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Caston RA, Fortini P, Chen K, Bauer J, Dogliotti E, Yin YW, Demple B. Maintenance of Flap Endonucleases for Long-Patch Base Excision DNA Repair in Mouse Muscle and Neuronal Cells Differentiated In Vitro. Int J Mol Sci 2023; 24:12715. [PMID: 37628896 PMCID: PMC10454756 DOI: 10.3390/ijms241612715] [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: 05/17/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
After cellular differentiation, nuclear DNA is no longer replicated, and many of the associated proteins are downregulated accordingly. These include the structure-specific endonucleases Fen1 and DNA2, which are implicated in repairing mitochondrial DNA (mtDNA). Two more such endonucleases, named MGME1 and ExoG, have been discovered in mitochondria. This category of nuclease is required for so-called "long-patch" (multinucleotide) base excision DNA repair (BER), which is necessary to process certain oxidative lesions, prompting the question of how differentiation affects the availability and use of these enzymes in mitochondria. In this study, we demonstrate that Fen1 and DNA2 are indeed strongly downregulated after differentiation of neuronal precursors (Cath.a-differentiated cells) or mouse myotubes, while the expression levels of MGME1 and ExoG showed minimal changes. The total flap excision activity in mitochondrial extracts of these cells was moderately decreased upon differentiation, with MGME1 as the predominant flap endonuclease and ExoG playing a lesser role. Unexpectedly, both differentiated cell types appeared to accumulate less oxidative or alkylation damage in mtDNA than did their proliferating progenitors. Finally, the overall rate of mtDNA repair was not significantly different between proliferating and differentiated cells. Taken together, these results indicate that neuronal cells maintain mtDNA repair upon differentiation, evidently relying on mitochondria-specific enzymes for long-patch BER.
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Affiliation(s)
- Rachel A. Caston
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Paola Fortini
- Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (P.F.)
| | - Kevin Chen
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jack Bauer
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Eugenia Dogliotti
- Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (P.F.)
| | - Y. Whitney Yin
- Department of Pharmacology and Toxicology, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Bruce Demple
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Radiation Oncology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
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2
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Lowder FC, Simmons LA. Bacillus subtilis encodes a discrete flap endonuclease that cleaves RNA-DNA hybrids. PLoS Genet 2023; 19:e1010585. [PMID: 37146086 PMCID: PMC10191290 DOI: 10.1371/journal.pgen.1010585] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/17/2023] [Accepted: 04/18/2023] [Indexed: 05/07/2023] Open
Abstract
The current model for Okazaki fragment maturation in bacteria invokes RNA cleavage by RNase H, followed by strand displacement synthesis and 5' RNA flap removal by DNA polymerase I (Pol I). RNA removal by Pol I is thought to occur through the 5'-3' flap endo/exonuclease (FEN) domain, located in the N-terminus of the protein. In addition to Pol I, many bacteria encode a second, Pol I-independent FEN. The contribution of Pol I and Pol I-independent FENs to DNA replication and genome stability remains unclear. In this work we purified Bacillus subtilis Pol I and FEN, then assayed these proteins on a variety of RNA-DNA hybrid and DNA-only substrates. We found that FEN is far more active than Pol I on nicked double-flap, 5' single flap, and nicked RNA-DNA hybrid substrates. We show that the 5' nuclease activity of B. subtilis Pol I is feeble, even during DNA synthesis when a 5' flapped substrate is formed modeling an Okazaki fragment intermediate. Examination of Pol I and FEN on DNA-only substrates shows that FEN is more active than Pol I on most substrates tested. Further experiments show that ΔpolA phenotypes are completely rescued by expressing the C-terminal polymerase domain while expression of the N-terminal 5' nuclease domain fails to complement ΔpolA. Cells lacking FEN (ΔfenA) show a phenotype in conjunction with an RNase HIII defect, providing genetic evidence for the involvement of FEN in Okazaki fragment processing. With these results, we propose a model where cells remove RNA primers using FEN while upstream Okazaki fragments are extended through synthesis by Pol I. Our model resembles Okazaki fragment processing in eukaryotes, where Pol δ catalyzes strand displacement synthesis followed by 5' flap cleavage using FEN-1. Together our work highlights the conservation of ordered steps for Okazaki fragment processing in cells ranging from bacteria to human.
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Affiliation(s)
- Frances Caroline Lowder
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lyle A. Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
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3
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Gu M, Yan Z, Wu X, Li Z, Dong Y, Wang GL. Trap remediation of CuBi 2O 4 nanopolyhedra via surface self-coordination by H 2O 2: an innovative signaling mode for cathodic photoelectrochemical bioassay. NANOSCALE 2023; 15:2954-2962. [PMID: 36722391 DOI: 10.1039/d2nr05588k] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
This work conveys a new philosophy of surface self-coordination mediated trap remediation for innovative cathodic photoelectrochemical (PEC) signal transduction. Initially, the surface trap states of CuBi2O4 nanopolyhedra resulting from dangling bonds can function as charge carrier recombination centers, which suppress the carrier separation efficiency and result in a low photocurrent output. Particularly, hydrogen peroxide (H2O2) spontaneously interacts with the uncoordinated Cu(II) on the surface of CuBi2O4, enabling efficient elimination of dangling bonds and remedy of trap states, thereby outputting intensified photocurrent readout. Exemplified by Flap endonuclease 1 (FEN1) as a model target, a tetrahedron DNA (THD)-based strand displacement amplification (SDA) was introduced to manipulate the formation of hemin impregnated G-quadruplex (G-quadruplex/hemin) DNAzyme and the resultant catalytic reduction for H2O2. In addition, a highly efficient and ultra-sensitive PEC sensing platform was achieved for FEN1 detection with a wide linear range from 1.0 fM to 100.0 pM and a detection limit of 0.3 fM (S/N = 3). This work not only establishes a new idea of cathodic PEC signal transduction, but also offers an efficient biosensing platform for FEN1.
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Affiliation(s)
- Mengmeng Gu
- Key Laboratory of Synthetic and Biological Colloids (Ministry of Education), School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122, China.
| | - Zhuying Yan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xiuming Wu
- Key Laboratory of Synthetic and Biological Colloids (Ministry of Education), School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122, China.
| | - Zaijun Li
- Key Laboratory of Synthetic and Biological Colloids (Ministry of Education), School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122, China.
| | - Yuming Dong
- Key Laboratory of Synthetic and Biological Colloids (Ministry of Education), School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122, China.
| | - Guang-Li Wang
- Key Laboratory of Synthetic and Biological Colloids (Ministry of Education), School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122, China.
- Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
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4
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Cheng X, Xia X, Ren D, Chen Q, Xu G, Wei F, Yang J, Wang L, Hu Q, Zou J, Cen Y. Programmable CRISPR-Cas12a and self-recruiting crRNA assisted dual biosensing platform for simultaneous detection of lung cancer biomarkers hOGG1 and FEN1. Anal Chim Acta 2023; 1240:340748. [PMID: 36641157 DOI: 10.1016/j.aca.2022.340748] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/18/2022] [Accepted: 12/22/2022] [Indexed: 12/27/2022]
Abstract
Human 8-oxoguanine DNA glycosylase (hOGG1) and flap endonuclease 1 (FEN1) are recognized as potential biomarkers in lung cancer investigations. Developing analytical platforms of simultaneously targeting hOGG1 and FEN1 with high selectivity, sensitivity, especially programmability and universality is highly valuable for clinical research. Herein, we established a signal-amplified platform for simultaneously detecting hOGG1 and FEN1 on the basis of cleavage-induced ligation of DNA dumbbell probes, rolling circle transcription (RCT) and CRISPR-Cas12a. A hOGG1 cleavable site and FEN1 cleavable flap were dexterously designed at the 5' end of DNA flapped dumbbell probes (FDP) for hOGG1 and FEN1. After cleavage, the resulting nick sites with juxtaposition of 5' phosphate and 3' hydroxyl terminus could be linked to closed DNA dumbbell probes (CDP) by DNA ligase. The CDP served as a template for RCT, producing plentiful crRNA repeats to activate the trans-cleavage activity of CRISPR-Cas12a which could cleave fluorophores (TAMRA and FAM) and quenchers (BHQ2 and BHQ1) double-labeled ssDNA reporters. Then, hOGG1 and FEN1 could be detected by the recovered fluorescence signal, allowing for the highly sensitive calculated detection limits of 0.0013 and 0.0052 U/mL, respectively. Additionally, this method made it possible to evaluate the inhibitory effects, even to measure hOGG1 and FEN1 activities at the single-cell level. This novel target enzyme-initiated, circles-transcription without promoters, real-time generation, and self-assembly features of FDP-RCT-Cas12a system suppressed nonspecific background remarkably and relieved rigorous requirement of protospacer adjacent motif site. Hence, the universality of FDP-RCT-Cas12a system toward various disease-related non-nucleic acid targets which are tested without using aptamers was extremely improved.
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Affiliation(s)
- Xia Cheng
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Department of Pharmacy, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, PR China
| | - Xinyi Xia
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Dandan Ren
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Qiutong Chen
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Guanhong Xu
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Fangdi Wei
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Jing Yang
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Lin Wang
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Qin Hu
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China.
| | - Jianjun Zou
- Department of Clinical Pharmacology, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, PR China.
| | - Yao Cen
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China.
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Laverde EE, Polyzos AA, Tsegay PP, Shaver M, Hutcheson JD, Balakrishnan L, McMurray CT, Liu Y. Flap Endonuclease 1 Endonucleolytically Processes RNA to Resolve R-Loops through DNA Base Excision Repair. Genes (Basel) 2022; 14:genes14010098. [PMID: 36672839 PMCID: PMC9859040 DOI: 10.3390/genes14010098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/30/2022] Open
Abstract
Flap endonuclease 1 (FEN1) is an essential enzyme that removes RNA primers and base lesions during DNA lagging strand maturation and long-patch base excision repair (BER). It plays a crucial role in maintaining genome stability and integrity. FEN1 is also implicated in RNA processing and biogenesis. A recent study from our group has shown that FEN1 is involved in trinucleotide repeat deletion by processing the RNA strand in R-loops through BER, further suggesting that the enzyme can modulate genome stability by facilitating the resolution of R-loops. However, it remains unknown how FEN1 can process RNA to resolve an R-loop. In this study, we examined the FEN1 cleavage activity on the RNA:DNA hybrid intermediates generated during DNA lagging strand processing and BER in R-loops. We found that both human and yeast FEN1 efficiently cleaved an RNA flap in the intermediates using its endonuclease activity. We further demonstrated that FEN1 was recruited to R-loops in normal human fibroblasts and senataxin-deficient (AOA2) fibroblasts, and its R-loop recruitment was significantly increased by oxidative DNA damage. We showed that FEN1 specifically employed its endonucleolytic cleavage activity to remove the RNA strand in an R-loop during BER. We found that FEN1 coordinated its DNA and RNA endonucleolytic cleavage activity with the 3'-5' exonuclease of APE1 to resolve the R-loop. Our results further suggest that FEN1 employed its unique tracking mechanism to endonucleolytically cleave the RNA strand in an R-loop by coordinating with other BER enzymes and cofactors during BER. Our study provides the first evidence that FEN1 endonucleolytic cleavage can result in the resolution of R-loops via the BER pathway, thereby maintaining genome integrity.
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Affiliation(s)
- Eduardo E. Laverde
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA
| | - Aris A. Polyzos
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Pawlos P. Tsegay
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA
| | - Mohammad Shaver
- Department of Biomedical Engineering, Florida International University, Miami, FL 33199, USA
| | - Joshua D. Hutcheson
- Department of Biomedical Engineering, Florida International University, Miami, FL 33199, USA
| | - Lata Balakrishnan
- Department of Biology, Indiana-Purdue University, Indianapolis, IN 46202, USA
| | - Cynthia T. McMurray
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yuan Liu
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
- Correspondence:
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6
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An ultrasensitive biosensing platform for FEN1 activity detection based on target-induced primer extension to trigger the collateral cleavage of CRISPR/Cas12a. Anal Chim Acta 2022; 1233:340519. [DOI: 10.1016/j.aca.2022.340519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/08/2022] [Accepted: 10/11/2022] [Indexed: 11/18/2022]
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Tang Y, Zhang D, Lu Y, Liu S, Zhang J, Pu Y, Wei W. Fluorescence imaging of FEN1 activity in living cells based on controlled-release of fluorescence probe from mesoporous silica nanoparticles. Biosens Bioelectron 2022; 214:114529. [DOI: 10.1016/j.bios.2022.114529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 06/10/2022] [Accepted: 06/29/2022] [Indexed: 11/02/2022]
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8
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Guo Y, Wang L, Qi Z, Liu Y, Tian K, Qiang H, Wang P, Zhou G, Zhang X, Xu S. A novel strategy for orthogonal genetic regulation on different RNA targeted loci simultaneously. RNA Biol 2022; 19:1172-1178. [PMID: 36350790 PMCID: PMC9648401 DOI: 10.1080/15476286.2022.2141507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
No current RNA-targeted interference tools have been reported to simultaneously up and down-regulate different gene expressions. Here we characterized an RNA-targeted genetic regulatory strategy composed of a flap endonuclease 1 (FEN1) and specific mis-hairpin DNA probes (mis-hpDNA), to realize the orthogonal genetic regulation. By targeting mRNA, the strategy hindered the translation and silenced genes in human cells with efficiencies of ~60%. By targeting miRNA, the strategy prevented the combination of miRNA to its specific mRNA and increased this mRNA expression by about 3-folds. In combination, we simultaneously performed CXCR4 gene knock-down (~50%) and EGFR gene activation (1.5-folds) in human cells. Although the functional property can be further improved, this RNA-targeted orthogonal genetic regulating strategy is complementary to classical tools.
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Affiliation(s)
- Yongjian Guo
- School of Basic Medical Science and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210000, China,School of Biopharmacy, China Pharmaceutical University, Nanjing, 210000, China
| | - Liang Wang
- School of Basic Medical Science and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210000, China,Institute of Binjiang, Zhejiang University, Hangzhou, 310053, China
| | - Zhen Qi
- School of Basic Medical Science and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210000, China,Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, 210000, China
| | - Yu Liu
- School of Basic Medical Science and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210000, China
| | - Kun Tian
- School of Basic Medical Science and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210000, China
| | - Huanran Qiang
- School of Basic Medical Science and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210000, China
| | - Pei Wang
- School of Basic Medical Science and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210000, China
| | - Guohua Zhou
- Department of Pharmacology, Jinling Hospital, Medical School, Nanjing University, Nanjing, 210000, China
| | - Xiaobo Zhang
- School of Basic Medical Science and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210000, China,CONTACT Xiaobo Zhang School of Basic Medical Science and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210000, China
| | - Shu Xu
- School of Basic Medical Science and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210000, China,Shu Xu School of Basic Medical Science and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210000, China
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Sobhy MA, Tehseen M, Takahashi M, Bralić A, De Biasio A, Hamdan SM. Implementing fluorescence enhancement, quenching, and FRET for investigating flap endonuclease 1 enzymatic reaction at the single-molecule level. Comput Struct Biotechnol J 2021; 19:4456-4471. [PMID: 34471492 PMCID: PMC8385120 DOI: 10.1016/j.csbj.2021.07.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/23/2021] [Accepted: 07/25/2021] [Indexed: 11/24/2022] Open
Abstract
Flap endonuclease 1 (FEN1) is an important component of the intricate molecular machinery for DNA replication and repair. FEN1 is a structure-specific 5' nuclease that cleaves nascent single-stranded 5' flaps during the maturation of Okazaki fragments. Here, we review our research primarily applying single-molecule fluorescence to resolve important mechanistic aspects of human FEN1 enzymatic reaction. The methodology presented in this review is aimed as a guide for tackling other biomolecular enzymatic reactions by fluorescence enhancement, quenching, and FRET and their combinations. Using these methods, we followed in real-time the structures of the substrate and product and 5' flap cleavage during catalysis. We illustrate that FEN1 actively bends the substrate to verify its features and continues to mold it to induce a protein disorder-to-order transitioning that controls active site assembly. This mechanism suppresses off-target cleavage of non-cognate substrates and promotes their dissociation with an accuracy that was underestimated from bulk assays. We determined that product release in FEN1 after the 5' flap release occurs in two steps; a brief binding to the bent nicked-product followed by longer binding to the unbent nicked-product before dissociation. Based on our cryo-electron microscopy structure of the human lagging strand replicase bound to FEN1, we propose how this two-step product release mechanism may regulate the final steps during the maturation of Okazaki fragments.
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Affiliation(s)
- Mohamed A Sobhy
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Muhammad Tehseen
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Masateru Takahashi
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Amer Bralić
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, 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
| | - Samir M Hamdan
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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10
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Yang H, Wang C, Xu E, Wei W, Liu Y, Liu S. Dual-Mode FEN1 Activity Detection Based on Nt.BstNBI-Induced Tandem Signal Amplification. Anal Chem 2021; 93:6567-6572. [PMID: 33847477 DOI: 10.1021/acs.analchem.1c00829] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Flap endonuclease 1 (FEN1) is a structure-specific nuclease that cleaves the 5' single-stranded protrusion (also known as 5' flap) during Okazaki fragment processing. It is overexpressed in various types of human cancer cells and has been considered as an important biomarker for cancer diagnosis. However, conventional methods for FEN1 assay usually suffer from complicated platform and laborious procedures with a limited sensitivity. Here, we developed a dual-signal method for sensitive detection of FEN1 on the basis of duplex-specific nuclease actuated cyclic enzymatic repairing-mediated signal amplification. Once the 5' flap of the double-flap DNA substrate was cleaved by target FEN1, the cleaved 5' flap initiated strand-displacement amplification to produce plenty of G-rich DNA (G) sequences. These G sequences that self-assembled into G-quadruplexes in the presence of hemin revealed horseradish-peroxidase-like catalytic activities as well as fluorescence enhancement of thioflavin T. The UV-vis signal showed a good linear relationship with the logarithm of FEN1 activity ranging from 0.03 to 1.5 U with a detection limit of 0.01 U. The fluorescence signal correlated linearly with the logarithm of FEN1 activity ranging from 0.001 to 1.5 U with a detection limit of 0.75 mU. In addition, FEN1 can be visualized not only by colorimetry but also by fluorescence (under ice-water mixture conditions). This reliable, accurate, and convenient method would be a potential powerful tool in point-of-care testing applications and therapeutic response assessment.
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Affiliation(s)
- Haitang Yang
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Chenchen Wang
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Ensheng Xu
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Wei Wei
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Yong Liu
- Henan Key Laboratory of Polyoxometalate Chemistry, College of Chemistry and Chemical Engineering, Henan University, Kaifeng 475004, China
| | - Songqin Liu
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
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11
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Li B, Xia A, Xie S, Lin L, Ji Z, Suo T, Zhang X, Huang H. Signal-Amplified Detection of the Tumor Biomarker FEN1 Based on Cleavage-Induced Ligation of a Dumbbell DNA Probe and Rolling Circle Amplification. Anal Chem 2021; 93:3287-3294. [PMID: 33529005 DOI: 10.1021/acs.analchem.0c05275] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Flap endonuclease 1 (FEN1), an endogenous nuclease with the ability to cleave the 5' overhang of branched dsDNA, is of significance in DNA replication and repair. The overexpression of FEN1 is common in cancer because of the ubiquitous upregulation of DNA replication; thus, FEN1 has been recognized as a potential biomarker in oncological investigations. However, few analytical methods targeting FEN1 with high sensitivity and simplicity have been developed. This work developed a signal-amplified detection of FEN1 based on the cleavage-induced ligation of a dumbbell DNA probe and rolling circle amplification (RCA). A flapped dumbbell DNA probe (FDP) was rationally designed with a FEN1 cleavable flap at the 5' end. The cleavage generated a nick site with juxtaposed 5' phosphate and 3' hydroxyl ends, which were linkable by T4 DNA ligase to form a closed dumbbell DNA probe (CDP) with a circular conformation. The CDP functioned as a template for RCA, which produced abundant DNA that could be probed using SYBR Green I. The highly sensitive detection of FEN1 with a limit of detection of 15 fM was achieved, and this method showed high specificity, which enabled the quantification of FEN1 in real samples. The inhibitory effects of chemicals on FEN1 were also evaluated. This study represents the first attempt to develop an FEN1 assay that involves signal amplification, and the novel biosensor method enriches the tools for FEN1-based diagnostics.
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Affiliation(s)
- Bingzhi Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Anqi Xia
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Siying Xie
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Lei Lin
- School of Environment, Nanjing Normal University, Nanjing 210023, China
| | - Zhirun Ji
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Tiying Suo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Xing Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
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12
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Tian K, Guo Y, Zou B, Wang L, Zhang Y, Qi Z, Zhou J, Wang X, Zhou G, Wei L, Xu S. DNA and RNA editing without sequence limitation using the flap endonuclease 1 guided by hairpin DNA probes. Nucleic Acids Res 2020; 48:e117. [PMID: 33051689 PMCID: PMC7672438 DOI: 10.1093/nar/gkaa843] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 09/11/2020] [Accepted: 09/19/2020] [Indexed: 12/26/2022] Open
Abstract
Here, we characterized a flap endonuclease 1 (FEN1) plus hairpin DNA probe (hpDNA) system, designated the HpSGN system, for both DNA and RNA editing without sequence limitation. The compact size of the HpSGN system make it an ideal candidate for in vivo delivery applications. In vitro biochemical studies showed that the HpSGN system required less nuclease to cleave ssDNA substrates than the SGN system we reported previously by a factor of ∼40. Also, we proved that the HpSGN system can efficiently cleave different RNA targets in vitro. The HpSGN system cleaved genomic DNA at an efficiency of ∼40% and ∼20% in bacterial and human cells, respectively, and knocked down specific mRNAs in human cells at a level of ∼25%. Furthermore, the HpSGN system was sensitive to the single base mismatch at the position next to the hairpin both in vitro and in vivo. Collectively, this study demonstrated the potential of developing the HpSGN system as a small, effective, and specific editing tool for manipulating both DNA and RNA without sequence limitation.
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Affiliation(s)
| | | | | | - Liang Wang
- School of Basic Medical Science and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210000, China
| | - Yun Zhang
- School of Basic Medical Science and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210000, China
| | - Zhen Qi
- School of Basic Medical Science and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210000, China
| | - Jieying Zhou
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA
| | - Xiaotang Wang
- Correspondence may also be addressed to Xiaotang Wang.
| | - Guohua Zhou
- Correspondence may also be addressed to Guohua Zhou.
| | - Libin Wei
- Correspondence may also be addressed to Libin Wei.
| | - Shu Xu
- To whom correspondence should be addressed.
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13
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Wang C, Zhang D, Tang Y, Wei W, Liu Y, Liu S. Label-Free Imaging of Flap Endonuclease 1 in Living Cells by Assembling Original and Multifunctional Nanoprobe. ACS APPLIED BIO MATERIALS 2020; 3:4573-4580. [DOI: 10.1021/acsabm.0c00494] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Chenchen Wang
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Duoduo Zhang
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Yunfei Tang
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Wei Wei
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Yong Liu
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng 475004, China
| | - Songqin Liu
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
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14
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Khristich AN, Mirkin SM. On the wrong DNA track: Molecular mechanisms of repeat-mediated genome instability. J Biol Chem 2020; 295:4134-4170. [PMID: 32060097 PMCID: PMC7105313 DOI: 10.1074/jbc.rev119.007678] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Expansions of simple tandem repeats are responsible for almost 50 human diseases, the majority of which are severe, degenerative, and not currently treatable or preventable. In this review, we first describe the molecular mechanisms of repeat-induced toxicity, which is the connecting link between repeat expansions and pathology. We then survey alternative DNA structures that are formed by expandable repeats and review the evidence that formation of these structures is at the core of repeat instability. Next, we describe the consequences of the presence of long structure-forming repeats at the molecular level: somatic and intergenerational instability, fragility, and repeat-induced mutagenesis. We discuss the reasons for gender bias in intergenerational repeat instability and the tissue specificity of somatic repeat instability. We also review the known pathways in which DNA replication, transcription, DNA repair, and chromatin state interact and thereby promote repeat instability. We then discuss possible reasons for the persistence of disease-causing DNA repeats in the genome. We describe evidence suggesting that these repeats are a payoff for the advantages of having abundant simple-sequence repeats for eukaryotic genome function and evolvability. Finally, we discuss two unresolved fundamental questions: (i) why does repeat behavior differ between model systems and human pedigrees, and (ii) can we use current knowledge on repeat instability mechanisms to cure repeat expansion diseases?
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Affiliation(s)
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, Massachusetts 02155.
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15
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Zheng L, Meng Y, Campbell JL, Shen B. Multiple roles of DNA2 nuclease/helicase in DNA metabolism, genome stability and human diseases. Nucleic Acids Res 2020; 48:16-35. [PMID: 31754720 PMCID: PMC6943134 DOI: 10.1093/nar/gkz1101] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 10/23/2019] [Accepted: 11/12/2019] [Indexed: 12/25/2022] Open
Abstract
DNA2 nuclease/helicase is a structure-specific nuclease, 5'-to-3' helicase, and DNA-dependent ATPase. It is involved in multiple DNA metabolic pathways, including Okazaki fragment maturation, replication of 'difficult-to-replicate' DNA regions, end resection, stalled replication fork processing, and mitochondrial genome maintenance. The participation of DNA2 in these different pathways is regulated by its interactions with distinct groups of DNA replication and repair proteins and by post-translational modifications. These regulatory mechanisms induce its recruitment to specific DNA replication or repair complexes, such as DNA replication and end resection machinery, and stimulate its efficient cleavage of various structures, for example, to remove RNA primers or to produce 3' overhangs at telomeres or double-strand breaks. Through these versatile activities at replication forks and DNA damage sites, DNA2 functions as both a tumor suppressor and promoter. In normal cells, it suppresses tumorigenesis by maintaining the genomic integrity. Thus, DNA2 mutations or functional deficiency may lead to cancer initiation. However, DNA2 may also function as a tumor promoter, supporting cancer cell survival by counteracting replication stress. Therefore, it may serve as an ideal target to sensitize advanced DNA2-overexpressing cancers to current chemo- and radiotherapy regimens.
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Affiliation(s)
- Li Zheng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Yuan Meng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Judith L Campbell
- Divisions of Chemistry and Chemical Engineering and Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
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16
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Muzzamal H, Ul Ain Q, Saeed MS, Rashid N. Gene cloning and characterization of Tk1281, a flap endonuclease 1 from Thermococcus kodakarensis. Folia Microbiol (Praha) 2019; 65:407-415. [PMID: 31401764 DOI: 10.1007/s12223-019-00745-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/29/2019] [Indexed: 11/25/2022]
Abstract
Flap endonuclease is a structure-specific nuclease which cleaves 5'-flap of bifurcated DNA substrates. Genome sequence of Thermococcus kodakarensis harbors an open reading frame, Tk1281, exhibiting high homology with archaeal flap endonucleases 1. The corresponding gene was cloned and expressed in Escherichia coli, and the gene product was purified to apparent homogeneity. Tk1281 was a monomer of 38 kDa and catalyzed the cleavage of 5'-flap from double-stranded DNA substrate containing single-stranded DNA flap. The highest cleavage activity was observed at 80 °C and pH 7.5. Under optimal conditions, Tk1281 exhibited apparent Vmax and Km values of 278 nmol/min/mg and 37 μM, respectively, against a 54-nucleotide double-stranded substrate containing a single-stranded 5'-flap of 27 nucleotides. A unique feature of Tk1281 is its highest activation in the presence of Co2+ and no activation with Mn2+. To the best of our knowledge, this is the first cloning and characterization of a flap endonuclease from the genus Thermococcus.
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Affiliation(s)
- Hira Muzzamal
- School of Biological Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Qurat Ul Ain
- School of Biological Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | | | - Naeem Rashid
- School of Biological Sciences, University of the Punjab, Lahore, 54590, Pakistan.
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17
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Zaher MS, Rashid F, Song B, Joudeh LI, Sobhy MA, Tehseen M, Hingorani MM, Hamdan SM. Missed cleavage opportunities by FEN1 lead to Okazaki fragment maturation via the long-flap pathway. Nucleic Acids Res 2019; 46:2956-2974. [PMID: 29420814 PMCID: PMC5888579 DOI: 10.1093/nar/gky082] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 01/27/2018] [Indexed: 12/11/2022] Open
Abstract
RNA–DNA hybrid primers synthesized by low fidelity DNA polymerase α to initiate eukaryotic lagging strand synthesis must be removed efficiently during Okazaki fragment (OF) maturation to complete DNA replication. In this process, each OF primer is displaced and the resulting 5′-single-stranded flap is cleaved by structure-specific 5′-nucleases, mainly Flap Endonuclease 1 (FEN1), to generate a ligatable nick. At least two models have been proposed to describe primer removal, namely short- and long-flap pathways that involve FEN1 or FEN1 along with Replication Protein A (RPA) and Dna2 helicase/nuclease, respectively. We addressed the question of pathway choice by studying the kinetic mechanism of FEN1 action on short- and long-flap DNA substrates. Using single molecule FRET and rapid quench-flow bulk cleavage assays, we showed that unlike short-flap substrates, which are bound, bent and cleaved within the first encounter between FEN1 and DNA, long-flap substrates can escape cleavage even after DNA binding and bending. Notably, FEN1 can access both substrates in the presence of RPA, but bending and cleavage of long-flap DNA is specifically inhibited. We propose that FEN1 attempts to process both short and long flaps, but occasional missed cleavage of the latter allows RPA binding and triggers the long-flap OF maturation pathway.
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Affiliation(s)
- Manal S Zaher
- King Abdullah University of Science and Technology, Division of Biological and Environmental Science and Engineering, Thuwal 23955, Saudi Arabia
| | - Fahad Rashid
- King Abdullah University of Science and Technology, Division of Biological and Environmental Science and Engineering, Thuwal 23955, Saudi Arabia
| | - Bo Song
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Luay I Joudeh
- King Abdullah University of Science and Technology, Division of Biological and Environmental Science and Engineering, Thuwal 23955, Saudi Arabia
| | - Mohamed A Sobhy
- King Abdullah University of Science and Technology, Division of Biological and Environmental Science and Engineering, Thuwal 23955, Saudi Arabia
| | - Muhammad Tehseen
- King Abdullah University of Science and Technology, Division of Biological and Environmental Science and Engineering, Thuwal 23955, Saudi Arabia
| | - Manju M Hingorani
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Samir M Hamdan
- King Abdullah University of Science and Technology, Division of Biological and Environmental Science and Engineering, Thuwal 23955, Saudi Arabia
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18
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Bennet IA, Finger LD, Baxter NJ, Ambrose B, Hounslow AM, Thompson MJ, Exell JC, Shahari NNBM, Craggs TD, Waltho JP, Grasby JA. Regional conformational flexibility couples substrate specificity and scissile phosphate diester selectivity in human flap endonuclease 1. Nucleic Acids Res 2019; 46:5618-5633. [PMID: 29718417 PMCID: PMC6009646 DOI: 10.1093/nar/gky293] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 04/09/2018] [Indexed: 02/07/2023] Open
Abstract
Human flap endonuclease-1 (hFEN1) catalyzes the divalent metal ion-dependent removal of single-stranded DNA protrusions known as flaps during DNA replication and repair. Substrate selectivity involves passage of the 5'-terminus/flap through the arch and recognition of a single nucleotide 3'-flap by the α2-α3 loop. Using NMR spectroscopy, we show that the solution conformation of free and DNA-bound hFEN1 are consistent with crystal structures; however, parts of the arch region and α2-α3 loop are disordered without substrate. Disorder within the arch explains how 5'-flaps can pass under it. NMR and single-molecule FRET data show a shift in the conformational ensemble in the arch and loop region upon addition of DNA. Furthermore, the addition of divalent metal ions to the active site of the hFEN1-DNA substrate complex demonstrates that active site changes are propagated via DNA-mediated allostery to regions key to substrate differentiation. The hFEN1-DNA complex also shows evidence of millisecond timescale motions in the arch region that may be required for DNA to enter the active site. Thus, hFEN1 regional conformational flexibility spanning a range of dynamic timescales is crucial to reach the catalytically relevant ensemble.
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Affiliation(s)
- Ian A Bennet
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
| | - L David Finger
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
| | - Nicola J Baxter
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S10 2TN, UK.,Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester M1 7DN, UK
| | - Benjamin Ambrose
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
| | - Andrea M Hounslow
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S10 2TN, UK
| | - Mark J Thompson
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
| | - Jack C Exell
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
| | - Nur Nazihah B Md Shahari
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
| | - Timothy D Craggs
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
| | - Jonathan P Waltho
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S10 2TN, UK.,Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester M1 7DN, UK
| | - Jane A Grasby
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
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19
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Algasaier SI, Finger LD, Bennet IA, Grasby JA. Flap Endonuclease 1 Mutations A159V and E160D Cause Genomic Instability by Slowing Reaction on Double-Flap Substrates. Biochemistry 2018; 57:6838-6847. [DOI: 10.1021/acs.biochem.8b00891] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Sana I. Algasaier
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Sheffield S3 7HF, U.K
| | - L. David Finger
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Sheffield S3 7HF, U.K
| | - Ian A. Bennet
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Sheffield S3 7HF, U.K
| | - Jane A. Grasby
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Sheffield S3 7HF, U.K
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20
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Mayanagi K, Ishino S, Shirai T, Oyama T, Kiyonari S, Kohda D, Morikawa K, Ishino Y. Direct visualization of DNA baton pass between replication factors bound to PCNA. Sci Rep 2018; 8:16209. [PMID: 30385773 PMCID: PMC6212441 DOI: 10.1038/s41598-018-34176-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 10/12/2018] [Indexed: 11/18/2022] Open
Abstract
In Eukarya and Archaea, the lagging strand synthesis is accomplished mainly by three key factors, DNA polymerase (Pol), flap endonuclease (FEN), and DNA ligase (Lig), in the DNA replication process. These three factors form important complexes with proliferating cell nuclear antigen (PCNA), thereby constructing a platform that enable each protein factor to act successively and smoothly on DNA. The structures of the Pol-PCNA-DNA and Lig-PCNA-DNA complexes alone have been visualized by single particle analysis. However, the FEN-PCNA-DNA complex structure remains unknown. In this report, we for the first time present this tertiary structure determined by single particle analysis. We also successfully visualized the structure of the FEN-Lig-PCNA-DNA complex, corresponding to a putative intermediate state between the removal of the DNA flap by FEN and the sealing of the nicked DNA by Lig. This structural study presents the direct visualization of the handing-over action, which proceeds between different replication factors on a single PCNA clamp bound to DNA. We detected a drastic conversion of the DNA from a bent form to a straight form, in addition to the dynamic motions of replication factors in the switching process.
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Affiliation(s)
- Kouta Mayanagi
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan.
| | - Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Tsuyoshi Shirai
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Tamura 1266, Nagahama, Shiga, 526-0829, Japan
| | - Takuji Oyama
- Faculty of Life and Environmental Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi, 400-8510, Japan
| | - Shinichi Kiyonari
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Daisuke Kohda
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Kosuke Morikawa
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Yoshida-konoemachi, Sakyo-ku, Kyoto, 606-8501, Japan.
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
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21
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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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22
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Rashid F, Harris PD, Zaher MS, Sobhy MA, Joudeh LI, Yan C, Piwonski H, Tsutakawa SE, Ivanov I, Tainer JA, Habuchi S, Hamdan SM. Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1. eLife 2017; 6. [PMID: 28230529 PMCID: PMC5358979 DOI: 10.7554/elife.21884] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 02/20/2017] [Indexed: 12/21/2022] Open
Abstract
Human flap endonuclease 1 (FEN1) and related structure-specific 5’nucleases precisely identify and incise aberrant DNA structures during replication, repair and recombination to avoid genomic instability. Yet, it is unclear how the 5’nuclease mechanisms of DNA distortion and protein ordering robustly mediate efficient and accurate substrate recognition and catalytic selectivity. Here, single-molecule sub-millisecond and millisecond analyses of FEN1 reveal a protein-DNA induced-fit mechanism that efficiently verifies substrate and suppresses off-target cleavage. FEN1 sculpts DNA with diffusion-limited kinetics to test DNA substrate. This DNA distortion mutually ‘locks’ protein and DNA conformation and enables substrate verification with extreme precision. Strikingly, FEN1 never misses cleavage of its cognate substrate while blocking probable formation of catalytically competent interactions with noncognate substrates and fostering their pre-incision dissociation. These findings establish FEN1 has practically perfect precision and that separate control of induced-fit substrate recognition sets up the catalytic selectivity of the nuclease active site for genome stability. DOI:http://dx.doi.org/10.7554/eLife.21884.001 When a cell divides it must copy its genetic information, which is found in the form of strands of DNA. Damage to the DNA may lead to cancer or a number of genetic diseases. However, every time a cell divides more than 10 million toxic “flaps” of excess DNA are generated. A protein called flap endonuclease 1 (FEN1) keeps the DNA in good repair by cutting off the flaps in a highly specific and selective manner. Many proteins that interact with DNA are attracted to specific genetic sequences within the DNA strands. However, this is not the case for FEN1 and several other “structure-specific” proteins that help to repair and replicate DNA strands. So how do these proteins select the correct regions of DNA to interact with? Rashid et al. used single-molecule fluorescence measurements to examine how purified FEN1 proteins interact with DNA flaps. The results show that FEN1 can perfectly recognize and correctly remove flaps through a process called “mutual-induced fit”, where the DNA and FEN1 are shaped by each other to produce a highly specific structure. Further work is now needed to examine whether other proteins that are related to FEN1 use a similar process to ensure that they always cut DNA in the same way. More detailed and direct examination of the structure of FEN1 through other experimental methods may also help to reveal how the mutual-induced fit process enables FEN1 to achieve such high levels of precision. This could increase our understanding of how problems with FEN1 and similar proteins lead to different genetic diseases. DOI:http://dx.doi.org/10.7554/eLife.21884.002
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Affiliation(s)
- Fahad Rashid
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Paul D Harris
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Manal S Zaher
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Mohamed A Sobhy
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Luay I Joudeh
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Chunli Yan
- Department of Chemistry, Georgia State University, Atlanta, United States.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, United States
| | - Hubert Piwonski
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | | | - Ivaylo Ivanov
- Department of Chemistry, Georgia State University, Atlanta, United States.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, United States
| | - John A Tainer
- Lawrence Berkeley National Laboratory, Berkeley, United States.,Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, United States
| | - Satoshi Habuchi
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Samir M Hamdan
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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23
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Ponce I, Aldunate C, Valenzuela L, Sepúlveda S, Garrido G, Kemmerling U, Cabrera G, Galanti N. A Flap Endonuclease (TcFEN1) Is Involved in Trypanosoma cruzi
Cell Proliferation, DNA Repair, and Parasite Survival. J Cell Biochem 2016; 118:1722-1732. [DOI: 10.1002/jcb.25830] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 12/07/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Ivan Ponce
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina; Universidad de Chile; Santiago 8380453 Chile
| | - Carmen Aldunate
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina; Universidad de Chile; Santiago 8380453 Chile
| | - Lucia Valenzuela
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina; Universidad de Chile; Santiago 8380453 Chile
| | - Sofia Sepúlveda
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina; Universidad de Chile; Santiago 8380453 Chile
| | - Gilda Garrido
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina; Universidad de Chile; Santiago 8380453 Chile
| | - Ulrike Kemmerling
- Programa de Anatomía y Biología del Desarrollo, Instituto de Ciencias Biomédicas, Facultad de Medicina; Universidad de Chile; Santiago 8380453 Chile
| | - Gonzalo Cabrera
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina; Universidad de Chile; Santiago 8380453 Chile
| | - Norbel Galanti
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina; Universidad de Chile; Santiago 8380453 Chile
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24
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He L, Zhang Y, Sun H, Jiang F, Yang H, Wu H, Zhou T, Hu S, Kathera CS, Wang X, Chen H, Li H, Shen B, Zhu Y, Guo Z. Targeting DNA Flap Endonuclease 1 to Impede Breast Cancer Progression. EBioMedicine 2016; 14:32-43. [PMID: 27852524 PMCID: PMC5161424 DOI: 10.1016/j.ebiom.2016.11.012] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 11/04/2016] [Accepted: 11/07/2016] [Indexed: 11/26/2022] Open
Abstract
DNA flap endonuclease 1 (FEN1) plays critical roles in maintaining genome stability and integrity by participating in both DNA replication and repair. Suppression of FEN1 in cells leads to the retardation of DNA replication and accumulation of unrepaired DNA intermediates, resulting in DNA double strand breaks (DSBs) and apoptosis. Therefore, targeting FEN1 could serve as a potent strategy for cancer therapy. In this study, we demonstrated that FEN1 is overexpressed in breast cancers and is essential for rapid proliferation of cancer cells. We showed that manipulating FEN1 levels in cells alters the response of cancer cells to chemotherapeutic drugs. Furthermore, we identified a small molecular compound, SC13 that specifically inhibits FEN1 activity, thereby interfering with DNA replication and repair in vitro and in cells. SC13 suppresses cancer cell proliferation and induces chromosome instability and cytotoxicity in cells. Importantly, SC13 sensitizes cancer cells to DNA damage-inducing therapeutic modalities and impedes cancer progression in a mouse model. These findings could establish a paradigm for the treatment of breast cancer and other cancers as well. FEN1 is overexpressed in cancer cells and essential for cancer cell growth; Down regulation of FEN1 leads to retarded cell growth and sensitizes cancer cells to chemotherapeutic agents; SC13, a FEN1 specific inhibitor, inhibits cancer growth in vitro and in xenograft tumor mice. Most anticancer agents used in clinic today kill cells by interfering DNA replication or inducing DNA damage, which in turn lead to cell apoptosis. However, cancer cells have evolved a compilation of highly effective DNA replication and repair systems to meet up the requirement of rapidly dividing of cancer cells and protect DNA against both endogenous and exogenous DNA damage. FEN1 has been shown to be an important factor in both DNA replication and repair pathways, making FEN1 a logical target for developing anticancer drugs as stand-alone agents for treating cancers that rely on its activity and as a therapy in combination with chemotherapeutic agents that cause DNA damage.
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Affiliation(s)
- Lingfeng He
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Yilan Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Hongfang Sun
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Feng Jiang
- Department of Thoracic Surgery, Jiangsu Cancer Hospital, Affiliated Cancer Hospital of Nanjing Medical University, Nanjing 210000, China
| | - Huan Yang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Huan Wu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Ting Zhou
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Sencai Hu
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, Hubei, China
| | - Chandra Sekhar Kathera
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Xiaojun Wang
- Isotope Laboratory, College of Life Science, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Haoyan Chen
- Division of Gastroenterology and Hepatology, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, China
| | - Hongzhi Li
- Department of Molecular Medicine, City of Hope National Medical Center and Beckman Research Institute, Duarte 91010, CA, USA
| | - Binghui Shen
- Department of Molecular Medicine, City of Hope National Medical Center and Beckman Research Institute, Duarte 91010, CA, USA; Department of Radiation Biology, City of Hope National Medical Center and Beckman Research Institute, Duarte 91010, CA, USA
| | - Yongqiang Zhu
- Center for New Drug Research & Development, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Zhigang Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China.
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25
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Sebesta M, Urulangodi M, Stefanovie B, Szakal B, Pacesa M, Lisby M, Branzei D, Krejci L. Esc2 promotes Mus81 complex-activity via its SUMO-like and DNA binding domains. Nucleic Acids Res 2016; 45:215-230. [PMID: 27694623 PMCID: PMC5224511 DOI: 10.1093/nar/gkw882] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 08/30/2016] [Accepted: 09/22/2016] [Indexed: 01/17/2023] Open
Abstract
Replication across damaged DNA templates is accompanied by transient formation of sister chromatid junctions (SCJs). Cells lacking Esc2, an adaptor protein containing no known enzymatic domains, are defective in the metabolism of these SCJs. However, how Esc2 is involved in the metabolism of SCJs remains elusive. Here we show interaction between Esc2 and a structure-specific endonuclease Mus81-Mms4 (the Mus81 complex), their involvement in the metabolism of SCJs, and the effects Esc2 has on the enzymatic activity of the Mus81 complex. We found that Esc2 specifically interacts with the Mus81 complex via its SUMO-like domains, stimulates enzymatic activity of the Mus81 complex in vitro, and is involved in the Mus81 complex-dependent resolution of SCJs in vivo. Collectively, our data point to the possibility that the involvement of Esc2 in the metabolism of SCJs is, in part, via modulation of the activity of the Mus81 complex.
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Affiliation(s)
- Marek Sebesta
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic.,Department of Biology, Masaryk University, Kamenice 5/A7, CZ-62500 Brno, Czech Republic.,IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, IT-20139 Milan, Italy
| | | | - Barbora Stefanovie
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic.,Department of Biology, Masaryk University, Kamenice 5/A7, CZ-62500 Brno, Czech Republic.,International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, Pekarska 53, CZ-656 91 Brno, Czech Republic
| | - Barnabas Szakal
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, IT-20139 Milan, Italy
| | - Martin Pacesa
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic
| | - Michael Lisby
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Dana Branzei
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, IT-20139 Milan, Italy
| | - Lumir Krejci
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic .,Department of Biology, Masaryk University, Kamenice 5/A7, CZ-62500 Brno, Czech Republic.,International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, Pekarska 53, CZ-656 91 Brno, Czech Republic
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26
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Xu S, Cao S, Zou B, Yue Y, Gu C, Chen X, Wang P, Dong X, Xiang Z, Li K, Zhu M, Zhao Q, Zhou G. An alternative novel tool for DNA editing without target sequence limitation: the structure-guided nuclease. Genome Biol 2016; 17:186. [PMID: 27634179 PMCID: PMC5025552 DOI: 10.1186/s13059-016-1038-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/05/2016] [Indexed: 01/31/2023] Open
Abstract
Engineered endonucleases are a powerful tool for editing DNA. However, sequence preferences may limit their application. We engineer a structure-guided endonuclease (SGN) composed of flap endonuclease-1 (FEN-1), which recognizes the 3′ flap structure, and the cleavage domain of Fok I (Fn1), which cleaves DNA strands. The SGN recognizes the target DNA on the basis of the 3′ flap structure formed between the target and the guide DNA (gDNA) and cut the target through its Fn1 dimerization. Our results show that the SGN, guided by a pair of gDNAs, cleaves transgenic reporter gene and endogenous genes in zebrafish embryonic genome.
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Affiliation(s)
- Shu Xu
- Department of Pharmacology, Jinling Hospital, School of Medicine, Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, People's Republic of China
| | - Shasha Cao
- MOE Key Laboratory of Model Animal for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing, 210061, People's Republic of China
| | - Bingjie Zou
- Department of Pharmacology, Jinling Hospital, School of Medicine, Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, People's Republic of China
| | - Yunyun Yue
- MOE Key Laboratory of Model Animal for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing, 210061, People's Republic of China
| | - Chun Gu
- MOE Key Laboratory of Model Animal for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing, 210061, People's Republic of China
| | - Xin Chen
- MOE Key Laboratory of Model Animal for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing, 210061, People's Republic of China
| | - Pei Wang
- MOE Key Laboratory of Model Animal for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing, 210061, People's Republic of China
| | - Xiaohua Dong
- MOE Key Laboratory of Model Animal for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing, 210061, People's Republic of China
| | - Zheng Xiang
- Department of Pharmacology, Jinling Hospital, School of Medicine, Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, People's Republic of China
| | - Kai Li
- College of Pharmaceutical Science, Soochow University, No. 199, Renai Road, Suzhou, 215123, People's Republic of China
| | - Minsheng Zhu
- MOE Key Laboratory of Model Animal for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing, 210061, People's Republic of China.
| | - Qingshun Zhao
- MOE Key Laboratory of Model Animal for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing, 210061, People's Republic of China.
| | - Guohua Zhou
- Department of Pharmacology, Jinling Hospital, School of Medicine, Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, People's Republic of China.
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27
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Uhler JP, Thörn C, Nicholls TJ, Matic S, Milenkovic D, Gustafsson CM, Falkenberg M. MGME1 processes flaps into ligatable nicks in concert with DNA polymerase γ during mtDNA replication. Nucleic Acids Res 2016; 44:5861-71. [PMID: 27220468 PMCID: PMC4937333 DOI: 10.1093/nar/gkw468] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 05/11/2016] [Accepted: 05/13/2016] [Indexed: 12/17/2022] Open
Abstract
Recently, MGME1 was identified as a mitochondrial DNA nuclease with preference for single-stranded DNA (ssDNA) substrates. Loss-of-function mutations in patients lead to mitochondrial disease with DNA depletion, deletions, duplications and rearrangements. Here, we assess the biochemical role of MGME1 in the processing of flap intermediates during mitochondrial DNA replication using reconstituted systems. We show that MGME1 can cleave flaps to enable efficient ligation of newly replicated DNA strands in combination with POLγ. MGME1 generates a pool of imprecisely cut products (short flaps, nicks and gaps) that are converted to ligatable nicks by POLγ through extension or excision of the 3'-end strand. This is dependent on the 3'-5' exonuclease activity of POLγ which limits strand displacement activity and enables POLγ to back up to the nick by 3'-5' degradation. We also demonstrate that POLγ-driven strand displacement is sufficient to generate DNA- but not RNA-flap substrates suitable for MGME1 cleavage and ligation during replication. Our findings have implications for RNA primer removal models, the 5'-end processing of nascent DNA at OriH, and DNA repair.
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Affiliation(s)
- Jay P Uhler
- Institute of Biomedicine, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Christian Thörn
- Institute of Biomedicine, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Thomas J Nicholls
- Institute of Biomedicine, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Stanka Matic
- Max Planck Institute for Biology of Ageing, 50391 Cologne, Germany
| | | | - Claes M Gustafsson
- Institute of Biomedicine, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Maria Falkenberg
- Institute of Biomedicine, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
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28
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Resolving individual steps of Okazaki-fragment maturation at a millisecond timescale. Nat Struct Mol Biol 2016; 23:402-8. [PMID: 27065195 PMCID: PMC4857878 DOI: 10.1038/nsmb.3207] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/18/2016] [Indexed: 11/08/2022]
Abstract
DNA polymerase delta (Pol δ) is responsible for elongation and maturation of Okazaki fragments. Pol δ and the flap endonuclease FEN1, coordinated by the PCNA clamp, remove RNA primers and produce ligatable nicks. We studied this process in the Saccharomyces cerevisiae machinery at millisecond resolution. During elongation, PCNA increased the Pol δ catalytic rate by >30-fold. When Pol δ invaded double-stranded RNA-DNA representing unmatured Okazaki fragments, the incorporation rate of each nucleotide decreased successively to 10-20% that of the preceding nucleotide. Thus, the nascent flap acts as a progressive molecular brake on the polymerase, and consequently FEN1 cuts predominantly single-nucleotide flaps. Kinetic and enzyme-trapping experiments support a model in which a stable PCNA-DNA-Pol δ-FEN1 complex moves processively through iterative steps of nick translation, ultimately completely removing primer RNA. Finally, whereas elongation rates are under dynamic dNTP control, maturation rates are buffered against changes in dNTP concentrations.
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29
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Cheng IC, Chen BC, Shuai HH, Chien FC, Chen P, Hsieh TS. Wuho Is a New Member in Maintaining Genome Stability through its Interaction with Flap Endonuclease 1. PLoS Biol 2016; 14:e1002349. [PMID: 26751069 PMCID: PMC4709127 DOI: 10.1371/journal.pbio.1002349] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 12/04/2015] [Indexed: 11/18/2022] Open
Abstract
Replication forks are vulnerable to wayward nuclease activities. We report here our discovery of a new member in guarding genome stability at replication forks. We previously isolated a Drosophila mutation, wuho (wh, no progeny), characterized by a severe fertility defect and affecting expression of a protein (WH) in a family of conserved proteins with multiple WD40 repeats. Knockdown of WH by siRNA in Drosophila, mouse, and human cultured cells results in DNA damage with strand breaks and apoptosis through ATM/Chk2/p53 signaling pathway. Mice with mWh knockout are early embryonic lethal and display DNA damage. We identify that the flap endonuclease 1 (FEN1) is one of the interacting proteins. Fluorescence microscopy showed the localization of WH at the site of nascent DNA synthesis along with other replication proteins, including FEN1 and PCNA. We show that WH is able to modulate FEN1's endonucleolytic activities depending on the substrate DNA structure. The stimulatory or inhibitory effects of WH on FEN1's flap versus gap endonuclease activities are consistent with the proposed WH's functions in protecting the integrity of replication fork. These results suggest that wh is a new member of the guardians of genome stability because it regulates FEN1's potential DNA cleavage threat near the site of replication.
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Affiliation(s)
- I-Cheng Cheng
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Betty Chamay Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Hung-Hsun Shuai
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Fan-Ching Chien
- Department of Optics and Photonics, National Central University, Chung-Li, Taiwan
| | - Peilin Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
| | - Tao-shih Hsieh
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.,Department of Biochemistry, Duke University, Durham, North Carolina, United States of America
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30
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Zhang Y, Wen C, Liu S, Zheng L, Shen B, Tao Y. Shade avoidance 6 encodes an Arabidopsis flap endonuclease required for maintenance of genome integrity and development. Nucleic Acids Res 2015; 44:1271-84. [PMID: 26721386 PMCID: PMC4756833 DOI: 10.1093/nar/gkv1474] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 12/03/2015] [Indexed: 12/01/2022] Open
Abstract
Flap endonuclease-1 (FEN1) belongs to the Rad2 family of structure-specific nucleases. It is required for several DNA metabolic pathways, including DNA replication and DNA damage repair. Here, we have identified a shade avoidance mutant, sav6, which reduces the mRNA splicing efficiency of SAV6. We have demonstrated that SAV6 is an FEN1 homologue that shows double-flap endonuclease and gap-dependent endonuclease activity, but lacks exonuclease activity. sav6 mutants are hypersensitive to DNA damage induced by ultraviolet (UV)-C radiation and reagents that induce double-stranded DNA breaks, but exhibit normal responses to chemicals that block DNA replication. Signalling components that respond to DNA damage are constitutively activated in sav6 mutants. These data indicate that SAV6 is required for DNA damage repair and the maintenance of genome integrity. Mutant sav6 plants also show reduced root apical meristem (RAM) size and defective quiescent centre (QC) development. The expression of SMR7, a cell cycle regulatory gene, and ERF115 and PSK5, regulators of QC division, is increased in sav6 mutants. Their constitutive induction is likely due to the elevated DNA damage responses in sav6 and may lead to defects in the development of the RAM and QC. Therefore, SAV6 assures proper root development through maintenance of genome integrity.
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Affiliation(s)
- Yijuan Zhang
- School of Life Sciences, Xiamen Plant Genetics Key Laboratory, Xiamen University, Xiamen 361102, China State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen 361102, China
| | - Chunhong Wen
- School of Life Sciences, Xiamen Plant Genetics Key Laboratory, Xiamen University, Xiamen 361102, China
| | - Songbai Liu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA College of Life Sciences, Zhejiang University, Hangzhou, China Suzhou Health College, Suzhou Key Laboratory of Biotechnology for Laboratory Medicine, Suzhou, 215009, Jiangsu Province, China
| | - Li Zheng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Yi Tao
- School of Life Sciences, Xiamen Plant Genetics Key Laboratory, Xiamen University, Xiamen 361102, China State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen 361102, China
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31
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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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32
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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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33
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Tarantino ME, Bilotti K, Huang J, Delaney S. Rate-determining Step of Flap Endonuclease 1 (FEN1) Reflects a Kinetic Bias against Long Flaps and Trinucleotide Repeat Sequences. J Biol Chem 2015; 290:21154-21162. [PMID: 26160176 DOI: 10.1074/jbc.m115.666438] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Indexed: 11/06/2022] Open
Abstract
Flap endonuclease 1 (FEN1) is a structure-specific nuclease responsible for removing 5'-flaps formed during Okazaki fragment maturation and long patch base excision repair. In this work, we use rapid quench flow techniques to examine the rates of 5'-flap removal on DNA substrates of varying length and sequence. Of particular interest are flaps containing trinucleotide repeats (TNR), which have been proposed to affect FEN1 activity and cause genetic instability. We report that FEN1 processes substrates containing flaps of 30 nucleotides or fewer at comparable single-turnover rates. However, for flaps longer than 30 nucleotides, FEN1 kinetically discriminates substrates based on flap length and flap sequence. In particular, FEN1 removes flaps containing TNR sequences at a rate slower than mixed sequence flaps of the same length. Furthermore, multiple-turnover kinetic analysis reveals that the rate-determining step of FEN1 switches as a function of flap length from product release to chemistry (or a step prior to chemistry). These results provide a kinetic perspective on the role of FEN1 in DNA replication and repair and contribute to our understanding of FEN1 in mediating genetic instability of TNR sequences.
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Affiliation(s)
- Mary E Tarantino
- Department of Chemistry, Brown University, Providence, Rhode Island 02912
| | - Katharina Bilotti
- Department of Chemistry, Brown University, Providence, Rhode Island 02912
| | - Ji Huang
- Department of Chemistry, Brown University, Providence, Rhode Island 02912
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, Rhode Island 02912.
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34
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Skoneczna A, Kaniak A, Skoneczny M. Genetic instability in budding and fission yeast-sources and mechanisms. FEMS Microbiol Rev 2015; 39:917-67. [PMID: 26109598 PMCID: PMC4608483 DOI: 10.1093/femsre/fuv028] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2015] [Indexed: 12/17/2022] Open
Abstract
Cells are constantly confronted with endogenous and exogenous factors that affect their genomes. Eons of evolution have allowed the cellular mechanisms responsible for preserving the genome to adjust for achieving contradictory objectives: to maintain the genome unchanged and to acquire mutations that allow adaptation to environmental changes. One evolutionary mechanism that has been refined for survival is genetic variation. In this review, we describe the mechanisms responsible for two biological processes: genome maintenance and mutation tolerance involved in generations of genetic variations in mitotic cells of both Saccharomyces cerevisiae and Schizosaccharomyces pombe. These processes encompass mechanisms that ensure the fidelity of replication, DNA lesion sensing and DNA damage response pathways, as well as mechanisms that ensure precision in chromosome segregation during cell division. We discuss various factors that may influence genome stability, such as cellular ploidy, the phase of the cell cycle, transcriptional activity of a particular region of DNA, the proficiency of DNA quality control systems, the metabolic stage of the cell and its respiratory potential, and finally potential exposure to endogenous or environmental stress. The stability of budding and fission yeast genomes is influenced by two contradictory factors: (1) the need to be fully functional, which is ensured through the replication fidelity pathways of nuclear and mitochondrial genomes through sensing and repairing DNA damage, through precise chromosome segregation during cell division; and (2) the need to acquire changes for adaptation to environmental challenges.
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Affiliation(s)
- Adrianna Skoneczna
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland
| | - Aneta Kaniak
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland
| | - Marek Skoneczny
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland
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35
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Liu S, Lu G, Ali S, Liu W, Zheng L, Dai H, Li H, Xu H, Hua Y, Zhou Y, Ortega J, Li GM, Kunkel TA, Shen B. Okazaki fragment maturation involves α-segment error editing by the mammalian FEN1/MutSα functional complex. EMBO J 2015; 34:1829-43. [PMID: 25921062 DOI: 10.15252/embj.201489865] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 04/14/2015] [Indexed: 11/09/2022] Open
Abstract
During nuclear DNA replication, proofreading-deficient DNA polymerase α (Pol α) initiates Okazaki fragment synthesis with lower fidelity than bulk replication by proofreading-proficient Pol δ or Pol ε. Here, we provide evidence that the exonuclease activity of mammalian flap endonuclease (FEN1) excises Pol α replication errors in a MutSα-dependent, MutLα-independent mismatch repair process we call Pol α-segment error editing (AEE). We show that MSH2 interacts with FEN1 and facilitates its nuclease activity to remove mismatches near the 5' ends of DNA substrates. Mouse cells and mice encoding FEN1 mutations display AEE deficiency, a strong mutator phenotype, enhanced cellular transformation, and increased cancer susceptibility. The results identify a novel role for FEN1 in a specialized mismatch repair pathway and a new cancer etiological mechanism.
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Affiliation(s)
- Songbai Liu
- Colleges of Life Sciences and Agriculture and Biotechnology, Zhejiang University, Hangzhou Zhejiang, China Departments of Radiation Biology and Molecular Medicine, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Guojun Lu
- Departments of Radiation Biology and Molecular Medicine, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Shafat Ali
- Departments of Radiation Biology and Molecular Medicine, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Wenpeng Liu
- Colleges of Life Sciences and Agriculture and Biotechnology, Zhejiang University, Hangzhou Zhejiang, China Departments of Radiation Biology and Molecular Medicine, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Li Zheng
- Departments of Radiation Biology and Molecular Medicine, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Huifang Dai
- Departments of Radiation Biology and Molecular Medicine, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Hongzhi Li
- Departments of Radiation Biology and Molecular Medicine, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Hong Xu
- Colleges of Life Sciences and Agriculture and Biotechnology, Zhejiang University, Hangzhou Zhejiang, China
| | - Yuejin Hua
- Colleges of Life Sciences and Agriculture and Biotechnology, Zhejiang University, Hangzhou Zhejiang, China
| | - Yajing Zhou
- Institute of Life Sciences, Jiangsu University, Zhen Jiang Jiangsu, China
| | - Janice Ortega
- Graduate Center for Toxicology, Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Guo-Min Li
- Graduate Center for Toxicology, Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC, USA
| | - Binghui Shen
- Departments of Radiation Biology and Molecular Medicine, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
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36
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Kim DH, Kim JH, Park BC, Lee DH, Cho S, Park SG. Human ChlR1 Stimulates Endonuclease Activity of hFen1 Independently of ATPase Activity. B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.10.3005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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37
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Archaeal genome guardians give insights into eukaryotic DNA replication and damage response proteins. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2014; 2014:206735. [PMID: 24701133 PMCID: PMC3950489 DOI: 10.1155/2014/206735] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 09/27/2013] [Accepted: 11/29/2013] [Indexed: 12/28/2022]
Abstract
As the third domain of life, archaea, like the eukarya and bacteria, must have robust DNA replication and repair complexes to ensure genome fidelity. Archaea moreover display a breadth of unique habitats and characteristics, and structural biologists increasingly appreciate these features. As archaea include extremophiles that can withstand diverse environmental stresses, they provide fundamental systems for understanding enzymes and pathways critical to genome integrity and stress responses. Such archaeal extremophiles provide critical data on the periodic table for life as well as on the biochemical, geochemical, and physical limitations to adaptive strategies allowing organisms to thrive under environmental stress relevant to determining the boundaries for life as we know it. Specifically, archaeal enzyme structures have informed the architecture and mechanisms of key DNA repair proteins and complexes. With added abilities to temperature-trap flexible complexes and reveal core domains of transient and dynamic complexes, these structures provide insights into mechanisms of maintaining genome integrity despite extreme environmental stress. The DNA damage response protein structures noted in this review therefore inform the basis for genome integrity in the face of environmental stress, with implications for all domains of life as well as for biomanufacturing, astrobiology, and medicine.
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Matsui E, Urushibata Y, Abe J, Matsui I. Serial intermediates with a 1 nt 3'-flap and 5' variable-length flaps are formed by cooperative functioning of Pyrococcus horikoshii FEN-1 with either B or D DNA polymerases. Extremophiles 2014; 18:415-27. [PMID: 24509689 DOI: 10.1007/s00792-014-0627-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 01/02/2014] [Indexed: 11/28/2022]
Abstract
Flap endonuclease-1 (FEN-1) plays important roles with DNA polymerases in DNA replication, repair and recombination. FEN-1 activity is elevated by the presence of a 1 nucleotide expansion at the 3' end in the upstream primer of substrates called "structures with a 1 nt 3'-flap", which appear to be the most preferable substrates for FEN-1; however, it is unclear how such substrates are generated in vivo. Here, we show that substrate production occurred by the cooperative function of FEN-1(phFEN-1) and Pyrococcus horikoshii DNA polymerase B (phPol B) or D (phPol D). Using various substrates, the activities of several phFEN-1 F79 mutants were compared with those of the wild type. Analysis of the activity profiles of these mutants led us to discriminate "structures with a 1 nt 3'-flap" from substrates with a 3' -projection longer than 2 nt or from those without a 3'-projection. When phFEN-1 processed a gap substrate with phPol B or phPol D, "structures with a 1 nt 3'-flap" were assumed the reaction intermediates. Furthermore, the phFEN-1 cleavage products with phPol B or D were from 1mer to 7mer, corresponding to the sizes of the strand-displacement products of these polymerases. This suggests that a series of 1 nt 3'-flap with 5'-variable length-flap configurations were generated as transient intermediates, in which the length of the 5'-flaps depended on the displacement distance of the downstream strand by phPol B or D. Therefore, phFEN-1 might act successively on displaced 5'-variable flaps.
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Affiliation(s)
- Eriko Matsui
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Higashi 1-1 Central 6-9, Tsukuba, Ibaraki, 305-8566, Japan,
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Craggs TD, Hutton RD, Brenlla A, White MF, Penedo JC. Single-molecule characterization of Fen1 and Fen1/PCNA complexes acting on flap substrates. Nucleic Acids Res 2014; 42:1857-72. [PMID: 24234453 PMCID: PMC3919604 DOI: 10.1093/nar/gkt1116] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Revised: 10/21/2013] [Accepted: 10/22/2013] [Indexed: 11/21/2022] Open
Abstract
Flap endonuclease 1 (Fen1) is a highly conserved structure-specific nuclease that catalyses a specific incision to remove 5' flaps in double-stranded DNA substrates. Fen1 plays an essential role in key cellular processes, such as DNA replication and repair, and mutations that compromise Fen1 expression levels or activity have severe health implications in humans. The nuclease activity of Fen1 and other FEN family members can be stimulated by processivity clamps such as proliferating cell nuclear antigen (PCNA); however, the exact mechanism of PCNA activation is currently unknown. Here, we have used a combination of ensemble and single-molecule Förster resonance energy transfer together with protein-induced fluorescence enhancement to uncouple and investigate the substrate recognition and catalytic steps of Fen1 and Fen1/PCNA complexes. We propose a model in which upon Fen1 binding, a highly dynamic substrate is bent and locked into an open flap conformation where specific Fen1/DNA interactions can be established. PCNA enhances Fen1 recognition of the DNA substrate by further promoting the open flap conformation in a step that may involve facilitated threading of the 5' ssDNA flap. Merging our data with existing crystallographic and molecular dynamics simulations we provide a solution-based model for the Fen1/PCNA/DNA ternary complex.
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Affiliation(s)
- Timothy D. Craggs
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK and Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9SS, UK
| | - Richard D. Hutton
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK and Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9SS, UK
| | - Alfonso Brenlla
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK and Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9SS, UK
| | - Malcolm F. White
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK and Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9SS, UK
| | - J. Carlos Penedo
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK and Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9SS, UK
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40
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Mitsunobu H, Zhu B, Lee SJ, Tabor S, Richardson CC. Flap endonuclease activity of gene 6 exonuclease of bacteriophage T7. J Biol Chem 2014; 289:5860-75. [PMID: 24394415 DOI: 10.1074/jbc.m113.538611] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Flap endonucleases remove flap structures generated during DNA replication. Gene 6 protein of bacteriophage T7 is a 5'-3'-exonuclease specific for dsDNA. Here we show that gene 6 protein also possesses a structure-specific endonuclease activity similar to known flap endonucleases. The flap endonuclease activity is less active relative to its exonuclease activity. The major cleavage by the endonuclease activity occurs at a position one nucleotide into the duplex region adjacent to a dsDNA-ssDNA junction. The efficiency of cleavage of the flap decreases with increasing length of the 5'-overhang. A 3'-single-stranded tail arising from the same end of the duplex as the 5'-tail inhibits gene 6 protein flap endonuclease activity. The released flap is not degraded further, but the exonuclease activity then proceeds to hydrolyze the 5'-terminal strand of the duplex. T7 gene 2.5 single-stranded DNA-binding protein stimulates the exonuclease and also the endonuclease activity. This stimulation is attributed to a specific interaction between the two proteins because Escherichia coli single-stranded DNA binding protein does not produce this stimulatory effect. The ability of gene 6 protein to remove 5'-terminal overhangs as well as to remove nucleotides from the 5'-termini enables it to effectively process the 5'-termini of Okazaki fragments before they are ligated.
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Affiliation(s)
- Hitoshi Mitsunobu
- From the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
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41
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Lin SHS, Wang X, Zhang S, Zhang Z, Lee EY, Lee MY. Dynamics of enzymatic interactions during short flap human Okazaki fragment processing by two forms of human DNA polymerase δ. DNA Repair (Amst) 2013; 12:922-35. [PMID: 24035200 PMCID: PMC3825817 DOI: 10.1016/j.dnarep.2013.08.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 07/30/2013] [Accepted: 08/21/2013] [Indexed: 12/22/2022]
Abstract
Lagging strand DNA replication requires the concerted actions of DNA polymerase δ, Fen1 and DNA ligase I for the removal of the RNA/DNA primers before ligation of Okazaki fragments. To better understand this process in human cells, we have reconstituted Okazaki fragment processing by the short flap pathway in vitro with purified human proteins and oligonucleotide substrates. We systematically characterized the key events in Okazaki fragment processing: the strand displacement, Pol δ/Fen1 combined reactions for removal of the RNA/DNA primer, and the complete reaction with DNA ligase I. Two forms of human DNA polymerase δ were studied: Pol δ4 and Pol δ3, which represent the heterotetramer and the heterotrimer lacking the p12 subunit, respectively. Pol δ3 exhibits very limited strand displacement activity in contrast to Pol δ4, and stalls on encounter with a 5'-blocking oligonucleotide. Pol δ4 and Pol δ3 exhibit different characteristics in the Pol δ/Fen1 reactions. While Pol δ3 produces predominantly 1 and 2 nt cleavage products irrespective of Fen1 concentrations, Pol δ4 produces cleavage fragments of 1-10 nts at low Fen1 concentrations. Pol δ3 and Pol δ4 exhibit comparable formation of ligated products in the complete system. While both are capable of Okazaki fragment processing in vitro, Pol δ3 exhibits ideal characteristics for a role in Okazaki fragment processing. Pol δ3 readily idles and in combination with Fen1 produces primarily 1 nt cleavage products, so that nick translation predominates in the removal of the blocking strand, avoiding the production of longer flaps that require additional processing. These studies represent the first analysis of the two forms of human Pol δ in Okazaki fragment processing. The findings provide evidence for the novel concept that Pol δ3 has a role in lagging strand synthesis, and that both forms of Pol δ may participate in DNA replication in higher eukaryotic cells.
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Affiliation(s)
- Szu Hua Sharon Lin
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595
| | - Xiaoxiao Wang
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595
| | - Sufang Zhang
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595
| | - Zhongtao Zhang
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595
| | - Ernest Y.C. Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595
| | - Marietta Y.W.T. Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595
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42
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Mir T, Huang SH, Kobryn K. The telomere resolvase of the Lyme disease spirochete, Borrelia burgdorferi, promotes DNA single-strand annealing and strand exchange. Nucleic Acids Res 2013; 41:10438-48. [PMID: 24049070 PMCID: PMC3905847 DOI: 10.1093/nar/gkt832] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Spirochetes of the genus Borrelia include the tick-transmitted causative agents of Lyme disease and relapsing fever. They possess unusual genomes composed mainly of linear replicons terminated by closed DNA hairpin telomeres. Hairpin telomeres present an uninterrupted DNA chain to the replication machinery overcoming the 'end-replication problem' for the linear replicons. Hairpin telomeres are formed from inverted repeat replicated telomere junctions by the telomere resolvase, ResT. ResT uses a reaction mechanism similar to that of the type IB topoisomerases and tyrosine recombinases. We report here that ResT also possesses single-strand annealing activity and a limited ability to promote DNA strand exchange reactions on partial duplex substrates. This combination of activities suggests ResT is a nexus between the seemingly distinct processes of telomere resolution and homologous recombination. Implications for hairpin telomere replication and linear plasmid recombination, including antigenic variation, are discussed.
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Affiliation(s)
- Taskia Mir
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, Academic Health Sciences Building, 107 Wiggins Rd, Saskatoon, SK S7N 5E5, Canada
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43
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Sobhy MA, Joudeh LI, Huang X, Takahashi M, Hamdan SM. Sequential and multistep substrate interrogation provides the scaffold for specificity in human flap endonuclease 1. Cell Rep 2013; 3:1785-94. [PMID: 23746444 DOI: 10.1016/j.celrep.2013.05.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 04/03/2013] [Accepted: 05/02/2013] [Indexed: 11/30/2022] Open
Abstract
Human flap endonuclease 1 (FEN1), one of the structure-specific 5' nucleases, is integral in replication, repair, and recombination of cellular DNA. The 5' nucleases share significant unifying features yet cleave diverse substrates at similar positions relative to 5' end junctions. Using single-molecule Förster resonance energy transfer, we find a multistep mechanism that verifies all substrate features before inducing the intermediary-DNA bending step that is believed to unify 5' nuclease mechanisms. This is achieved by coordinating threading of the 5' flap of a nick junction into the conserved capped-helical gateway, overseeing the active site, and bending by binding at the base of the junction. We propose that this sequential and multistep substrate recognition process allows different 5' nucleases to recognize different substrates and restrict the induction of DNA bending to the last common step. Such mechanisms would also ensure the protection of DNA junctions from nonspecific bending and cleavage.
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Affiliation(s)
- Mohamed A Sobhy
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
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44
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Abstract
First discovered as a structure-specific endonuclease that evolved to cut at the base of single-stranded flaps, flap endonuclease (FEN1) is now recognized as a central component of cellular DNA metabolism. Substrate specificity allows FEN1 to process intermediates of Okazaki fragment maturation, long-patch base excision repair, telomere maintenance, and stalled replication fork rescue. For Okazaki fragments, the RNA primer is displaced into a 5' flap and then cleaved off. FEN1 binds to the flap base and then threads the 5' end of the flap through its helical arch and active site to create a configuration for cleavage. The threading requirement prevents this active nuclease from cutting the single-stranded template between Okazaki fragments. FEN1 efficiency and specificity are critical to the maintenance of genome fidelity. Overall, recent advances in our knowledge of FEN1 suggest that it was an ancient protein that has been fine-tuned over eons to coordinate many essential DNA transactions.
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Affiliation(s)
- Lata Balakrishnan
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA.
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45
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Kantartzis A, Williams GM, Balakrishnan L, Roberts RL, Surtees JA, Bambara RA. Msh2-Msh3 interferes with Okazaki fragment processing to promote trinucleotide repeat expansions. Cell Rep 2012; 2:216-22. [PMID: 22938864 DOI: 10.1016/j.celrep.2012.06.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 05/31/2012] [Accepted: 06/28/2012] [Indexed: 11/17/2022] Open
Abstract
Trinucleotide repeat (TNR) expansions are the underlying cause of more than 40 neurodegenerative and neuromuscular diseases, including myotonic dystrophy and Huntington's disease. Although genetic evidence points to errors in DNA replication and/or repair as the cause of these diseases, clear molecular mechanisms have not been described. Here, we focused on the role of the mismatch repair complex Msh2-Msh3 in promoting TNR expansions. We demonstrate that Msh2-Msh3 promotes CTG and CAG repeat expansions in vivo in Saccharomyces cerevisiae. Furthermore, we provide biochemical evidence that Msh2-Msh3 directly interferes with normal Okazaki fragment processing by flap endonuclease1 (Rad27) and DNA ligase I (Cdc9) in the presence of TNR sequences, thereby producing small, incremental expansion events. We believe that this is the first mechanistic evidence showing the interplay of replication and repair proteins in the expansion of sequences during lagging-strand DNA replication.
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Affiliation(s)
- Athena Kantartzis
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, NY 14642, USA
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46
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Shin YK, Amangyeld T, Nguyen TA, Munashingha PR, Seo YS. Human MUS81 complexes stimulate flap endonuclease 1. FEBS J 2012; 279:2412-30. [PMID: 22551069 DOI: 10.1111/j.1742-4658.2012.08620.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The yeast heterodimeric Mus81-Mms4 complex possesses a structure-specific endonuclease activity that is critical for the restart of stalled replication forks and removal of toxic recombination intermediates. Previously, we reported that Mus81-Mms4 and Rad27 (yeast FEN1, another structure-specific endonuclease) showed mutual stimulation of nuclease activity. In this study, we investigated the interactions between human FEN1 and MUS81-EME1 or MUS81-EME2, the human homologs of the yeast Mus81-Mms4 complex. We found that both MUS81-EME1 and MUS81-EME2 increased the activity of FEN1, but FEN1 did not stimulate the activity of MUS81-EME1/EME2. The MUS81 subunit alone and its N-terminal half were able to bind to FEN1 and stimulate its endonuclease activity. A truncated FEN1 fragment lacking the C-terminal region that retained catalytic activity was not stimulated by MUS81. Michaelis-Menten kinetic analysis revealed that MUS81 increased the interaction between FEN1 and its substrates, resulting in increased turnover. We also showed that, after DNA damage in human cells, FEN1 co-localizes with MUS81. These findings indicate that the human proteins and yeast homologs act similarly, except that the human FEN1 does not stimulate the nuclease activities of MUS81-EME1 or MUS81-EME2. Thus, the mammalian MUS81 complexes and FEN1 collaborate to remove the various flap structures that arise during many DNA transactions, including Okazaki fragment processing.
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Affiliation(s)
- Yong-Keol Shin
- Department of Biological Sciences, Center for DNA Replication and Genome Instability, Korea Advanced Institute of Science and Technology, Daejeon, Korea
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47
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Gloor JW, Balakrishnan L, Campbell JL, Bambara RA. Biochemical analyses indicate that binding and cleavage specificities define the ordered processing of human Okazaki fragments by Dna2 and FEN1. Nucleic Acids Res 2012; 40:6774-86. [PMID: 22570407 PMCID: PMC3413157 DOI: 10.1093/nar/gks388] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In eukaryotic Okazaki fragment processing, the RNA primer is displaced into a single-stranded flap prior to removal. Evidence suggests that some flaps become long before they are cleaved, and that this cleavage involves the sequential action of two nucleases. Strand displacement characteristics of the polymerase show that a short gap precedes the flap during synthesis. Using biochemical techniques, binding and cleavage assays presented here indicate that when the flap is ∼30 nt long the nuclease Dna2 can bind with high affinity to the flap and downstream double strand and begin cleavage. When the polymerase idles or dissociates the Dna2 can reorient for additional contacts with the upstream primer region, allowing the nuclease to remain stably bound as the flap is further shortened. The DNA can then equilibrate to a double flap that can bind Dna2 and flap endonuclease (FEN1) simultaneously. When Dna2 shortens the flap even more, FEN1 can displace the Dna2 and cleave at the flap base to make a nick for ligation.
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Affiliation(s)
- Jason W Gloor
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
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48
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Liu Y, Wilson SH. DNA base excision repair: a mechanism of trinucleotide repeat expansion. Trends Biochem Sci 2012; 37:162-72. [PMID: 22285516 DOI: 10.1016/j.tibs.2011.12.002] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 12/15/2011] [Accepted: 12/23/2011] [Indexed: 12/16/2022]
Abstract
The expansion of trinucleotide repeat (TNR) sequences in human DNA is considered to be a key factor in the pathogenesis of more than 40 neurodegenerative diseases. TNR expansion occurs during DNA replication and also, as suggested by recent studies, during the repair of DNA lesions produced by oxidative stress. In particular, the oxidized guanine base 8-oxoguanine within sequences containing CAG repeats may induce formation of pro-expansion intermediates through strand slippage during DNA base excision repair (BER). In this article, we describe how oxidized DNA lesions are repaired by BER and discuss the importance of the coordinated activities of the key repair enzymes, such as DNA polymerase β, flap endonuclease 1 (FEN1) and DNA ligase, in preventing strand slippage and TNR expansion.
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Affiliation(s)
- Yuan Liu
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
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49
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Finger LD, Atack JM, Tsutakawa S, Classen S, Tainer J, Grasby J, Shen B. The wonders of flap endonucleases: structure, function, mechanism and regulation. Subcell Biochem 2012; 62:301-26. [PMID: 22918592 PMCID: PMC3728657 DOI: 10.1007/978-94-007-4572-8_16] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Processing of Okazaki fragments to complete lagging strand DNA synthesis requires coordination among several proteins. RNA primers and DNA synthesised by DNA polymerase α are displaced by DNA polymerase δ to create bifurcated nucleic acid structures known as 5'-flaps. These 5'-flaps are removed by Flap Endonuclease 1 (FEN), a structure-specific nuclease whose divalent metal ion-dependent phosphodiesterase activity cleaves 5'-flaps with exquisite specificity. FENs are paradigms for the 5' nuclease superfamily, whose members perform a wide variety of roles in nucleic acid metabolism using a similar nuclease core domain that displays common biochemical properties and structural features. A detailed review of FEN structure is undertaken to show how DNA substrate recognition occurs and how FEN achieves cleavage at a single phosphate diester. A proposed double nucleotide unpairing trap (DoNUT) is discussed with regards to FEN and has relevance to the wider 5' nuclease superfamily. The homotrimeric proliferating cell nuclear antigen protein (PCNA) coordinates the actions of DNA polymerase, FEN and DNA ligase by facilitating the hand-off intermediates between each protein during Okazaki fragment maturation to maximise through-put and minimise consequences of intermediates being released into the wider cellular environment. FEN has numerous partner proteins that modulate and control its action during DNA replication and is also controlled by several post-translational modification events, all acting in concert to maintain precise and appropriate cleavage of Okazaki fragment intermediates during DNA replication.
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Affiliation(s)
- L. David Finger
- Department of Chemistry, Centre for Chemical Biology, Krebs Institute, University of Sheffield, Sheffield S3 7HF, UK
| | - John M. Atack
- Department of Chemistry, Centre for Chemical Biology, Krebs Institute, University of Sheffield, Sheffield S3 7HF, UK
| | - Susan Tsutakawa
- Life Sciences Division, Lawrence Berkeley National, Laboratory, Berkeley, CA 94720, USA
| | - Scott Classen
- Physical Biosciences Division, The Scripps Research, Institute, La Jolla, CA 92037, USA
| | - John Tainer
- Life Sciences Division, Lawrence Berkeley, National Laboratory, Berkeley, CA 94720, USA, Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA, Skaggs Institute for Chemical Biology, La Jolla, CA 92037, USA
| | - Jane Grasby
- Department of Chemistry, Centre for Chemical Biology, Krebs Institute, University of Sheffield, Sheffield S3 7HF, UK
| | - Binghui Shen
- Division of Radiation Biology, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA 91010, USA, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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Grasby JA, Finger LD, Tsutakawa SE, Atack JM, Tainer JA. Unpairing and gating: sequence-independent substrate recognition by FEN superfamily nucleases. Trends Biochem Sci 2011; 37:74-84. [PMID: 22118811 DOI: 10.1016/j.tibs.2011.10.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2011] [Revised: 10/07/2011] [Accepted: 10/14/2011] [Indexed: 01/13/2023]
Abstract
Structure-specific 5'-nucleases form a superfamily of evolutionarily conserved phosphodiesterases that catalyse a precise incision of a diverse range of DNA and RNA substrates in a sequence-independent manner. Superfamily members, such as flap endonucleases, exonuclease 1, DNA repair protein XPG, endonuclease GEN1 and the 5'-3'-exoribonucleases, play key roles in many cellular processes such as DNA replication and repair, recombination, transcription, RNA turnover and RNA interference. In this review, we discuss recent results that highlight the conserved architectures and active sites of the structure-specific 5'-nucleases. Despite substrate diversity, a common gating mechanism for sequence-independent substrate recognition and incision emerges, whereby double nucleotide unpairing of substrates is required to access the active site.
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Affiliation(s)
- Jane A Grasby
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Sheffield S3 7HF, UK.
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