts as a progressive molecular break that provides both time and opportunity for the flap endonuclease 1 (FEN1) to access the nascent flap and cut it. The iterative action of Pol δ and FEN1 is coordinated by the replication clamp PCNA and produces a regulated degradation of the RNA primer, thereby preventing the formation of long-strand displacement flaps. Occasional long flaps are further processed by backup nucleases including Dna2.
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Affiliation(s)
- Joseph L Stodola
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO, USA
| | - Peter M Burgers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO, USA.
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12
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Ren Y, Lai Y, Laverde EE, Lei R, Rein HL, Liu Y. Modulation of trinucleotide repeat instability by DNA polymerase β polymorphic variant R137Q. PLoS One 2017; 12:e0177299. [PMID: 28475635 PMCID: PMC5419657 DOI: 10.1371/journal.pone.0177299] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/25/2017] [Indexed: 12/13/2022] Open
Abstract
Trinucleotide repeat (TNR) instability is associated with human neurodegenerative diseases and cancer. Recent studies have pointed out that DNA base excision repair (BER) mediated by DNA polymerase β (pol β) plays a crucial role in governing somatic TNR instability in a damage-location dependent manner. It has been shown that the activities and function of BER enzymes and cofactors can be modulated by their polymorphic variations. This could alter the function of BER in regulating TNR instability. However, the roles of BER polymorphism in modulating TNR instability remain to be elucidated. A previous study has shown that a pol β polymorphic variant, polβR137Q is associated with cancer due to its impaired polymerase activity and its deficiency in interacting with a BER cofactor, proliferating cell nuclear antigen (PCNA). In this study, we have studied the effect of the pol βR137Q variant on TNR instability. We showed that pol βR137Q exhibited weak DNA synthesis activity to cause TNR deletion during BER. We demonstrated that similar to wild-type pol β, the weak DNA synthesis activity of pol βR137Q allowed it to skip over a small loop formed on the template strand, thereby facilitating TNR deletion during BER. Our results further suggest that carriers with pol βR137Q polymorphic variant may not exhibit an elevated risk of developing human diseases that are associated with TNR instability.
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Affiliation(s)
- Yaou Ren
- Biochemistry Ph.D. Program, Florida International University, Miami, Florida, United States of America
| | - Yanhao Lai
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Eduardo E. Laverde
- Biochemistry Ph.D. Program, Florida International University, Miami, Florida, United States of America
| | - Ruipeng Lei
- Biochemistry Ph.D. Program, Florida International University, Miami, Florida, United States of America
| | - Hayley L. Rein
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Yuan Liu
- Biochemistry Ph.D. Program, Florida International University, Miami, Florida, United States of America
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- * E-mail:
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13
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Trasviña-Arenas CH, Cardona-Felix CS, Azuara-Liceaga E, Díaz-Quezada C, Brieba LG. Proliferating cell nuclear antigen restores the enzymatic activity of a DNA ligase I deficient in DNA binding. FEBS Open Bio 2017; 7:659-674. [PMID: 28469979 PMCID: PMC5407892 DOI: 10.1002/2211-5463.12209] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 02/13/2017] [Accepted: 02/16/2017] [Indexed: 11/16/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) coordinates multienzymatic reactions by interacting with a variety of protein partners. Family I DNA ligases are multidomain proteins involved in sealing of DNA nicks during Okazaki fragment maturation and DNA repair. The interaction of DNA ligases with the interdomain connector loop (IDCL) of PCNA through its PCNA‐interacting peptide (PIP box) is well studied but the role of the interacting surface between both proteins is not well characterized. In this work, we used a minimal DNA ligase I and two N‐terminal deletions to establish that DNA binding and nick‐sealing stimulation of DNA ligase I by PCNA are not solely dependent on the PIP box–IDCL interaction. We found that a truncated DNA ligase I with a deleted PIP box is stimulated by PCNA. Furthermore, the activity of a DNA ligase defective in DNA binding is rescued upon PCNA addition. As the rate constants for single‐turnover ligation for the full‐length and truncated DNA ligases are not affected by PCNA, our data suggest that PCNA stimulation is achieved by increasing the affinity for nicked DNA substrate and not by increasing catalytic efficiency. Surprisingly C‐terminal mutants of PCNA are not able to stimulate nick‐sealing activity of Entamoeba histolytica DNA ligase I. Our data support the notion that the C‐terminal region of PCNA may be involved in promoting an allosteric transition in E. histolytica DNA ligase I from a spread‐shaped to a ring‐shaped structure. This study suggests that the ring‐shaped PCNA is a binding platform able to stabilize coevolved protein–protein interactions, in this case an interaction with DNA ligase I.
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Affiliation(s)
- Carlos H Trasviña-Arenas
- Laboratorio Nacional de Genómica para la Biodiversidad Centro de Investigación y de Estudios Avanzados Irapuato Guanajuato México
| | - Cesar S Cardona-Felix
- Laboratorio Nacional de Genómica para la Biodiversidad Centro de Investigación y de Estudios Avanzados Irapuato Guanajuato México.,Present address: Centro Interdisciplinario de Ciencias Marinas (CICIMAR-IPN) Av. Instituto Politécnico Nacional. s/n.La Paz Baja California Sur 23096 Mexico.,Present address: Cátedras CONACyT Dirección Adjunta de Desarrollo Científico Consejo Nacional de Ciencia y Tecnología Av. Insurgentes Sur 1582 Ciudad de Mexico 03940 Mexico
| | - Elisa Azuara-Liceaga
- Posgrado en Ciencias Genómicas Universidad Autónoma de la Ciudad de México México
| | - Corina Díaz-Quezada
- Laboratorio Nacional de Genómica para la Biodiversidad Centro de Investigación y de Estudios Avanzados Irapuato Guanajuato México
| | - Luis G Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad Centro de Investigación y de Estudios Avanzados Irapuato Guanajuato México
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14
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Balliano AJ, Hayes JJ. Base excision repair in chromatin: Insights from reconstituted systems. DNA Repair (Amst) 2015; 36:77-85. [PMID: 26411876 DOI: 10.1016/j.dnarep.2015.09.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The process of base excision repair has been completely reconstituted in vitro and structural and biochemical properties of the component enzymes thoroughly studied on naked DNA templates. More recent work in this field aims to understand how BER operates on the natural substrate, chromatin [1,2]. Toward this end, a number of researchers, including the Smerdon group, have focused attention to understand how individual enzymes and reconstituted BER operate on nucleosome substrates. While nucleosomes were once thought to completely restrict access of DNA-dependent factors, the surprising finding from these studies suggests that at least some BER components can utilize target DNA bound within nucleosomes as substrates for their enzymatic processes. This data correlates well with both structural studies of these enzymes and our developing understanding of nucleosome conformation and dynamics. While more needs to be learned, these studies highlight the utility of reconstituted BER and chromatin systems to inform our understanding of in vivo biological processes.
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Affiliation(s)
- Angela J Balliano
- University of Rochester Medical Center, 601 Elmwood Ave., Box 712, Rochester, NY 14642, United States
| | - Jeffrey J Hayes
- University of Rochester Medical Center, 601 Elmwood Ave., Box 712, Rochester, NY 14642, United States.
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15
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Strzalka WK, Aggarwal C, Krzeszowiec W, Jakubowska A, Sztatelman O, Banas AK. Arabidopsis PCNAs form complexes with selected D-type cyclins. FRONTIERS IN PLANT SCIENCE 2015; 6:516. [PMID: 26379676 PMCID: PMC4550699 DOI: 10.3389/fpls.2015.00516] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/26/2015] [Indexed: 05/29/2023]
Abstract
Proliferating Cell Nuclear Antigen (PCNA) is a key nuclear protein of eukaryotic cells. It has been shown to form complexes with cyclin dependent kinases, cyclin dependent kinase inhibitors and the D-type cyclins which are involved in the cell cycle control. In Arabidopsis two genes coding for PCNA1 and PCNA2 proteins have been identified. In this study by analyzing Arabidopsis PCNA/CycD complexes we tested the possible functional differentiation of PCNA1/2 proteins in cell cycle control. Most out of the 10 cyclins investigated showed only nuclear localization except CycD2;1, CycD4;1, and CycD4;2 which were observed both in the nucleus and cytoplasm. Using the Y2H, BiFC and FLIM-FRET techniques we identified D-type cyclins which formed complexes with either PCNA1 or PCNA2. Among the candidates tested only CycD1;1, CycD3;1, and CycD3;3 were not detected in a complex with the PCNA proteins. Moreover, our results indicate that the formation of CycD3;2/PCNA and CycD4;1/PCNA complexes can be regulated by other as yet unidentified factor(s). Additionally, FLIM-FRET analyses suggested that in planta the distance between PCNA1/CycD4;1, PCNA1/CycD6;1, PCNA1/CycD7;1, and PCNA2/CycD4;2 proteins was shorter than that between PCNA2/CycD4;1, PCNA2/CycD6;1, PCNA2/CycD7;1, and PCNA1/CycD4;2 pairs. These data indicate that the nine amino acid differences between PCNA1 and PCNA2 have an impact on the architecture of Arabidopsis CycD/PCNA complexes.
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Affiliation(s)
- Wojciech K. Strzalka
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian UniversityKrakow, Poland
- The Bioremediation Department, Malopolska Centre of Biotechnology, Jagiellonian UniversityKrakow, Poland
| | - Chhavi Aggarwal
- Department of Gene Expression, Faculty of Biology, Adam Mickiewicz UniversityPoznan, Poland
| | - Weronika Krzeszowiec
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian UniversityKrakow, Poland
| | - Agata Jakubowska
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian UniversityKrakow, Poland
| | - Olga Sztatelman
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian UniversityKrakow, Poland
| | - Agnieszka K. Banas
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian UniversityKrakow, Poland
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16
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Levikova M, Cejka P. The Saccharomyces cerevisiae Dna2 can function as a sole nuclease in the processing of Okazaki fragments in DNA replication. Nucleic Acids Res 2015; 43:7888-97. [PMID: 26175049 PMCID: PMC4652754 DOI: 10.1093/nar/gkv710] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Accepted: 07/01/2015] [Indexed: 01/30/2023] Open
Abstract
During DNA replication, synthesis of the lagging strand occurs in stretches termed Okazaki fragments. Before adjacent fragments are ligated, any flaps resulting from the displacement of the 5' DNA end of the Okazaki fragment must be cleaved. Previously, Dna2 was implicated to function upstream of flap endonuclease 1 (Fen1 or Rad27) in the processing of long flaps bound by the replication protein A (RPA). Here we show that Dna2 efficiently cleaves long DNA flaps exactly at or directly adjacent to the base. A fraction of the flaps cleaved by Dna2 can be immediately ligated. When coupled with DNA replication, the flap processing activity of Dna2 leads to a nearly complete Okazaki fragment maturation at sub-nanomolar Dna2 concentrations. Our results indicate that a subsequent nucleolytic activity of Fen1 is not required in most cases. In contrast Dna2 is completely incapable to cleave short flaps. We show that also Dna2, like Fen1, interacts with proliferating cell nuclear antigen (PCNA). We propose a model where Dna2 alone is responsible for cleaving of RPA-bound long flaps, while Fen1 or exonuclease 1 (Exo1) cleave short flaps. Our results argue that Dna2 can function in a separate, rather than in a Fen1-dependent pathway.
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Affiliation(s)
- Maryna Levikova
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Petr Cejka
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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17
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Khanam T, Rai N, Ramachandran R. Mycobacterium tuberculosis class II apurinic/apyrimidinic-endonuclease/3'-5' exonuclease III exhibits DNA regulated modes of interaction with the sliding DNA β-clamp. Mol Microbiol 2015; 98:46-68. [PMID: 26103519 DOI: 10.1111/mmi.13102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2015] [Indexed: 11/30/2022]
Abstract
The class-II AP-endonuclease (XthA) acts on abasic sites of damaged DNA in bacterial base excision repair. We identified that the sliding DNA β-clamp forms in vivo and in vitro complexes with XthA in Mycobacterium tuberculosis. A novel 239 QLRFPKK245 motif in the DNA-binding domain of XthA was found to be important for the interactions. Likewise, the peptide binding-groove (PBG) and the C-terminal of β-clamp located on different domains interact with XthA. The β-clamp-XthA complex can be disrupted by clamp binding peptides and also by a specific bacterial clamp inhibitor that binds at the PBG. We also identified that β-clamp stimulates the activities of XthA primarily by increasing its affinity for the substrate and its processivity. Additionally, loading of the β-clamp onto DNA is required for activity stimulation. A reduction in XthA activity stimulation was observed in the presence of β-clamp binding peptides supporting that direct interactions between the proteins are necessary to cause stimulation. Finally, we found that in the absence of DNA, the PBG located on the second domain of the β-clamp is important for interactions with XthA, while the C-terminal domain predominantly mediates functional interactions in the substrate's presence.
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Affiliation(s)
- Taran Khanam
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh, 226031, India
| | - Niyati Rai
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh, 226031, India
| | - Ravishankar Ramachandran
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh, 226031, India
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18
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Ishino Y, Ishino S. Rapid progress of DNA replication studies in Archaea, the third domain of life. SCIENCE CHINA-LIFE SCIENCES 2012; 55:386-403. [PMID: 22645083 DOI: 10.1007/s11427-012-4324-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 04/20/2012] [Indexed: 02/04/2023]
Abstract
Archaea, the third domain of life, are interesting organisms to study from the aspects of molecular and evolutionary biology. Archaeal cells have a unicellular ultrastructure without a nucleus, resembling bacterial cells, but the proteins involved in genetic information processing pathways, including DNA replication, transcription, and translation, share strong similarities with those of Eukaryota. Therefore, archaea provide useful model systems to understand the more complex mechanisms of genetic information processing in eukaryotic cells. Moreover, the hyperthermophilic archaea provide very stable proteins, which are especially useful for the isolation of replisomal multicomplexes, to analyze their structures and functions. This review focuses on the history, current status, and future directions of archaeal DNA replication studies.
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Affiliation(s)
- Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan.
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19
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Kukshal V, Khanam T, Chopra D, Singh N, Sanyal S, Ramachandran R. M. tuberculosis sliding β-clamp does not interact directly with the NAD+-dependent DNA ligase. PLoS One 2012; 7:e35702. [PMID: 22545130 PMCID: PMC3335792 DOI: 10.1371/journal.pone.0035702] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 03/20/2012] [Indexed: 11/26/2022] Open
Abstract
The sliding β-clamp, an important component of the DNA replication and repair machinery, is drawing increasing attention as a therapeutic target. We report the crystal structure of the M. tuberculosis β-clamp (Mtbβ-clamp) to 3.0 Å resolution. The protein crystallized in the space group C222(1) with cell-dimensions a = 72.7, b = 234.9 & c = 125.1 Å respectively. Mtbβ-clamp is a dimer, and exhibits head-to-tail association similar to other bacterial clamps. Each monomer folds into three domains with similar structures respectively and associates with its dimeric partner through 6 salt-bridges and about 21 polar interactions. Affinity experiments involving a blunt DNA duplex, primed-DNA and nicked DNA respectively show that Mtbβ-clamp binds specifically to primed DNA about 1.8 times stronger compared to the other two substrates and with an apparent K(d) of 300 nM. In bacteria like E. coli, the β-clamp is known to interact with subunits of the clamp loader, NAD(+)-dependent DNA ligase (LigA) and other partners. We tested the interactions of the Mtbβ-clamp with MtbLigA and the γ-clamp loader subunit through radioactive gel shift assays, size exclusion chromatography, yeast-two hybrid experiments and also functionally. Intriguingly while Mtbβ-clamp interacts in vitro with the γ-clamp loader, it does not interact with MtbLigA unlike in bacteria like E. coli where it does. Modeling studies involving earlier peptide complexes reveal that the peptide-binding site is largely conserved despite lower sequence identity between bacterial clamps. Overall the results suggest that other as-yet-unidentified factors may mediate interactions between the clamp, LigA and DNA in mycobacteria.
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Affiliation(s)
- Vandna Kukshal
- Molecular and Structural Biology Division, Central Drug Research Institute (Council of Scientific and Industrial Research), Lucknow, Uttar Pradesh, India
| | - Taran Khanam
- Molecular and Structural Biology Division, Central Drug Research Institute (Council of Scientific and Industrial Research), Lucknow, Uttar Pradesh, India
| | - Deepti Chopra
- Molecular and Structural Biology Division, Central Drug Research Institute (Council of Scientific and Industrial Research), Lucknow, Uttar Pradesh, India
| | - Nidhi Singh
- Drug Target Discovery and Development Division, Central Drug Research Institute (Council of Scientific and Industrial Research), Lucknow, Uttar Pradesh, India
| | - Sabyasachi Sanyal
- Drug Target Discovery and Development Division, Central Drug Research Institute (Council of Scientific and Industrial Research), Lucknow, Uttar Pradesh, India
| | - Ravishankar Ramachandran
- Molecular and Structural Biology Division, Central Drug Research Institute (Council of Scientific and Industrial Research), Lucknow, Uttar Pradesh, India
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20
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Abstract
Multiple DNA ligation events are required to join the Okazaki fragments generated during lagging strand DNA synthesis. In eukaryotes, this is primarily carried out by members of the DNA ligase I family. The C-terminal catalytic region of these enzymes is composed of three domains: a DNA binding domain, an adenylation domain and an OB-fold domain. In the absence of DNA, these domains adopt an extended structure but transition into a compact ring structure when they engage a DNA nick, with each of the domains contacting the DNA. The non-catalytic N-terminal region of eukaryotic DNA ligase I is responsible for the specific participation of these enzymes in DNA replication. This proline-rich unstructured region contains the nuclear localization signal and a PCNA interaction motif that is critical for localization to replication foci and efficient joining of Okazaki fragments. DNA ligase I initially engages the PCNA trimer via this interaction motif which is located at the extreme N-terminus of this flexible region. It is likely that this facilitates an additional interaction between the DNA binding domain and the PCNA ring. The similar size and shape of the rings formed by the PCNA trimer and the DNA ligase I catalytic region when it engages a DNA nick suggest that these proteins interact to form a double-ring structure during the joining of Okazaki fragments. DNA ligase I also interacts with replication factor C, the factor that loads the PCNA trimeric ring onto DNA. This interaction, which is regulated by phosphorylation of the non-catalytic N-terminus of DNA ligase I, also appears to be critical for DNA replication.
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Affiliation(s)
- Timothy R L Howes
- Biomedical Sciences Graduate Program, University of New Mexico, Cancer Research Facility MSC08 4640, 1 University of New Mexico, Albuquerque, NM, 87131-0001, USA,
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21
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Kirchmaier AL. Ub-family modifications at the replication fork: Regulating PCNA-interacting components. FEBS Lett 2011; 585:2920-8. [DOI: 10.1016/j.febslet.2011.08.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 08/05/2011] [Accepted: 08/05/2011] [Indexed: 11/29/2022]
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22
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Cardona-Felix CS, Lara-Gonzalez S, Brieba LG. Structure and biochemical characterization of proliferating cellular nuclear antigen from a parasitic protozoon. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:497-505. [PMID: 21636889 DOI: 10.1107/s0907444911010547] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 03/21/2011] [Indexed: 11/10/2022]
Abstract
Proliferating cellular nuclear antigen (PCNA) is a toroidal-shaped protein that is involved in cell-cycle control, DNA replication and DNA repair. Parasitic protozoa are early-diverged eukaryotes that are responsible for neglected diseases. In this work, a PCNA from a parasitic protozoon was identified, cloned and biochemically characterized and its crystal structure was determined. Structural and biochemical studies demonstrate that PCNA from Entamoeba histolytica assembles as a homotrimer that is able to interact with and stimulate the activity of a PCNA-interacting peptide-motif protein from E. histolytica, EhDNAligI. The data indicate a conservation of the biochemical mechanisms of PCNA-mediated interactions between metazoa, yeast and parasitic protozoa.
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Affiliation(s)
- Cesar S Cardona-Felix
- Grupo de Bioquímica Estructural, Laboratorio Nacional de Genomica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Guanajuato, México
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23
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Zhang W, Qin Z, Zhang X, Xiao W. Roles of sequential ubiquitination of PCNA in DNA-damage tolerance. FEBS Lett 2011; 585:2786-94. [PMID: 21536034 DOI: 10.1016/j.febslet.2011.04.044] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 04/16/2011] [Accepted: 04/18/2011] [Indexed: 11/15/2022]
Abstract
Living organisms not only repair DNA damage induced by environmental agents and endogenous cellular metabolites, but have also developed mechanisms to survive in the presence of otherwise lethal lesions. DNA-damage tolerance (DDT) is considered such a mechanism that resumes DNA synthesis in the presence of replication-blocking lesions. Recent studies revealed that DDT in budding yeast is achieved through sequential ubiquitination of DNA polymerase processivity factor, proliferating cell nuclear antigen (PCNA). It is generally believed that monoubiquitinated PCNA promotes translesion DNA synthesis, whereas polyubiquitinated PCNA mediates an error-free mode of lesion bypass. This review will discuss how ubiquitinated PCNA modulates different means of lesion bypass.
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Affiliation(s)
- Weiwei Zhang
- College of Life Sciences, Capital Normal University, Beijing 100048, China
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24
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The role of the DNA sliding clamp in Okazaki fragment maturation in archaea and eukaryotes. Biochem Soc Trans 2011; 39:70-6. [DOI: 10.1042/bst0390070] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Efficient processing of Okazaki fragments generated during discontinuous lagging-strand DNA replication is critical for the maintenance of genome integrity. In eukaryotes, a number of enzymes co-ordinate to ensure the removal of initiating primers from the 5′-end of each fragment and the generation of a covalently linked daughter strand. Studies in eukaryotic systems have revealed that the co-ordination of DNA polymerase δ and FEN-1 (Flap Endonuclease 1) is sufficient to remove the majority of primers. Other pathways such as that involving Dna2 also operate under certain conditions, although, notably, Dna2 is not universally conserved between eukaryotes and archaea, unlike the other core factors. In addition to the catalytic components, the DNA sliding clamp, PCNA (proliferating-cell nuclear antigen), plays a pivotal role in binding and co-ordinating these enzymes at sites of lagging-strand replication. Structural studies in eukaryotic and archaeal systems have revealed that PCNA-binding proteins can adopt different conformations when binding PCNA. This conformational malleability may be key to the co-ordination of these enzymes' activities.
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25
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DNA replication: changing faces, trading places. Nat Chem Biol 2010; 6:701-2. [PMID: 20852606 DOI: 10.1038/nchembio.444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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Zhu Y, Wu Z, Cardoso MC, Parris DS. Processing of lagging-strand intermediates in vitro by herpes simplex virus type 1 DNA polymerase. J Virol 2010; 84:7459-72. [PMID: 20444887 PMCID: PMC2897638 DOI: 10.1128/jvi.01875-09] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Accepted: 04/28/2010] [Indexed: 12/14/2022] Open
Abstract
The processing of lagging-strand intermediates has not been demonstrated in vitro for herpes simplex virus type 1 (HSV-1). Human flap endonuclease-1 (Fen-1) was examined for its ability to produce ligatable products with model lagging-strand intermediates in the presence of the wild-type or exonuclease-deficient (exo(-)) HSV-1 DNA polymerase (pol). Primer/templates were composed of a minicircle single-stranded DNA template annealed to primers that contained 5' DNA flaps or 5' annealed DNA or RNA sequences. Gapped DNA primer/templates were extended but not significantly strand displaced by the wild-type HSV-1 pol, although significant strand displacement was observed with exo(-) HSV-1 pol. Nevertheless, the incubation of primer/templates containing 5' flaps with either wild-type or exo(-) HSV-1 pol and Fen-1 led to the efficient production of nicks that could be sealed with DNA ligase I. Both polymerases stimulated the nick translation activity of Fen-1 on DNA- or RNA-containing primer/templates, indicating that the activities were coordinated. Further evidence for Fen-1 involvement in HSV-1 DNA synthesis is suggested by the ability of a transiently expressed green fluorescent protein fusion with Fen-1 to accumulate in viral DNA replication compartments in infected cells and by the ability of endogenous Fen-1 to coimmunoprecipitate with an essential viral DNA replication protein in HSV-1-infected cells.
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Affiliation(s)
- Yali Zhu
- Department of Molecular Virology, Immunology, and Medical Genetics, Program in Molecular, Cellular, and Developmental Biology, Ohio State University, Columbus, Ohio 43210, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, D-64287 Darmstadt, Germany
| | - Zetang Wu
- Department of Molecular Virology, Immunology, and Medical Genetics, Program in Molecular, Cellular, and Developmental Biology, Ohio State University, Columbus, Ohio 43210, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, D-64287 Darmstadt, Germany
| | - M. Cristina Cardoso
- Department of Molecular Virology, Immunology, and Medical Genetics, Program in Molecular, Cellular, and Developmental Biology, Ohio State University, Columbus, Ohio 43210, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, D-64287 Darmstadt, Germany
| | - Deborah S. Parris
- Department of Molecular Virology, Immunology, and Medical Genetics, Program in Molecular, Cellular, and Developmental Biology, Ohio State University, Columbus, Ohio 43210, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, D-64287 Darmstadt, Germany
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27
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Balakrishnan L, Gloor JW, Bambara RA. Reconstitution of eukaryotic lagging strand DNA replication. Methods 2010; 51:347-57. [PMID: 20178844 DOI: 10.1016/j.ymeth.2010.02.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Revised: 02/15/2010] [Accepted: 02/17/2010] [Indexed: 11/17/2022] Open
Abstract
Eukaryotic DNA replication is a complex process requiring the proper functioning of a multitude of proteins to create error-free daughter DNA strands and maintain genome integrity. Even though synthesis and joining of Okazaki fragments on the lagging strand involves only half the DNA in the nucleus, the complexity associated with processing these fragments is about twice that needed for leading strand synthesis. Flap endonuclease 1 (FEN1) is the central component of the Okazaki fragment maturation pathway. FEN1 cleaves flaps that are displaced by DNA polymerase delta (pol delta), to create a nick that is effectively joined by DNA ligase I. The Pif1 helicase and Dna2 helicase/nuclease contribute to the maturation process by elongating the flap displaced by pol delta. Though the reason for generating long flaps is still a matter of debate, genetic studies have shown that Dna2 and Pif1 are both important components of DNA replication. Our current knowledge of the exact enzymatic steps that govern Okazaki fragment maturation has heavily derived from reconstitution reactions in vitro, which have augmented genetic information, to yield current mechanistic models. In this review, we describe both the design of specific DNA substrates that simulate intermediates of fragment maturation and protocols for reconstituting partial and complete lagging strand replication.
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Affiliation(s)
- Lata Balakrishnan
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
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28
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López Castel A, Tomkinson AE, Pearson CE. CTG/CAG repeat instability is modulated by the levels of human DNA ligase I and its interaction with proliferating cell nuclear antigen: a distinction between replication and slipped-DNA repair. J Biol Chem 2009; 284:26631-45. [PMID: 19628465 PMCID: PMC2785351 DOI: 10.1074/jbc.m109.034405] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Revised: 07/21/2009] [Indexed: 11/06/2022] Open
Abstract
Mechanisms contributing to disease-associated trinucleotide repeat instability are poorly understood. DNA ligation is an essential step common to replication and repair, both potential sources of repeat instability. Using derivatives of DNA ligase I (hLigI)-deficient human cells (46BR.1G1), we assessed the effect of hLigI activity, overexpression, and its interaction with proliferating cell nuclear antigen (PCNA) upon the ability to replicate and repair trinucleotide repeats. Compared with LigI(+/+), replication progression through repeats was poor, and repair tracts were broadened beyond the slipped-repeat for all mutant extracts. Increased repeat instability was linked only to hLigI overexpression and expression of a mutant hLigI incapable of interacting with PCNA. The endogenous mutant version of hLigI with reduced ligation activity did not alter instability. We distinguished the DNA processes through which hLigI contributes to trinucleotide instability. The highest levels of repeat instability were observed under the hLigI overexpression and were linked to reduced slipped-DNAs repair efficiencies. Therefore, the replication-mediated instability can partly be attributed to errors during replication but also to the poor repair of slipped-DNAs formed during this process. However, repair efficiencies were unaffected by expression of a PCNA interaction mutant of hLigI, limiting this instability to the replication process. The addition of purified proteins suggests that disruption of LigI and PCNA interactions influences trinucleotide repeat instability. The variable levels of age- and tissue-specific trinucleotide repeat instability observed in myotonic dystrophy patients and transgenic mice may be influenced by varying steady state levels of DNA ligase I in these tissues and during different developmental windows.
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Affiliation(s)
- Arturo López Castel
- From the Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
| | - Alan E. Tomkinson
- the Radiation Oncology Research Laboratory, Department of Radiation Oncology, and Marlene and Stewart Greenebaum Cancer Center, School of Medicine, University of Maryland, Baltimore, Maryland 21201
| | - Christopher E. Pearson
- From the Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
- the Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, and
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29
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C-terminal flap endonuclease (rad27) mutations: lethal interactions with a DNA ligase I mutation (cdc9-p) and suppression by proliferating cell nuclear antigen (POL30) in Saccharomyces cerevisiae. Genetics 2009; 183:63-78. [PMID: 19596905 DOI: 10.1534/genetics.109.103937] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During lagging-strand DNA replication in eukaryotic cells primers are removed from Okazaki fragments by the flap endonuclease and DNA ligase I joins nascent fragments. Both enzymes are brought to the replication fork by the sliding clamp proliferating cell nuclear antigen (PCNA). To understand the relationship among these three components, we have carried out a synthetic lethal screen with cdc9-p, a DNA ligase mutation with two substitutions (F43A/F44A) in its PCNA interaction domain. We recovered the flap endonuclease mutation rad27-K325* with a stop codon at residue 325. We created two additional rad27 alleles, rad27-A358* with a stop codon at residue 358 and rad27-pX8 with substitutions of all eight residues of the PCNA interaction domain. rad27-pX8 is temperature lethal and rad27-A358* grows slowly in combination with cdc9-p. Tests of mutation avoidance, DNA repair, and compatibility with DNA repair mutations showed that rad27-K325* confers severe phenotypes similar to rad27Delta, rad27-A358* confers mild phenotypes, and rad27-pX8 confers phenotypes intermediate between the other two alleles. High-copy expression of POL30 (PCNA) suppresses the canavanine mutation rate of all the rad27 alleles, including rad27Delta. These studies show the importance of the C terminus of the flap endonuclease in DNA replication and repair and, by virtue of the initial screen, show that this portion of the enzyme helps coordinate the entry of DNA ligase during Okazaki fragment maturation.
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30
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The DNA binding domain of human DNA ligase I interacts with both nicked DNA and the DNA sliding clamps, PCNA and hRad9-hRad1-hHus1. DNA Repair (Amst) 2009; 8:912-9. [PMID: 19523882 DOI: 10.1016/j.dnarep.2009.05.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Revised: 05/08/2009] [Accepted: 05/11/2009] [Indexed: 11/20/2022]
Abstract
The participation of the DNA ligase (hLigI) encoded by the human LIG1 gene in DNA replication and repair is mediated by an interaction with proliferating cell nuclear antigen (PCNA), a homotrimeric DNA sliding clamp. Interestingly, the catalytic fragment of hLigI encircles a DNA nick forming a ring that is similar in size and shape to the PCNA ring. Here we show that the DNA binding domain (DBD) within the hLigI catalytic fragment interacts with both PCNA and the heterotrimeric cell-cycle checkpoint clamp, hRad9-hRad1-hHus1 (9-1-1). The DBD preferentially binds to trimeric PCNA and the hRad1 subunit of 9-1-1. Unlike the majority of PCNA interacting proteins, the DBD does not interact with the interdomain connector loop region of PCNA but instead appears to interact with regions adjacent to the intersubunit interfaces within the PCNA trimer. Notably, the DBD not only binds specifically to DNA nicks but also mediates the formation of DNA protein complexes with PCNA. Based on these results, we suggest that the interface between the DBD and PCNA acts as a pivot facilitating the transition of the hLigI catalytic region fragment from an extended conformation to a ring structure when it engages a DNA nick.
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31
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Phosphorylation of human DNA ligase I regulates its interaction with replication factor C and its participation in DNA replication and DNA repair. Mol Cell Biol 2009; 29:2042-52. [PMID: 19223468 DOI: 10.1128/mcb.01732-08] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Human DNA ligase I (hLigI) participates in DNA replication and excision repair via an interaction with proliferating cell nuclear antigen (PCNA), a DNA sliding clamp. In addition, hLigI interacts with and is inhibited by replication factor C (RFC), the clamp loader complex that loads PCNA onto DNA. Here we show that a mutant version of hLigI, which mimics the hyperphosphorylated M-phase form of hLigI, does not interact with and is not inhibited by RFC, demonstrating that inhibition of ligation is dependent upon the interaction between hLigI and RFC. To examine the biological relevance of hLigI phosphorylation, we isolated derivatives of the hLigI-deficient cell line 46BR.1G1 that stably express mutant versions of hLigI in which four serine residues phosphorylated in vivo were replaced with either alanine or aspartic acid. The cell lines expressing the phosphorylation site mutants of hLigI exhibited a dramatic reduction in proliferation and DNA synthesis and were also hypersensitive to DNA damage. The dominant-negative effects of the hLigI phosphomutants on replication and repair are due to the activation of cellular senescence, presumably because of DNA damage arising from replication abnormalities. Thus, appropriate phosphorylation of hLigI is critical for its participation in DNA replication and repair.
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32
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Bloom LB. Loading clamps for DNA replication and repair. DNA Repair (Amst) 2009; 8:570-8. [PMID: 19213612 DOI: 10.1016/j.dnarep.2008.12.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Accepted: 12/19/2008] [Indexed: 01/25/2023]
Abstract
Sliding clamps and clamp loaders were initially identified as DNA polymerase processivity factors. Sliding clamps are ring-shaped protein complexes that encircle and slide along duplex DNA, and clamp loaders are enzymes that load these clamps onto DNA. When bound to a sliding clamp, DNA polymerases remain tightly associated with the template being copied, but are able to translocate along DNA at rates limited by rates of nucleotide incorporation. Many different enzymes required for DNA replication and repair use sliding clamps. Clamps not only increase the processivity of these enzymes, but may also serve as an attachment point to coordinate the activities of enzymes required for a given process. Clamp loaders are members of the AAA+ family of ATPases and use energy from ATP binding and hydrolysis to catalyze the mechanical reaction of loading clamps onto DNA. Many structural and functional features of clamps and clamp loaders are conserved across all domains of life. Here, the mechanism of clamp loading is reviewed by comparing features of prokaryotic and eukaryotic clamps and clamp loaders.
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Affiliation(s)
- Linda B Bloom
- Department of Biochemistry & Molecular Biology, University of Florida, Gainesville, FL 32610-0245, United States.
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33
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Abstract
DNA replication is a complex mechanism that functions due to the co-ordinated interplay of several dozen protein factors. In the last few years, numerous studies suggested a tight implication of DNA replication factors in several DNA transaction events that maintain the integrity of the genome. Therefore, DNA replication fork proteins have also to be considered as part of a general process aiming at replicating and protecting the genome in order to allow the correct function of a cell and of its eventual daughter cells. This is illustrated by several DNA repair pathways such as base excision repair, nucleotide excision repair, double-strand break repair, and mismatch repair. Furthermore, several of the replication proteins have also been shown to be essential in sensing and transducing DNA damages through the checkpoint cascade pathways. This review will summarize the properties of DNA replication proteins that function exclusively at the replication fork.
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34
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Abstract
DNA ligases are required for DNA replication, repair, and recombination. In eukaryotes, there are three families of ATP-dependent DNA ligases. Members of the DNA ligase I and IV families are found in all eukaryotes, whereas DNA ligase III family members are restricted to vertebrates. These enzymes share a common catalytic region comprising a DNA-binding domain, a nucleotidyltransferase (NTase) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The catalytic region encircles nicked DNA with each of the domains contacting the DNA duplex. The unique segments adjacent to the catalytic region of eukaryotic DNA ligases are involved in specific protein-protein interactions with a growing number of DNA replication and repair proteins. These interactions determine the specific cellular functions of the DNA ligase isozymes. In mammals, defects in DNA ligation have been linked with an increased incidence of cancer and neurodegeneration.
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Affiliation(s)
- Tom Ellenberger
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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35
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Kiyonari S, Uchimura M, Shirai T, Ishino Y. Physical and functional interactions between uracil-DNA glycosylase and proliferating cell nuclear antigen from the euryarchaeon Pyrococcus furiosus. J Biol Chem 2008; 283:24185-93. [PMID: 18562313 PMCID: PMC3259797 DOI: 10.1074/jbc.m802837200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Revised: 06/10/2008] [Indexed: 01/27/2023] Open
Abstract
Uracil-DNA glycosylase (UDG) is an important repair enzyme in all organisms to remove uracil bases from DNA. Recent biochemical studies have revealed that human nuclear UDG (UNG2) forms a multiprotein complex in replication foci and initiates the base excision repair pathway by interacting with proliferating cell nuclear antigen (PCNA). Here, we show the physical and functional interactions between UDG and PCNA from the hyperthermophilic euryarchaeon, Pyrococcus furiosus. The physical interaction between the two proteins was identified by a surface plasmon resonance analysis. Furthermore, the uracil glycosylase activity of P. furiosus UDG is stimulated by P. furiosus PCNA (PfuPCNA) in vitro. This stimulatory effect was observed only when wild type PfuPCNA, but not a monomeric PCNA mutant, was present in the reaction. Mutational analyses revealed that our predicted PCNA-binding region (AKTLF) in P. furiosus UDG is actually important for the interaction with PfuPCNA. This is the first report describing the functional interaction between archaeal UDG and PCNA.
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Affiliation(s)
- Shinichi Kiyonari
- Department of Genetic
Resources Technology, Faculty of Agriculture, Kyushu University, and
BIRD-Japan Science and Technology
Agency, 6-10-1 Hakozaki, Fukuoka-shi, Fukuoka 812-8581, Japan and the
Department of Bioscience, Nagahama
Institute of Bio-Science and Technology and
BIRD-Japan Science and Technology
Agency, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
| | - Maiko Uchimura
- Department of Genetic
Resources Technology, Faculty of Agriculture, Kyushu University, and
BIRD-Japan Science and Technology
Agency, 6-10-1 Hakozaki, Fukuoka-shi, Fukuoka 812-8581, Japan and the
Department of Bioscience, Nagahama
Institute of Bio-Science and Technology and
BIRD-Japan Science and Technology
Agency, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
| | - Tsuyoshi Shirai
- Department of Genetic
Resources Technology, Faculty of Agriculture, Kyushu University, and
BIRD-Japan Science and Technology
Agency, 6-10-1 Hakozaki, Fukuoka-shi, Fukuoka 812-8581, Japan and the
Department of Bioscience, Nagahama
Institute of Bio-Science and Technology and
BIRD-Japan Science and Technology
Agency, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
| | - Yoshizumi Ishino
- Department of Genetic
Resources Technology, Faculty of Agriculture, Kyushu University, and
BIRD-Japan Science and Technology
Agency, 6-10-1 Hakozaki, Fukuoka-shi, Fukuoka 812-8581, Japan and the
Department of Bioscience, Nagahama
Institute of Bio-Science and Technology and
BIRD-Japan Science and Technology
Agency, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
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36
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Johansson VM, Miniotis MF, Hegardt C, Jönsson G, Staaf J, Berntsson PSH, Oredsson SM, Alm K. Effect of polyamine deficiency on proteins involved in Okazaki fragment maturation. Cell Biol Int 2008; 32:1467-77. [PMID: 18786645 DOI: 10.1016/j.cellbi.2008.08.018] [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] [Indexed: 11/17/2022]
Abstract
Polyamine depletion causes S phase prolongation, and earlier studies indicate that the elongation step of DNA replication is affected. This led us to investigate the effects of polyamine depletion on enzymes crucial for Okazaki fragment maturation in the two breast cancer cell lines MCF-7 and L56Br-C1. In MCF-7 cells, treatment with N(1),N(11)-diethylnorspermine (DENSPM) causes S phase prolongation. In L56Br-C1 cells the prolongation is followed by massive apoptosis. In the present study we show that L56Br-C1 cells have substantially lower basal expressions of two Okazaki fragment maturation key proteins, DNA ligase I and FEN1, than MCF-7 cells. Thus, these two proteins might be promising markers for prediction of polyamine depletion sensitivity, something that can be useful for cancer treatment with polyamine analogues. DENSPM treatment affects the cellular distribution of FEN1 in L56Br-C1 cells, but not in MCF-7 cells, implying that FEN1 is affected by or involved in DENSPM-induced apoptosis.
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Affiliation(s)
- Veronica M Johansson
- Department of Cell and Organism Biology, Lund University, Helgonavägen 3B, SE-223 62 Lund, Sweden.
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37
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Song W, Levin DS, Varkey J, Post S, Bermudez VP, Hurwitz J, Tomkinson AE. A Conserved Physical and Functional Interaction between the Cell Cycle Checkpoint Clamp Loader and DNA Ligase I of Eukaryotes. J Biol Chem 2007; 282:22721-30. [PMID: 17561505 DOI: 10.1074/jbc.m703774200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA ligase I joins Okazaki fragments during DNA replication and completes certain excision repair pathways. The participation of DNA ligase I in these transactions is directed by physical and functional interactions with proliferating cell nuclear antigen, a DNA sliding clamp, and, replication factor C (RFC), the clamp loader. Here we show that DNA ligase I also interacts with the hRad17 subunit of the hRad17-RFC cell cycle checkpoint clamp loader, and with each of the subunits of its DNA sliding clamp, the heterotrimeric hRad9-hRad1-hHus1 complex. In contrast to the inhibitory effect of RFC, hRad17-RFC stimulates joining by DNA ligase I. Similar results were obtained with the homologous Saccharomyces cerevisiae proteins indicating that the interaction between the replicative DNA ligase and checkpoint clamp is conserved in eukaryotes. Notably, we show that hRad17 preferentially interacts with and specifically stimulates dephosphorylated DNA ligase I. Moreover, there is an increased association between DNA ligase I and hRad17 in S phase following DNA damage and replication blockage that occurs concomitantly with DNA damage-induced dephosphorylation of chromatin-associated DNA ligase I. Thus, our results suggest that the in vivo interaction between DNA ligase I and the checkpoint clamp loader is regulated by post-translational modification of DNA ligase I.
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Affiliation(s)
- Wei Song
- Molecular Medicine Graduate Program, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
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38
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Buguliskis JS, Casta LJ, Butz CE, Matsumoto Y, Taraschi TF. Expression and biochemical characterization of Plasmodium falciparum DNA ligase I. Mol Biochem Parasitol 2007; 155:128-37. [PMID: 17688957 PMCID: PMC2692355 DOI: 10.1016/j.molbiopara.2007.06.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2007] [Revised: 06/21/2007] [Accepted: 06/22/2007] [Indexed: 11/18/2022]
Abstract
We report that Plasmodium falciparum (Pf) encodes a 912 amino acid ATP-dependent DNA ligase. Protein sequence analysis of Pf DNA ligase I indicates a strong sequence similarity, particularly in the C-terminal region, to DNA ligase I homologues. The activity of recombinant Pf DNA ligase I (PfLigI) was investigated using protein expressed in HEK293 cells. The PfLigI gene product is approximately 94kDa and catalyzes phosphodiester bond formation on a singly nicked DNA substrate. The enzyme is most active at alkaline pH (8.5) and with Mg(2+) or Mn(2+) and ATP as cofactors. Kinetic studies of PfLigI revealed that the enzyme has similar substrate affinity (K(m) 2.6nM) as compared to human DNA ligase I and k(cat) (2.3x10(-3)s(-1)) and k(cat)/K(m) (8.8x10(5)M(-1)s(-1)) which are similar to other ATP-dependent DNA ligases. PfLigI was able to join RNA-DNA substrates only when the RNA sequence was upstream of the nick, confirming that it is DNA ligase I and has no associated DNA ligase III like activity.
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Affiliation(s)
- Jeffrey S. Buguliskis
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Louis J. Casta
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Charles E. Butz
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Yoshihiro Matsumoto
- Medical Science Division, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111
| | - Theodore F. Taraschi
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
- Address Correspondence: Theodore F. Taraschi, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, Pennsylvania, 19107-6731, Tel. 215-503-5020 Fax. 215-503-0206 E-mail:
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39
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Kiyonari S, Kamigochi T, Ishino Y. A single amino acid substitution in the DNA-binding domain of Aeropyrum pernix DNA ligase impairs its interaction with proliferating cell nuclear antigen. Extremophiles 2007; 11:675-84. [PMID: 17487442 DOI: 10.1007/s00792-007-0083-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2007] [Accepted: 04/09/2007] [Indexed: 11/25/2022]
Abstract
Proliferating cell nuclear antigen (PCNA) is known as a DNA sliding clamp that acts as a platform for the assembly of enzymes involved in DNA replication and repair. Previously, it was reported that a crenarchaeal PCNA formed a heterotrimeric structure, and that each PCNA subunit has distinct binding specificity to PCNA-binding proteins. Here we describe the PCNA-binding properties of a DNA ligase from the hyperthermophilic crenarchaeon Aeropyrum pernix K1. Based on our findings on the Pyrococcus furiosus DNA ligase-PCNA interaction, we predicted that the aromatic residue, Phe132, in the DNA-binding domain of A. pernix DNA ligase (ApeLig) would play a critical role in binding to A. pernix PCNA (ApePCNA). Surface plasmon resonance analyses revealed that the ApeLig F132A mutant does not interact with an immobilized subunit of ApePCNA. Furthermore, we could not detect any stimulation of the ligation activity of the ApeLig F132A protein by ApePCNA in vitro. These results indicated that the phenylalanine, which is located in our predicted PCNA-binding region in ApeLig, has a critical role for the physical and functional interaction with ApePCNA.
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Affiliation(s)
- Shinichi Kiyonari
- Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka-shi, Fukuoka, 812-8581, Japan
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40
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Abstract
Inheritance requires genome duplication, reproduction of chromatin and its epigenetic information, mechanisms to ensure genome integrity, and faithful transmission of the information to progeny. Proliferating cell nuclear antigen (PCNA)-a cofactor of DNA polymerases that encircles DNA-orchestrates several of these functions by recruiting crucial players to the replication fork. Remarkably, many factors that are involved in replication-linked processes interact with a particular face of PCNA and through the same interaction domain, indicating that these interactions do not occur simultaneously during replication. Switching of PCNA partners may be triggered by affinity-driven competition, phosphorylation, proteolysis, and modification of PCNA by ubiquitin and SUMO.
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Affiliation(s)
- George-Lucian Moldovan
- Department of Molecular Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18 82152 Martinsried, Germany
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41
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Almeida KH, Sobol RW. A unified view of base excision repair: lesion-dependent protein complexes regulated by post-translational modification. DNA Repair (Amst) 2007; 6:695-711. [PMID: 17337257 PMCID: PMC1995033 DOI: 10.1016/j.dnarep.2007.01.009] [Citation(s) in RCA: 306] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2007] [Accepted: 01/22/2007] [Indexed: 12/29/2022]
Abstract
Base excision repair (BER) proteins act upon a significantly broad spectrum of DNA lesions that result from endogenous and exogenous sources. Multiple sub-pathways of BER (short-path or long-patch) and newly designated DNA repair pathways (e.g., SSBR and NIR) that utilize BER proteins complicate any comprehensive understanding of BER and its role in genome maintenance, chemotherapeutic response, neuro-degeneration, cancer or aging. Herein, we propose a unified model of BER, comprised of three functional processes: Lesion Recognition/Strand Scission, Gap Tailoring and DNA Synthesis/Ligation, each represented by one or more multi-protein complexes and coordinated via the XRCC1/DNA Ligase III and PARP1 scaffold proteins. BER therefore may be represented by a series of repair complexes that assemble at the site of the DNA lesion and mediates repair in a coordinated fashion involving protein-protein interactions that dictate subsequent steps or sub-pathway choice. Complex formation is influenced by post-translational protein modifications that arise from the cellular state or the DNA damage response, providing an increase in specificity and efficiency to the BER pathway. In this review, we have summarized the reported BER protein-protein interactions and protein post-translational modifications and discuss the impact on DNA repair capacity and complex formation.
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Affiliation(s)
- Karen H. Almeida
- Department of Physical Sciences, Rhode Island College, 600 Mt. Pleasant Ave., Providence RI 02908-1991
| | - Robert W. Sobol
- Department of Pharmacology, University of Pittsburgh School of Medicine & University of Pittsburgh Cancer Institute, Hillman Cancer Center, Research Pavilion, Suite 2.6, 5117 Centre Avenue, Pittsburgh, PA 15213-1863
- *To whom correspondence should be addressed: Robert W. Sobol, Ph.D., Tel. 412-623-7764, Fax 412-623-7761, e-mail
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42
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Sokhansanj BA, Wilson DM. Estimating the effect of human base excision repair protein variants on the repair of oxidative DNA base damage. Cancer Epidemiol Biomarkers Prev 2006; 15:1000-8. [PMID: 16702383 DOI: 10.1158/1055-9965.epi-05-0817] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Epidemiologic studies have revealed a complex association between human genetic variance and cancer risk. Quantitative biological modeling based on experimental data can play a critical role in interpreting the effect of genetic variation on biochemical pathways relevant to cancer development and progression. Defects in human DNA base excision repair (BER) proteins can reduce cellular tolerance to oxidative DNA base damage caused by endogenous and exogenous sources, such as exposure to toxins and ionizing radiation. If not repaired, DNA base damage leads to cell dysfunction and mutagenesis, consequently leading to cancer, disease, and aging. Population screens have identified numerous single-nucleotide polymorphism variants in many BER proteins and some have been purified and found to exhibit mild kinetic defects. Epidemiologic studies have led to conflicting conclusions on the association between single-nucleotide polymorphism variants in BER proteins and cancer risk. Using experimental data for cellular concentration and the kinetics of normal and variant BER proteins, we apply a previously developed and tested human BER pathway model to (i) estimate the effect of mild variants on BER of abasic sites and 8-oxoguanine, a prominent oxidative DNA base modification, (ii) identify ranges of variation associated with substantial BER capacity loss, and (iii) reveal nonintuitive consequences of multiple simultaneous variants. Our findings support previous work suggesting that mild BER variants have a minimal effect on pathway capacity whereas more severe defects and simultaneous variation in several BER proteins can lead to inefficient repair and potentially deleterious consequences of cellular damage.
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Affiliation(s)
- Bahrad A Sokhansanj
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA.
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43
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Doré AS, Kilkenny ML, Jones SA, Oliver AW, Roe SM, Bell SD, Pearl LH. Structure of an archaeal PCNA1-PCNA2-FEN1 complex: elucidating PCNA subunit and client enzyme specificity. Nucleic Acids Res 2006; 34:4515-26. [PMID: 16945955 PMCID: PMC1636371 DOI: 10.1093/nar/gkl623] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The archaeal/eukaryotic proliferating cell nuclear antigen (PCNA) toroidal clamp interacts with a host of DNA modifying enzymes, providing a stable anchorage and enhancing their respective processivities. Given the broad range of enzymes with which PCNA has been shown to interact, relatively little is known about the mode of assembly of functionally meaningful combinations of enzymes on the PCNA clamp. We have determined the X-ray crystal structure of the Sulfolobus solfataricus PCNA1-PCNA2 heterodimer, bound to a single copy of the flap endonuclease FEN1 at 2.9 A resolution. We demonstrate the specificity of interaction of the PCNA subunits to form the PCNA1-PCNA2-PCNA3 heterotrimer, as well as providing a rationale for the specific interaction of the C-terminal PIP-box motif of FEN1 for the PCNA1 subunit. The structure explains the specificity of the individual archaeal PCNA subunits for selected repair enzyme 'clients', and provides insights into the co-ordinated assembly of sequential enzymatic steps in PCNA-scaffolded DNA repair cascades.
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Affiliation(s)
- Andrew S Doré
- CR-UK DNA Repair Enzymes Group, Section of Structural Biology, The Institute of Cancer Research, 237 Fulham Road, Chelsea, London, SW3 6JB, UK.
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44
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Kiyonari S, Takayama K, Nishida H, Ishino Y. Identification of a novel binding motif in Pyrococcus furiosus DNA ligase for the functional interaction with proliferating cell nuclear antigen. J Biol Chem 2006; 281:28023-32. [PMID: 16829513 DOI: 10.1074/jbc.m603403200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA ligase is an essential enzyme for all organisms and catalyzes a nick-joining reaction in the final step of the DNA replication, repair, and recombination processes. Herein, we show the physical and functional interaction between DNA ligase and proliferating cell nuclear antigen (PCNA) from the hyperthermophilic Euryarchaea Pyrococcus furiosus. The stimulatory effect of P. furiosus PCNA on the enzyme activity of P. furiosus DNA ligase was observed not at low ionic strength, but at a high salt concentration, at which a DNA ligase alone cannot bind to a nicked DNA substrate. On the basis of mutational analyses, we identified the amino acid residues that are critical for PCNA binding in a loop structure located in the N-terminal DNA-binding domain of P. furiosus DNA ligase. We propose that the pentapeptide motif QKSFF is involved in the PCNA-interacting motifs, in which Gln and the first Phe are especially important for stable binding with PCNA.
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Affiliation(s)
- Shinichi Kiyonari
- Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Japan
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Wang W, Lindsey-Boltz LA, Sancar A, Bambara RA. Mechanism of stimulation of human DNA ligase I by the Rad9-rad1-Hus1 checkpoint complex. J Biol Chem 2006; 281:20865-20872. [PMID: 16731526 DOI: 10.1074/jbc.m602289200] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Accumulating evidence suggests that the Rad9-Rad1-Hus1 (9-1-1) checkpoint complex, known to be a sensor of DNA damage, is also a component of DNA repair systems. Recent results show that 9-1-1 interacts with several base excision repair proteins. It binds the DNA glycosylase MutY homolog, and stimulates DNA polymerase beta, flap endonuclease 1, and DNA ligase I. 9-1-1 resembles proliferating cell nuclear antigen (PCNA), which stimulates some of these same repair enzymes, and is loaded onto DNA in a similar manner. The complex of 9-1-1 with DNA ligase I can be immunoprecipitated from human cells. Moreover, UV irradiation stimulates 9-1-1.ligase I complex formation, suggesting a role for 9-1-1 in DNA repair. Examining the nature of 9-1-1 interaction with DNA ligase I, we show that there is a similar degree of stimulation on ligation substrates with different structures, and that there is specificity for DNA ligase I. 9-1-1 improves the binding of DNA ligase I to nicked double strand DNA. Furthermore, although high concentrations of casein kinase II strongly inhibits DNA ligase I activity, it does not affect the ability of 9-1-1 to stimulate. This suggests that 9-1-1 is also an activator of DNA ligase I during DNA damage. Unlike PCNA, 9-1-1 stimulates DNA ligase I activity to the same extent on both linear and circular substrates, indicating that encirclement is not a requirement for stimulation. These data are consistent with a direct role for 9-1-1 in DNA repair, but possibly employing a different mechanism than PCNA.
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Affiliation(s)
- Wensheng Wang
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Laura A Lindsey-Boltz
- Department of Biochemistry and Biophysics, CB 7260, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, CB 7260, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599
| | - Robert A Bambara
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642.
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Puebla-Osorio N, Lacey DB, Alt FW, Zhu C. Early embryonic lethality due to targeted inactivation of DNA ligase III. Mol Cell Biol 2006; 26:3935-41. [PMID: 16648486 PMCID: PMC1489003 DOI: 10.1128/mcb.26.10.3935-3941.2006] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2005] [Revised: 12/21/2005] [Accepted: 03/02/2006] [Indexed: 11/20/2022] Open
Abstract
DNA ligases catalyze the joining of strand breaks in the phosphodiester backbone of duplex DNA and play essential roles in DNA replication, recombination, repair, and maintenance of genomic integrity. Three mammalian DNA ligase genes have been identified, and their corresponding ligases play distinct roles in DNA metabolism. DNA ligase III is proposed to be involved in the repairing of DNA single-strand breaks, but its precise role has not yet been demonstrated directly. To determine its role in DNA repair, cellular growth, and embryonic development, we introduced targeted interruption of the DNA ligase III (LIG3) gene into the mouse. Mice homozygous for LIG3 disruption showed early embryonic lethality. We found that the mutant embryonic developmental process stops at 8.5 days postcoitum (dpc), and excessive cell death occurs at 9.5 dpc. LIG3 mutant cells have relatively normal XRCC1 levels but elevated sister chromatid exchange. These findings indicate that DNA ligase III is involved in essential DNA repair activities required for early embryonic development and therefore cannot be replaced by other DNA ligases.
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Affiliation(s)
- Nahum Puebla-Osorio
- Department of Immunology, Unit 902, The University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Blvd., Houston, Texas 77030, USA
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Rossi ML, Purohit V, Brandt PD, Bambara RA. Lagging strand replication proteins in genome stability and DNA repair. Chem Rev 2006; 106:453-73. [PMID: 16464014 DOI: 10.1021/cr040497l] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Marie L Rossi
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, New York 14642, USA
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Tomkinson AE, Vijayakumar S, Pascal JM, Ellenberger T. DNA ligases: structure, reaction mechanism, and function. Chem Rev 2006; 106:687-99. [PMID: 16464020 DOI: 10.1021/cr040498d] [Citation(s) in RCA: 203] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Alan E Tomkinson
- Radiation Oncology Research Laboratory and Marlene and Stewart Greenebaum Cancer Center, Molecular and Cellular Biology Graduate Program, University of Maryland School of Medicine, Baltimore, 21201, USA.
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Dyrkheeva NS, Lomzov AA, Pyshnyi DV, Khodyreva SN, Lavrik OI. Efficiency of exonucleolytic action of apurinic/apyrimidinic endonuclease 1 towards matched and mismatched dNMP at the 3' terminus of different oligomeric DNA structures correlates with thermal stability of DNA duplexes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:699-706. [PMID: 16481227 DOI: 10.1016/j.bbapap.2006.01.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2005] [Revised: 01/05/2006] [Accepted: 01/05/2006] [Indexed: 11/20/2022]
Abstract
Human DNA apurinic/apyrimidinic endonuclease 1 (APE1) is involved in the DNA base excision repair process. In addition to its AP (apurinic/apyrimidinic) endonucleolytic function, APE1 possesses 3' phosphodiesterase and 3'-5' exonuclease activities. The 3'-5' exonuclease activity is considered important in proofreading of DNA synthesis catalyzed by DNA polymerase beta. Here, we examine the removal of matched and mismatched dNMP from the 3' terminus of the 3'-recessed and nicked DNA by the APE1 activity using two different reaction buffers. To investigate whether the ability of APE1 to excise nucleotides from the 3' terminus depends on the thermal stability of the DNA duplex, we studied this characteristic of the DNAs that were used in the exonuclease assays in these two buffers. Our data confirm that APE1 removes mismatched nucleotides from the 3' terminus of DNA more efficiently than matched pairs. Both the efficiency of the 3'-5' exonuclease activity of APE1 and the thermal stability of DNA duplexes varied depending on the nature of the flanking group at the 5' margin of the nick. The 3'-5' exonuclease activity of APE1 shows a preference for substrates with a hydroxyl group at the 5' margin of the nick as well as for flapped and recessed DNAs.
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Affiliation(s)
- Nadezhda S Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, pr. Lavrenteva 8, Novosibirsk 630090, Russia
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