1
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Peñafiel-Ayala A, Peralta-Castro A, Mora-Garduño J, García-Medel P, Zambrano-Pereira AG, Díaz-Quezada C, Abraham-Juárez MJ, Benítez-Cardoza CG, Sloan DB, Brieba LG. Plant Organellar MSH1 Is a Displacement Loop-Specific Endonuclease. PLANT & CELL PHYSIOLOGY 2024; 65:560-575. [PMID: 37756637 DOI: 10.1093/pcp/pcad112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/09/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023]
Abstract
MutS HOMOLOG 1 (MSH1) is an organellar-targeted protein that obstructs ectopic recombination and the accumulation of mutations in plant organellar genomes. MSH1 also modulates the epigenetic status of nuclear DNA, and its absence induces a variety of phenotypic responses. MSH1 is a member of the MutS family of DNA mismatch repair proteins but harbors an additional GIY-YIG nuclease domain that distinguishes it from the rest of this family. How MSH1 hampers recombination and promotes fidelity in organellar DNA inheritance is unknown. Here, we elucidate its enzymatic activities by recombinantly expressing and purifying full-length MSH1 from Arabidopsis thaliana (AtMSH1). AtMSH1 is a metalloenzyme that shows a strong binding affinity for displacement loops (D-loops). The DNA-binding abilities of AtMSH1 reside in its MutS domain and not in its GIY-YIG domain, which is the ancillary nickase of AtMSH1. In the presence of divalent metal ions, AtMSH1 selectively executes multiple incisions at D-loops, but not other DNA structures including Holliday junctions or dsDNA, regardless of the presence or absence of mismatches. The selectivity of AtMSH1 to dismantle D-loops supports the role of this enzyme in preventing recombination between short repeats. Our results suggest that plant organelles have evolved novel DNA repair routes centered around the anti-recombinogenic activity of MSH1.
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Affiliation(s)
- Alejandro Peñafiel-Ayala
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, Irapuato, Guanajuato 36821, México
| | - Antolin Peralta-Castro
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, Irapuato, Guanajuato 36821, México
| | - Josue Mora-Garduño
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, Irapuato, Guanajuato 36821, México
| | - Paola García-Medel
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, Irapuato, Guanajuato 36821, México
| | - Angie G Zambrano-Pereira
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, Irapuato, Guanajuato 36821, México
| | - Corina Díaz-Quezada
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, Irapuato, Guanajuato 36821, México
| | - María Jazmín Abraham-Juárez
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, Irapuato, Guanajuato 36821, México
| | - Claudia G Benítez-Cardoza
- Laboratorio de Investigación Bioquímica, Programa Institucional en Biomedicina Molecular ENMyH-IPN, Guillermo Massieu Helguera No. 239, La Escalera Ticoman 07320 DF, México
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Luis G Brieba
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, Irapuato, Guanajuato 36821, México
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2
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Wang L, Xue Y, Yang S, Bo T, Xu J, Wang W. Mismatch Repair Protein Msh2 Is Necessary for Macronuclear Stability and Micronuclear Division in Tetrahymena thermophila. Int J Mol Sci 2023; 24:10559. [PMID: 37445734 DOI: 10.3390/ijms241310559] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
Mismatch repair (MMR) is a conserved mechanism that is primarily responsible for the repair of DNA mismatches during DNA replication. Msh2 forms MutS heterodimer complexes that initiate the MMR in eukaryotes. The function of Msh2 is less clear under different chromatin structures. Tetrahymena thermophila contains a transcriptionally active macronucleus (MAC) and a transcriptionally silent micronucleus (MIC) in the same cytoplasm. Msh2 is localized in the MAC and MIC during vegetative growth. Msh2 is localized in the perinuclear region around the MIC and forms a spindle-like structure as the MIC divides. During the early conjugation stage, Msh2 is localized in the MIC and disappears from the parental MAC. Msh2 is localized in the new MAC and new MIC during the late conjugation stage. Msh2 also forms a spindle-like structure with a meiotic MIC and mitotic gametic nucleus. MSH2 knockdown inhibits the division of MAC and MIC during vegetative growth and affects cellular proliferation. MSH2 knockdown mutants are sensitive to cisplatin treatment. MSH2 knockdown also affects micronuclear meiosis and gametogenesis during sexual development. Furthermore, Msh2 interacts with MMR-dependent and MMR-independent factors. Therefore, Msh2 is necessary for macronuclear stability, as well as micronuclear mitosis and meiosis in Tetrahymena.
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Affiliation(s)
- Lin Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Yuhuan Xue
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Sitong Yang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Tao Bo
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
- Shanxi Key Laboratory of Biotechnology, Taiyuan 030006, China
| | - Jing Xu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
- School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Wei Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
- Shanxi Key Laboratory of Biotechnology, Taiyuan 030006, China
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3
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Walens A, Van Alsten SC, Olsson LT, Smith MA, Lockhart A, Gao X, Hamilton AM, Kirk EL, Love MI, Gupta GP, Perou CM, Vaziri C, Hoadley KA, Troester MA. RNA-Based Classification of Homologous Recombination Deficiency in Racially Diverse Patients with Breast Cancer. Cancer Epidemiol Biomarkers Prev 2022; 31:2136-2147. [PMID: 36129803 PMCID: PMC9720427 DOI: 10.1158/1055-9965.epi-22-0590] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/03/2022] [Accepted: 09/14/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Aberrant expression of DNA repair pathways such as homologous recombination (HR) can lead to DNA repair imbalance, genomic instability, and altered chemotherapy response. DNA repair imbalance may predict prognosis, but variation in DNA repair in diverse cohorts of breast cancer patients is understudied. METHODS To identify RNA-based patterns of DNA repair expression, we performed unsupervised clustering on 51 DNA repair-related genes in the Cancer Genome Atlas Breast Cancer [TCGA BRCA (n = 1,094)] and Carolina Breast Cancer Study [CBCS (n = 1,461)]. Using published DNA-based HR deficiency (HRD) scores (high-HRD ≥ 42) from TCGA, we trained an RNA-based supervised classifier. Unsupervised and supervised HRD classifiers were evaluated in association with demographics, tumor characteristics, and clinical outcomes. RESULTS : Unsupervised clustering on DNA repair genes identified four clusters of breast tumors, with one group having high expression of HR genes. Approximately 39.7% of CBCS and 29.3% of TCGA breast tumors had this unsupervised high-HRD (U-HRD) profile. A supervised HRD classifier (S-HRD) trained on TCGA had 84% sensitivity and 73% specificity to detect HRD-high samples. Both U-HRD and S-HRD tumors in CBCS had higher frequency of TP53 mutant-like status (45% and 41% enrichment) and basal-like subtype (63% and 58% enrichment). S-HRD high was more common among black patients. Among chemotherapy-treated participants, recurrence was associated with S-HRD high (HR: 2.38, 95% confidence interval = 1.50-3.78). CONCLUSIONS HRD is associated with poor prognosis and enriched in the tumors of black women. IMPACT RNA-level indicators of HRD are predictive of breast cancer outcomes in diverse populations.
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Affiliation(s)
- Andrea Walens
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Sarah C. Van Alsten
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Linnea T. Olsson
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Markia A. Smith
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Alex Lockhart
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Xiaohua Gao
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Alina M. Hamilton
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Erin L. Kirk
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Michael I. Love
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Gaorav P. Gupta
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Charles M. Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Katherine A. Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Melissa A. Troester
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
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4
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MutS recognition of mismatches within primed DNA replication intermediates. DNA Repair (Amst) 2022; 119:103392. [PMID: 36095926 DOI: 10.1016/j.dnarep.2022.103392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 11/24/2022]
Abstract
MutS initiates mismatch repair by recognizing mismatches in newly replicated DNA. Specific interactions between MutS and mismatches within double-stranded DNA promote ADP-ATP exchange and a conformational change into a sliding clamp. Here, we demonstrated that MutS from Pseudomonas aeruginosa associates with primed DNA replication intermediates. The predicted structure of this MutS-DNA complex revealed a new DNA binding site, in which Asn 279 and Arg 272 appeared to directly interact with the 3'-OH terminus of primed DNA. Mutation of these residues resulted in a noticeable defect in the interaction of MutS with primed DNA substrates. Remarkably, MutS interaction with a mismatch within primed DNA induced a compaction of the protein structure and impaired the formation of an ATP-bound sliding clamp. Our findings reveal a novel DNA binding mode, conformational change and intramolecular signaling for MutS recognition of mismatches within primed DNA structures.
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5
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Fukui K, Inoue M, Murakawa T, Baba S, Kumasaka T, Yano T. Structural and functional insights into the mechanism by which MutS2 recognizes a DNA junction. Structure 2022; 30:973-982.e4. [DOI: 10.1016/j.str.2022.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/11/2022] [Accepted: 03/23/2022] [Indexed: 10/18/2022]
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6
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Elez M. Mismatch Repair: From Preserving Genome Stability to Enabling Mutation Studies in Real-Time Single Cells. Cells 2021; 10:cells10061535. [PMID: 34207040 PMCID: PMC8235422 DOI: 10.3390/cells10061535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/11/2021] [Accepted: 06/15/2021] [Indexed: 12/18/2022] Open
Abstract
Mismatch Repair (MMR) is an important and conserved keeper of the maintenance of genetic information. Miroslav Radman's contributions to the field of MMR are multiple and tremendous. One of the most notable was to provide, along with Bob Wagner and Matthew Meselson, the first direct evidence for the existence of the methyl-directed MMR. The purpose of this review is to outline several aspects and biological implications of MMR that his work has helped unveil, including the role of MMR during replication and recombination editing, and the current understanding of its mechanism. The review also summarizes recent discoveries related to the visualization of MMR components and discusses how it has helped shape our understanding of the coupling of mismatch recognition to replication. Finally, the author explains how visualization of MMR components has paved the way to the study of spontaneous mutations in living cells in real time.
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Affiliation(s)
- Marina Elez
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France;
- Laboratoire Jean Perrin (LJP), Institut de Biologie Paris-Seine (IBPS), CNRS, Sorbonne Université, F-75005 Paris, France
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7
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Mackenroth B, Alani E. Collaborations between chromatin and nuclear architecture to optimize DNA repair fidelity. DNA Repair (Amst) 2021; 97:103018. [PMID: 33285474 PMCID: PMC8486310 DOI: 10.1016/j.dnarep.2020.103018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/18/2020] [Accepted: 11/05/2020] [Indexed: 01/22/2023]
Abstract
Homologous recombination (HR), considered the highest fidelity DNA double-strand break (DSB) repair pathway that a cell possesses, is capable of repairing multiple DSBs without altering genetic information. However, in "last resort" scenarios, HR can be directed to low fidelity subpathways which often use non-allelic donor templates. Such repair mechanisms are often highly mutagenic and can also yield chromosomal rearrangements and/or deletions. While the choice between HR and its less precise counterpart, non-homologous end joining (NHEJ), has received much attention, less is known about how cells manage and prioritize HR subpathways. In this review, we describe work focused on how chromatin and nuclear architecture orchestrate subpathway choice and repair template usage to maintain genome integrity without sacrificing cell survival. Understanding the relationships between nuclear architecture and recombination mechanics will be critical to understand these cellular repair decisions.
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Affiliation(s)
- Beata Mackenroth
- Department of Molecular Biology and Genetics, Cornell University, 459 Biotechnology Building, Ithaca, NY, 14853-2703, United States
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, 459 Biotechnology Building, Ithaca, NY, 14853-2703, United States.
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8
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Shah SS, Hartono SR, Chédin F, Heyer WD. Bisulfite treatment and single-molecule real-time sequencing reveal D-loop length, position, and distribution. eLife 2020; 9:59111. [PMID: 33185185 PMCID: PMC7695462 DOI: 10.7554/elife.59111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/27/2020] [Indexed: 01/01/2023] Open
Abstract
Displacement loops (D-loops) are signature intermediates formed during homologous recombination. Numerous factors regulate D-loop formation and disruption, thereby influencing crucial aspects of DNA repair, including donor choice and the possibility of crossover outcome. While D-loop detection methods exist, it is currently unfeasible to assess the relationship between D-loop editors and D-loop characteristics such as length and position. Here, we developed a novel in vitro assay to characterize the length and position of individual D-loops with near base-pair resolution and deep coverage, while also revealing their distribution in a population. Non-denaturing bisulfite treatment modifies the cytosines on the displaced strand of the D-loop to uracil, leaving a permanent signature for the displaced strand. Subsequent single-molecule real-time sequencing uncovers the cytosine conversion patch as a D-loop footprint. The D-loop Mapping Assay is widely applicable with different substrates and donor types and can be used to study factors that influence D-loop properties.
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Affiliation(s)
- Shanaya Shital Shah
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, United States
| | - Stella R Hartono
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, United States.,Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
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9
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Blackwell AR, Dluzewska J, Szymanska-Lejman M, Desjardins S, Tock AJ, Kbiri N, Lambing C, Lawrence EJ, Bieluszewski T, Rowan B, Higgins JD, Ziolkowski PA, Henderson IR. MSH2 shapes the meiotic crossover landscape in relation to interhomolog polymorphism in Arabidopsis. EMBO J 2020; 39:e104858. [PMID: 32935357 PMCID: PMC7604573 DOI: 10.15252/embj.2020104858] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 08/12/2020] [Accepted: 08/19/2020] [Indexed: 11/09/2022] Open
Abstract
During meiosis, DNA double-strand breaks undergo interhomolog repair to yield crossovers between homologous chromosomes. To investigate how interhomolog sequence polymorphism affects crossovers, we sequenced multiple recombinant populations of the model plant Arabidopsis thaliana. Crossovers were elevated in the diverse pericentromeric regions, showing a local preference for polymorphic regions. We provide evidence that crossover association with elevated diversity is mediated via the Class I crossover formation pathway, although very high levels of diversity suppress crossovers. Interhomolog polymorphism causes mismatches in recombining molecules, which can be detected by MutS homolog (MSH) mismatch repair protein heterodimers. Therefore, we mapped crossovers in a msh2 mutant, defective in mismatch recognition, using multiple hybrid backgrounds. Although total crossover numbers were unchanged in msh2 mutants, recombination was remodelled from the diverse pericentromeres towards the less-polymorphic sub-telomeric regions. Juxtaposition of megabase heterozygous and homozygous regions causes crossover remodelling towards the heterozygous regions in wild type Arabidopsis, but not in msh2 mutants. Immunostaining showed that MSH2 protein accumulates on meiotic chromosomes during prophase I, consistent with MSH2 regulating meiotic recombination. Our results reveal a pro-crossover role for MSH2 in regions of higher sequence diversity in A. thaliana.
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Affiliation(s)
| | - Julia Dluzewska
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Maja Szymanska-Lejman
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Stuart Desjardins
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Andrew J Tock
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Nadia Kbiri
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | | | - Emma J Lawrence
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Tomasz Bieluszewski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Beth Rowan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - James D Higgins
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Piotr A Ziolkowski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
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10
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Rajapakse A, Suraweera A, Boucher D, Naqi A, O'Byrne K, Richard DJ, Croft LV. Redox Regulation in the Base Excision Repair Pathway: Old and New Players as Cancer Therapeutic Targets. Curr Med Chem 2020; 27:1901-1921. [PMID: 31258058 DOI: 10.2174/0929867326666190430092732] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 02/09/2019] [Accepted: 04/05/2019] [Indexed: 01/03/2023]
Abstract
BACKGROUND Reactive Oxygen Species (ROS) are by-products of normal cellular metabolic processes, such as mitochondrial oxidative phosphorylation. While low levels of ROS are important signalling molecules, high levels of ROS can damage proteins, lipids and DNA. Indeed, oxidative DNA damage is the most frequent type of damage in the mammalian genome and is linked to human pathologies such as cancer and neurodegenerative disorders. Although oxidative DNA damage is cleared predominantly through the Base Excision Repair (BER) pathway, recent evidence suggests that additional pathways such as Nucleotide Excision Repair (NER) and Mismatch Repair (MMR) can also participate in clearance of these lesions. One of the most common forms of oxidative DNA damage is the base damage 8-oxoguanine (8-oxoG), which if left unrepaired may result in G:C to A:T transversions during replication, a common mutagenic feature that can lead to cellular transformation. OBJECTIVE Repair of oxidative DNA damage, including 8-oxoG base damage, involves the functional interplay between a number of proteins in a series of enzymatic reactions. This review describes the role and the redox regulation of key proteins involved in the initial stages of BER of 8-oxoG damage, namely Apurinic/Apyrimidinic Endonuclease 1 (APE1), human 8-oxoguanine DNA glycosylase-1 (hOGG1) and human single-stranded DNA binding protein 1 (hSSB1). Moreover, the therapeutic potential and modalities of targeting these key proteins in cancer are discussed. CONCLUSION It is becoming increasingly apparent that some DNA repair proteins function in multiple repair pathways. Inhibiting these factors would provide attractive strategies for the development of more effective cancer therapies.
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Affiliation(s)
- Aleksandra Rajapakse
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Cancer and Ageing Research Program, Translational Research Institute, Brisbane, QLD, Australia.,School of Natural Sciences, Griffith University, Nathan, QLD, Australia
| | - Amila Suraweera
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Cancer and Ageing Research Program, Translational Research Institute, Brisbane, QLD, Australia
| | - Didier Boucher
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Cancer and Ageing Research Program, Translational Research Institute, Brisbane, QLD, Australia
| | - Ali Naqi
- Department of Chemistry, Pennsylvania State University, United States
| | - Kenneth O'Byrne
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Cancer and Ageing Research Program, Translational Research Institute, Brisbane, QLD, Australia.,Cancer Services, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Derek J Richard
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Cancer and Ageing Research Program, Translational Research Institute, Brisbane, QLD, Australia
| | - Laura V Croft
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Cancer and Ageing Research Program, Translational Research Institute, Brisbane, QLD, Australia
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11
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Gonzalez V, Spampinato CP. The mismatch repair protein MSH6 regulates somatic recombination in Arabidopsis thaliana. DNA Repair (Amst) 2020; 87:102789. [PMID: 31945543 DOI: 10.1016/j.dnarep.2020.102789] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 11/29/2019] [Accepted: 01/08/2020] [Indexed: 11/28/2022]
Abstract
The mismatch repair (MMR) pathway promotes genome stability by controlling the fidelity of replication and recombination. The first step of the pathway involves recognition of the mismatch by heterodimers composed of MutS homologs (MSH). Although MSH6 has been well characterized in yeasts and humans, the role of the plant protein has not been extensively studied. We first analyzed gene expression in Arabidopsis thaliana. The use of transgenic plants expressing the β-glucuronidase (GUS) reporter gene under the control of approximately 1-kb region upstream of the start codon of the AtMSH6 gene demonstrated that MSH6 is preferentially expressed in undifferentiated cells with an intense cell division rate. We then examined protein function in meiotic and somatic recombination. Suppression of AtMSH6 did not affect the rate of meiotic recombination, but increased the frequency of recombination between two homeologous repeats of a marker gene by 3-fold relative to wild-type plants. Expression of the AtMSH6 gene under the control of its own promoter in msh6 homozygous mutant plants rescued the altered somatic recombination phenotype. We conclude that MSH6 shows a functional conservation across different biological kingdoms and a functional specificity in plants.
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Affiliation(s)
- Valentina Gonzalez
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Claudia P Spampinato
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina.
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12
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Hum YF, Jinks-Robertson S. Mismatch recognition and subsequent processing have distinct effects on mitotic recombination intermediates and outcomes in yeast. Nucleic Acids Res 2019; 47:4554-4568. [PMID: 30809658 PMCID: PMC6511840 DOI: 10.1093/nar/gkz126] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/12/2019] [Accepted: 02/23/2019] [Indexed: 01/25/2023] Open
Abstract
The post-replicative mismatch repair (MMR) system has anti-recombination activity that limits interactions between diverged sequences by recognizing mismatches in strand-exchange intermediates. In contrast to their equivalent roles during replication-error repair, mismatch recognition is more important for anti-recombination than subsequent mismatch processing. To obtain insight into this difference, ectopic substrates with 2% sequence divergence were used to examine mitotic recombination outcome (crossover or noncrossover; CO and NCO, respectively) and to infer molecular intermediates formed during double-strand break repair in Saccharomyces cerevisiae. Experiments were performed in an MMR-proficient strain, a strain with compromised mismatch-recognition activity (msh6Δ) and a strain that retained mismatch-recognition activity but was unable to process mismatches (mlh1Δ). While the loss of either mismatch binding or processing elevated the NCO frequency to a similar extent, CO events increased only when mismatch binding was compromised. The molecular features of NCOs, however, were altered in fundamentally different ways depending on whether mismatch binding or processing was eliminated. These data suggest a model in which mismatch recognition reverses strand-exchange intermediates prior to the initiation of end extension, while subsequent mismatch processing that is linked to end extension specifically destroys NCO intermediates that contain conflicting strand-discrimination signals for mismatch removal.
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Affiliation(s)
- Yee Fang Hum
- University Program in Genetics and Genomics, Duke University, Durham, NC, USA
| | - Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
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13
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Liu Q, Tan YQ. Advances in Identification of Susceptibility Gene Defects of Hereditary Colorectal Cancer. J Cancer 2019; 10:643-653. [PMID: 30719162 PMCID: PMC6360424 DOI: 10.7150/jca.28542] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 12/08/2018] [Indexed: 12/17/2022] Open
Abstract
Colorectal cancer (CRC) is a common malignant tumor of the digestive system worldwide, associated with hereditary genetic features. CRC with a Mendelian genetic predisposition accounts for approximately 5-10% of total CRC cases, mainly caused by a single germline mutation of a CRC susceptibility gene. The main subtypes of hereditary CRC are hereditary non-polyposis colorectal cancer (HNPCC) and familial adenomatous polyposis (FAP). With the rapid development of genetic testing methods, especially next-generation sequencing technology, multiple genes have now been confirmed to be pathogenic, including DNA repair or DNA mismatch repair genes such as APC, MLH1, and MSH2. Since familial CRC patients have poor clinical outcomes, timely clinical diagnosis and mutation screening of susceptibility genes will aid clinicians in establishing appropriate risk assessment and treatment interventions at a personal level. Here, we systematically summarize the susceptibility genes identified to date and the potential pathogenic mechanism of HNPCC and FAP development. Moreover, clinical recommendations for susceptibility gene screening, diagnosis, and treatment of HNPCC and FAP are discussed.
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Affiliation(s)
- Qiang Liu
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan cancer Hospital and The Affiliated Cancer of Xiangya School of Medicine, Central South University, Changsha, China.,Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Yue-Qiu Tan
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
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14
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Fukui K, Harada A, Wakamatsu T, Minobe A, Ohshita K, Ashiuchi M, Yano T. The GIY-YIG endonuclease domain of Arabidopsis MutS homolog 1 specifically binds to branched DNA structures. FEBS Lett 2018; 592:4066-4077. [PMID: 30372520 DOI: 10.1002/1873-3468.13279] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/16/2018] [Accepted: 10/24/2018] [Indexed: 01/18/2023]
Abstract
In plant organelle genomes, homeologous recombination between heteroallelic positions of repetitive sequences is increased by dysfunction of the gene encoding MutS homolog 1 (MSH1), a plant organelle-specific homolog of bacterial mismatch-binding protein MutS1. The C-terminal region of plant MSH1 contains the GIY-YIG endonuclease motif. The biochemical characteristics of plant MSH1 have not been investigated; accordingly, the molecular mechanism by which plant MSH1 suppresses homeologous recombination is unknown. Here, we characterized the recombinant GIY-YIG domain of Arabidopsis thaliana MSH1, showing that the domain possesses branched DNA-specific DNA-binding activity. Interestingly, the domain exhibited no endonuclease activity, suggesting that the mismatch-binding domain is required for DNA incision. Based on these results, we propose a possible mechanism for MSH1-dependent suppression of homeologous recombination.
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Affiliation(s)
- Kenji Fukui
- Department of Biochemistry, Osaka Medical College, Takatsuki, Japan
| | - Akiko Harada
- Department of Biology, Osaka Medical College, Takatsuki, Japan
| | - Taisuke Wakamatsu
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, Nankoku, Japan
| | - Ai Minobe
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, Nankoku, Japan
| | - Koki Ohshita
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, Nankoku, Japan
| | - Makoto Ashiuchi
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, Nankoku, Japan
| | - Takato Yano
- Department of Biochemistry, Osaka Medical College, Takatsuki, Japan
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15
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Gopalakrishnan V, Dahal S, Radha G, Sharma S, Raghavan SC, Choudhary B. Characterization of DNA double-strand break repair pathways in diffuse large B cell lymphoma. Mol Carcinog 2018; 58:219-233. [DOI: 10.1002/mc.22921] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/18/2018] [Accepted: 10/07/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Vidya Gopalakrishnan
- Institute of Bioinformatics and Applied Biotechnology; Electronics City; Bangalore India
- Manipal Academy of Higher Education; Manipal Karnataka India
| | - Sumedha Dahal
- Department of Biochemistry; Indian Institute of Science; Bangalore India
| | - Gudapureddy Radha
- Department of Biochemistry; Indian Institute of Science; Bangalore India
| | - Shivangi Sharma
- Department of Biochemistry; Indian Institute of Science; Bangalore India
| | | | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology; Electronics City; Bangalore India
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16
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Hanne J, Britton BM, Park J, Liu J, Martín-López J, Jones N, Schoffner M, Klajner P, Bundschuh R, Lee JB, Fishel R. MutS homolog sliding clamps shield the DNA from binding proteins. J Biol Chem 2018; 293:14285-14294. [PMID: 30072380 DOI: 10.1074/jbc.ra118.002264] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 07/31/2018] [Indexed: 11/06/2022] Open
Abstract
Sliding clamps on DNA consist of evolutionarily conserved enzymes that coordinate DNA replication, repair, and the cellular DNA damage response. MutS homolog (MSH) proteins initiate mismatch repair (MMR) by recognizing mispaired nucleotides and in the presence of ATP form stable sliding clamps that randomly diffuse along the DNA. The MSH sliding clamps subsequently load MutL homolog (MLH/PMS) proteins that form a second extremely stable sliding clamp, which together coordinate downstream MMR components with the excision-initiation site that may be hundreds to thousands of nucleotides distant from the mismatch. Specific or nonspecific binding of other proteins to the DNA between the mismatch and the distant excision-initiation site could conceivably obstruct the free diffusion of these MMR sliding clamps, inhibiting their ability to initiate repair. Here, we employed bulk biochemical analysis, single-molecule fluorescence imaging, and mathematical modeling to determine how sliding clamps might overcome such hindrances along the DNA. Using both bacterial and human MSH proteins, we found that increasing the number of MSH sliding clamps on a DNA decreased the association of the Escherichia coli transcriptional repressor LacI to its cognate promoter LacO. Our results suggest a simple mechanism whereby thermal diffusion of MSH sliding clamps along the DNA alters the association kinetics of other DNA-binding proteins over extended distances. These observations appear generally applicable to any stable sliding clamp that forms on DNA.
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Affiliation(s)
- Jeungphill Hanne
- From the Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43210
| | - Brooke M Britton
- From the Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43210
| | - Jonghyun Park
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang 790-784 Korea
| | - Jiaquan Liu
- From the Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43210
| | - Juana Martín-López
- From the Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43210
| | - Nathan Jones
- From the Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43210.,Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210
| | - Matthew Schoffner
- From the Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43210
| | - Piotr Klajner
- From the Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43210
| | - Ralf Bundschuh
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, .,Department of Physics, The Ohio State University, Columbus, Ohio 43210.,Department of Chemistry and Biochemistry, Division of Hematology, Department of Internal Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, and
| | - Jong-Bong Lee
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang 790-784 Korea, .,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang 790-784 Korea
| | - Richard Fishel
- From the Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43210, .,Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210
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17
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Li S, Wehrenberg B, Waldman BC, Waldman AS. Mismatch tolerance during homologous recombination in mammalian cells. DNA Repair (Amst) 2018; 70:25-36. [PMID: 30103093 DOI: 10.1016/j.dnarep.2018.07.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/19/2018] [Accepted: 07/30/2018] [Indexed: 12/13/2022]
Abstract
We investigated the homology dependency of recombination in thymidine kinase (tk)-deficient mouse fibroblasts. Cells were transfected with DNA constructs harboring a herpes tk gene (the "recipient") rendered non-functional by an oligonucleotide containing the recognition site for endonuclease I-SceI. Constructs also contained a "donor" tk sequence that could restore function to the recipient gene through spontaneous gene conversion or via repair of a double-strand break (DSB) at the I-SceI site. Recombination events were recoverable by selection for tk-positive clones. Three different donors were used containing 16, 25, or 33 mismatches relative to the recipient. The mismatches were clustered, forming an interval of "homeology" relative to the recipient sequences. We show that when homeologous sequences were surrounded by high homology, mismatches were frequently included in gene conversion events. Notably, conversion tracts from spontaneous recombination included either all or none of the mismatches, suggesting that recombination must begin and end in high homology. This requirement was relaxed for events that occurred near an induced DSB, as a significant number of these latter conversion tracts had one end positioned within homeology. Knock-down of mismatch repair showed that incorporation of mismatches into gene conversion tracts can involve repair of mismatched heteroduplex intermediates, indicating that mismatch repair does not necessarily impede homeologous genetic exchange. Our results illustrate (1) genetic exchange between homeologous sequences in a mammalian genome is enabled by nearby homology, (2) proximity to a DSB impacts the homology requirements for where genetic exchange may begin and end, and (3) mismatch correction and previously documented anti-recombination activity are separable functions of the mismatch repair machinery in mammalian cells.
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Affiliation(s)
- Shen Li
- Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, 700 Sumter Street, Columbia, South Carolina, 29208, USA
| | - Bryan Wehrenberg
- Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, 700 Sumter Street, Columbia, South Carolina, 29208, USA
| | - Barbara C Waldman
- Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, 700 Sumter Street, Columbia, South Carolina, 29208, USA
| | - Alan S Waldman
- Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, 700 Sumter Street, Columbia, South Carolina, 29208, USA.
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18
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Deshmukh AL, Chandra S, Singh DK, Siddiqi MI, Banerjee D. Identification of human flap endonuclease 1 (FEN1) inhibitors using a machine learning based consensus virtual screening. MOLECULAR BIOSYSTEMS 2018; 13:1630-1639. [PMID: 28685785 DOI: 10.1039/c7mb00118e] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Human Flap endonuclease1 (FEN1) is an enzyme that is indispensable for DNA replication and repair processes and inhibition of its Flap cleavage activity results in increased cellular sensitivity to DNA damaging agents (cisplatin, temozolomide, MMS, etc.), with the potential to improve cancer prognosis. Reports of the high expression levels of FEN1 in several cancer cells support the idea that FEN1 inhibitors may target cancer cells with minimum side effects to normal cells. In this study, we used large publicly available, high-throughput screening data of small molecule compounds targeted against FEN1. Two machine learning algorithms, Support Vector Machine (SVM) and Random Forest (RF), were utilized to generate four classification models from huge PubChem bioassay data containing probable FEN1 inhibitors and non-inhibitors. We also investigated the influence of randomly selected Zinc-database compounds as negative data on the outcome of classification modelling. The results show that the SVM model with inactive compounds was superior to RF with Matthews's correlation coefficient (MCC) of 0.67 for the test set. A Maybridge database containing approximately 53 000 compounds was screened and top ranking 5 compounds were selected for enzyme and cell-based in vitro screening. The compound JFD00950 was identified as a novel FEN1 inhibitor with in vitro inhibition of flap cleavage activity as well as cytotoxic activity against a colon cancer cell line, DLD-1.
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Affiliation(s)
- Amit Laxmikant Deshmukh
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Janakipuram Extension, Sitapur Road, Lucknow, 226031, India.
| | - Sharat Chandra
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Janakipuram Extension, Sitapur Road, Lucknow, 226031, India. and AcSIR (Academy of Scientific and Innovative Research), India
| | - Deependra Kumar Singh
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Janakipuram Extension, Sitapur Road, Lucknow, 226031, India.
| | - Mohammad Imran Siddiqi
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Janakipuram Extension, Sitapur Road, Lucknow, 226031, India. and AcSIR (Academy of Scientific and Innovative Research), India
| | - Dibyendu Banerjee
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Janakipuram Extension, Sitapur Road, Lucknow, 226031, India. and AcSIR (Academy of Scientific and Innovative Research), India
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19
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León-Ortiz AM, Panier S, Sarek G, Vannier JB, Patel H, Campbell PJ, Boulton SJ. A Distinct Class of Genome Rearrangements Driven by Heterologous Recombination. Mol Cell 2018; 69:292-305.e6. [PMID: 29351848 PMCID: PMC5783719 DOI: 10.1016/j.molcel.2017.12.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/02/2017] [Accepted: 12/18/2017] [Indexed: 11/25/2022]
Abstract
Erroneous DNA repair by heterologous recombination (Ht-REC) is a potential threat to genome stability, but evidence supporting its prevalence is lacking. Here we demonstrate that recombination is possible between heterologous sequences and that it is a source of chromosomal alterations in mitotic and meiotic cells. Mechanistically, we find that the RTEL1 and HIM-6/BLM helicases and the BRCA1 homolog BRC-1 counteract Ht-REC in Caenorhabditis elegans, whereas mismatch repair does not. Instead, MSH-2/6 drives Ht-REC events in rtel-1 and brc-1 mutants and excessive crossovers in rtel-1 mutant meioses. Loss of vertebrate Rtel1 also causes a variety of unusually large and complex structural variations, including chromothripsis, breakage-fusion-bridge events, and tandem duplications with distant intra-chromosomal insertions, whose structure are consistent with a role for RTEL1 in preventing Ht-REC during break-induced replication. Our data establish Ht-REC as an unappreciated source of genome instability that underpins a novel class of complex genome rearrangements that likely arise during replication stress.
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Affiliation(s)
- Ana María León-Ortiz
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stephanie Panier
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Grzegorz Sarek
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jean-Baptiste Vannier
- Telomere Replication and Stability Group, MRC London Institute of Medical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Harshil Patel
- Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Peter J Campbell
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Simon J Boulton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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20
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Chen CC, Avdievich E, Zhang Y, Zhang Y, Wei K, Lee K, Edelmann W, Jasin M, LaRocque JR. EXO1 suppresses double-strand break induced homologous recombination between diverged sequences in mammalian cells. DNA Repair (Amst) 2017; 57:98-106. [PMID: 28711786 DOI: 10.1016/j.dnarep.2017.07.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 07/05/2017] [Accepted: 07/07/2017] [Indexed: 11/17/2022]
Abstract
DNA double-strand breaks (DSBs) can be repaired through several mechanisms, including homologous recombination (HR). While HR between identical sequences is robust in mammalian cells, HR between diverged sequences is suppressed by DNA mismatch-repair (MMR) components such as MSH2. Exonuclease I (EXO1) interacts with the MMR machinery and has been proposed to act downstream of the mismatch recognition proteins in mismatch correction. EXO1 has also been shown to participate in extensive DSB end resection, an initial step in the HR pathway. To assess the contribution of EXO1 to HR in mammalian cells, DSB-inducible reporters were introduced into Exo1-/- mouse embryonic stem cells, including a novel GFP reporter containing several silent polymorphisms to monitor HR between diverged sequences. Compared to HR between identical sequences which was not clearly affected, HR between diverged sequences was substantially increased in Exo1-/- cells although to a lesser extent than seen in Msh2-/- cells. Thus, like canonical MMR proteins, EXO1 can restrain aberrant HR events between diverged sequence elements in the genome.
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Affiliation(s)
- Chun-Chin Chen
- Developmental Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Ave., New York, NY, 10065, USA; Weill Cornell Graduate School of Medical Sciences, New York, NY, 10065, USA
| | - Elena Avdievich
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, New York, 10461, USA
| | - Yongwei Zhang
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, New York, 10461, USA
| | - Yu Zhang
- Developmental Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Ave., New York, NY, 10065, USA
| | - Kaichun Wei
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, New York, 10461, USA
| | - Kyeryoung Lee
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, New York, 10461, USA
| | - Winfried Edelmann
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, New York, 10461, USA.
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Ave., New York, NY, 10065, USA.
| | - Jeannine R LaRocque
- Developmental Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Ave., New York, NY, 10065, USA; Department of Human Science, Georgetown University Medical Center, 3700 Reservoir Rd. NW, Washington, D.C., 20057, USA.
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21
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Abstract
The exchange of DNA strands between broken and intact molecules lies at the heart of fundamental cellular processes ranging from repairing DNA damage by homologous recombination to generation of genetic diversity during sexual reproduction. New work by Lee and colleagues utilizes the DNA curtain method, an elegant single-molecule technique, to demonstrate common and idiosyncratic features in the DNA strand exchange mechanisms of three RecA-family recombinases, bacterial RecA, and eukaryotic Rad51 and Dmc1 proteins.
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Affiliation(s)
- Maria Spies
- From the Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242
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22
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Chakraborty U, Alani E. Understanding how mismatch repair proteins participate in the repair/anti-recombination decision. FEMS Yeast Res 2016; 16:fow071. [PMID: 27573382 PMCID: PMC5976031 DOI: 10.1093/femsyr/fow071] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/24/2016] [Accepted: 08/24/2016] [Indexed: 01/06/2023] Open
Abstract
Mismatch repair (MMR) systems correct DNA mismatches that result from DNA polymerase misincorporation errors. Mismatches also appear in heteroduplex DNA intermediates formed during recombination between nearly identical sequences, and can be corrected by MMR or removed through an unwinding mechanism, known as anti-recombination or heteroduplex rejection. We review studies, primarily in baker's yeast, which support how specific factors can regulate the MMR/anti-recombination decision. Based on recent advances, we present models for how DNA structure, relative amounts of key repair proteins, the timely localization of repair proteins to DNA substrates and epigenetic marks can modulate this critical decision.
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Affiliation(s)
- Ujani Chakraborty
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA
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23
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Wu CG, Spies M. G-quadruplex recognition and remodeling by the FANCJ helicase. Nucleic Acids Res 2016; 44:8742-8753. [PMID: 27342280 PMCID: PMC5062972 DOI: 10.1093/nar/gkw574] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 06/15/2016] [Indexed: 12/16/2022] Open
Abstract
Guanine rich nucleic acid sequences can form G-quadruplex (G4) structures that interfere with DNA replication, repair and RNA transcription. The human FANCJ helicase contributes to maintaining genomic integrity by promoting DNA replication through G4-forming DNA regions. Here, we combined single-molecule and ensemble biochemical analysis to show that FANCJ possesses a G4-specific recognition site. Through this interaction, FANCJ targets G4-containing DNA where its helicase and G4-binding activities enable repeated rounds of stepwise G4-unfolding and refolding. In contrast to other G4-remodeling enzymes, FANCJ partially stabilizes the G-quadruplex. This would preserve the substrate for the REV1 translesion DNA synthesis polymerase to incorporate cytosine across from a replication-stalling G-quadruplex. The residues responsible for G-quadruplex recognition also participate in interaction with MLH1 mismatch-repair protein, suggesting that the FANCJ activity supporting replication and its participation in DNA interstrand crosslink repair and/or heteroduplex rejection are mutually exclusive. Our findings not only describe the mechanism by which FANCJ recognizes G-quadruplexes and mediates their stepwise unfolding, but also explain how FANCJ chooses between supporting DNA repair versus promoting DNA replication through G-rich sequences.
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Affiliation(s)
- Colin G Wu
- Department of Biochemistry, University of Iowa Carver College of Medicine, 51 Newton Rd., 4-532 BSB, Iowa City, IA 52242, USA
| | - Maria Spies
- Department of Biochemistry, University of Iowa Carver College of Medicine, 51 Newton Rd., 4-532 BSB, Iowa City, IA 52242, USA
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24
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Brown MW, Kim Y, Williams GM, Huck JD, Surtees JA, Finkelstein IJ. Dynamic DNA binding licenses a repair factor to bypass roadblocks in search of DNA lesions. Nat Commun 2016; 7:10607. [PMID: 26837705 PMCID: PMC4742970 DOI: 10.1038/ncomms10607] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 01/04/2016] [Indexed: 12/17/2022] Open
Abstract
DNA-binding proteins search for specific targets via facilitated diffusion along a crowded genome. However, little is known about how crowded DNA modulates facilitated diffusion and target recognition. Here we use DNA curtains and single-molecule fluorescence imaging to investigate how Msh2-Msh3, a eukaryotic mismatch repair complex, navigates on crowded DNA. Msh2-Msh3 hops over nucleosomes and other protein roadblocks, but maintains sufficient contact with DNA to recognize a single lesion. In contrast, Msh2-Msh6 slides without hopping and is largely blocked by protein roadblocks. Remarkably, the Msh3-specific mispair-binding domain (MBD) licences a chimeric Msh2-Msh6(3MBD) to bypass nucleosomes. Our studies contrast how Msh2-Msh3 and Msh2-Msh6 navigate on a crowded genome and suggest how Msh2-Msh3 locates DNA lesions outside of replication-coupled repair. These results also provide insights into how DNA repair factors search for DNA lesions in the context of chromatin.
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Affiliation(s)
- Maxwell W Brown
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Yoori Kim
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Gregory M Williams
- Department of Biochemistry, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York 14214, USA
| | - John D Huck
- Department of Biochemistry, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York 14214, USA
| | - Jennifer A Surtees
- Department of Biochemistry, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York 14214, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, USA
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Kolodner RD. A personal historical view of DNA mismatch repair with an emphasis on eukaryotic DNA mismatch repair. DNA Repair (Amst) 2016; 38:3-13. [PMID: 26698650 PMCID: PMC4740188 DOI: 10.1016/j.dnarep.2015.11.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 10/30/2015] [Accepted: 11/30/2015] [Indexed: 01/12/2023]
Affiliation(s)
- Richard D Kolodner
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Moores-UCSD Cancer Center and Institute for Molecular Medicine, University of CA, San Diego School of Medicine, La Jolla, CA 92093-0669, United States.
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Quantifying the Assembly of Multicomponent Molecular Machines by Single-Molecule Total Internal Reflection Fluorescence Microscopy. Methods Enzymol 2016; 581:105-145. [PMID: 27793278 PMCID: PMC5403009 DOI: 10.1016/bs.mie.2016.08.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Large, dynamic macromolecular complexes play essential roles in many cellular processes. Knowing how the components of these complexes associate with one another and undergo structural rearrangements is critical to understanding how they function. Single-molecule total internal reflection fluorescence (TIRF) microscopy is a powerful approach for addressing these fundamental issues. In this article, we first discuss single-molecule TIRF microscopes and strategies to immobilize and fluorescently label macromolecules. We then review the use of single-molecule TIRF microscopy to study the formation of binary macromolecular complexes using one-color imaging and inhibitors. We conclude with a discussion of the use of TIRF microscopy to examine the formation of higher-order (i.e., ternary) complexes using multicolor setups. The focus throughout this article is on experimental design, controls, data acquisition, and data analysis. We hope that single-molecule TIRF microscopy, which has largely been the province of specialists, will soon become as common in the tool box of biophysicists and biochemists as structural approaches have become today.
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Moses M, Hedegård P, Hatzakis N. Quantification of Functional Dynamics of Membrane Proteins Reconstituted in Nanodiscs Membranes by Single Turnover Functional Readout. Methods Enzymol 2016; 581:227-256. [DOI: 10.1016/bs.mie.2016.08.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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A Delicate Balance Between Repair and Replication Factors Regulates Recombination Between Divergent DNA Sequences in Saccharomyces cerevisiae. Genetics 2015; 202:525-40. [PMID: 26680658 DOI: 10.1534/genetics.115.184093] [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: 10/27/2015] [Accepted: 12/07/2015] [Indexed: 11/18/2022] Open
Abstract
Single-strand annealing (SSA) is an important homologous recombination mechanism that repairs DNA double strand breaks (DSBs) occurring between closely spaced repeat sequences. During SSA, the DSB is acted upon by exonucleases to reveal complementary sequences that anneal and are then repaired through tail clipping, DNA synthesis, and ligation steps. In baker's yeast, the Msh DNA mismatch recognition complex and the Sgs1 helicase act to suppress SSA between divergent sequences by binding to mismatches present in heteroduplex DNA intermediates and triggering a DNA unwinding mechanism known as heteroduplex rejection. Using baker's yeast as a model, we have identified new factors and regulatory steps in heteroduplex rejection during SSA. First we showed that Top3-Rmi1, a topoisomerase complex that interacts with Sgs1, is required for heteroduplex rejection. Second, we found that the replication processivity clamp proliferating cell nuclear antigen (PCNA) is dispensable for heteroduplex rejection, but is important for repairing mismatches formed during SSA. Third, we showed that modest overexpression of Msh6 results in a significant increase in heteroduplex rejection; this increase is due to a compromise in Msh2-Msh3 function required for the clipping of 3' tails. Thus 3' tail clipping during SSA is a critical regulatory step in the repair vs. rejection decision; rejection is favored before the 3' tails are clipped. Unexpectedly, Msh6 overexpression, through interactions with PCNA, disrupted heteroduplex rejection between divergent sequences in another recombination substrate. These observations illustrate the delicate balance that exists between repair and replication factors to optimize genome stability.
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Mismatch repair and homeologous recombination. DNA Repair (Amst) 2015; 38:75-83. [PMID: 26739221 DOI: 10.1016/j.dnarep.2015.11.010] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 10/26/2015] [Accepted: 11/30/2015] [Indexed: 12/27/2022]
Abstract
DNA mismatch repair influences the outcome of recombination events between diverging DNA sequences. Here we discuss how mismatch repair proteins are active in different homologous recombination subpathways and specific reaction steps, resulting in differential modulation of these recombination events, with a focus on the mechanism of heteroduplex rejection during the inhibition of recombination between slightly diverged (homeologous) DNA sequences.
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30
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Manova V, Gruszka D. DNA damage and repair in plants - from models to crops. FRONTIERS IN PLANT SCIENCE 2015; 6:885. [PMID: 26557130 PMCID: PMC4617055 DOI: 10.3389/fpls.2015.00885] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 10/05/2015] [Indexed: 05/17/2023]
Abstract
The genomic integrity of every organism is constantly challenged by endogenous and exogenous DNA-damaging factors. Mutagenic agents cause reduced stability of plant genome and have a deleterious effect on development, and in the case of crop species lead to yield reduction. It is crucial for all organisms, including plants, to develop efficient mechanisms for maintenance of the genome integrity. DNA repair processes have been characterized in bacterial, fungal, and mammalian model systems. The description of these processes in plants, in contrast, was initiated relatively recently and has been focused largely on the model plant Arabidopsis thaliana. Consequently, our knowledge about DNA repair in plant genomes - particularly in the genomes of crop plants - is by far more limited. However, the relatively small size of the Arabidopsis genome, its rapid life cycle and availability of various transformation methods make this species an attractive model for the study of eukaryotic DNA repair mechanisms and mutagenesis. Moreover, abnormalities in DNA repair which proved to be lethal for animal models are tolerated in plant genomes, although sensitivity to DNA damaging agents is retained. Due to the high conservation of DNA repair processes and factors mediating them among eukaryotes, genes and proteins that have been identified in model species may serve to identify homologous sequences in other species, including crop plants, in which these mechanisms are poorly understood. Crop breeding programs have provided remarkable advances in food quality and yield over the last century. Although the human population is predicted to "peak" by 2050, further advances in yield will be required to feed this population. Breeding requires genetic diversity. The biological impact of any mutagenic agent used for the creation of genetic diversity depends on the chemical nature of the induced lesions and on the efficiency and accuracy of their repair. More recent targeted mutagenesis procedures also depend on host repair processes, with different pathways yielding different products. Enhanced understanding of DNA repair processes in plants will inform and accelerate the engineering of crop genomes via both traditional and targeted approaches.
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Affiliation(s)
- Vasilissa Manova
- Department of Molecular Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of SciencesSofia
| | - Damian Gruszka
- Department of Genetics, Faculty of Biology and Environment Protection, University of SilesiaKatowice, Poland
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Abstract
Homologous recombination (HR) and mismatch repair (MMR) are inextricably linked. HR pairs homologous chromosomes before meiosis I and is ultimately responsible for generating genetic diversity during sexual reproduction. HR is initiated in meiosis by numerous programmed DNA double-strand breaks (DSBs; several hundred in mammals). A characteristic feature of HR is the exchange of DNA strands, which results in the formation of heteroduplex DNA. Mismatched nucleotides arise in heteroduplex DNA because the participating parental chromosomes contain nonidentical sequences. These mismatched nucleotides may be processed by MMR, resulting in nonreciprocal exchange of genetic information (gene conversion). MMR and HR also play prominent roles in mitotic cells during genome duplication; MMR rectifies polymerase misincorporation errors, whereas HR contributes to replication fork maintenance, as well as the repair of spontaneous DSBs and genotoxic lesions that affect both DNA strands. MMR suppresses HR when the heteroduplex DNA contains excessive mismatched nucleotides, termed homeologous recombination. The regulation of homeologous recombination by MMR ensures the accuracy of DSB repair and significantly contributes to species barriers during sexual reproduction. This review discusses the history, genetics, biochemistry, biophysics, and the current state of studies on the role of MMR in homologous and homeologous recombination from bacteria to humans.
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Affiliation(s)
- Maria Spies
- Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242
| | - Richard Fishel
- Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University Medical Center and Comprehensive Cancer Center, Columbus, Ohio 43210 Human Genetics Institute, The Ohio State University Medical Center, Columbus, Ohio 43210 Physics Department, The Ohio State University, Columbus, Ohio 43210
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Zhang J, Yin D, Li H. hMSH2 expression is associated with paclitaxel resistance in ovarian carcinoma, and inhibition of hMSH2 expression in vitro restores paclitaxel sensitivity. Oncol Rep 2014; 32:2199-206. [PMID: 25175513 DOI: 10.3892/or.2014.3430] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 07/25/2014] [Indexed: 11/06/2022] Open
Abstract
The objective of the present study was to investigate the association between paclitaxel resistance, gene copy number, and gene expression in ovarian carcinoma, and to restore paclitaxel sensitivity in a paclitaxel-resistant ovarian carcinoma cell line by using hMSH2-targeting siRNA. Paclitaxel-resistant ovarian carcinoma cell lines OC3/TAX300 and OC3/TAX50 and their parental cell lines were analyzed by comparative genomic hybridization, and the expression levels of hMSH2 in ovarian carcinoma cell lines and tissues were determined. An siRNA targeted to hMSH2 mRNA was used to transfect a paclitaxel-resistant cell line. We assessed the morphological features, proliferation, and susceptibility to apoptosis of the transfected cells after paclitaxel treatment. Chromosome 2p21 (gene locus of hMSH2) was amplified in OC3/TAX300 cells. hMSH2 was overexpressed in 93.9 and 47.6% of paclitaxel-treated and untreated ovarian carcinoma tissue samples (P=0.0001), respectively. hMSH2 was overexpressed in 93.3 and 54.2% of low-differentiated and moderate-to-highly differentiated ovarian carcinoma tissue samples (P=0.0008), respectively. hMSH2 expression was inhibited in the OC3/TAX300 cells transfected with hMSH2 siRNA. hMSH2 siRNA increased paclitaxel sensitivity, inhibited OC3/TAX300 cell proliferation (G2/M arrest), and increased susceptibility to apoptosis. hMSH2 expression was upregulated in ovarian carcinoma cell lines and tissues after paclitaxel treatment. hMSH2 overexpression is related to paclitaxel resistance and poor prognosis. Inhibition of hMSH2 expression in vitro restores paclitaxel sensitivity in paclitaxel‑resistant ovarian carcinoma cell lines and indicates a new direction in adjuvant therapy for ovarian carcinoma.
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Affiliation(s)
- Jin Zhang
- Department of Obstetrics and Gynecology, Beijing Shijitan Hospital, Capital Medical University, Haidian, Beijing 100038, P.R. China
| | - Dongmei Yin
- Department of Gynecology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Dongcheng, Beijing 100006, P.R. China
| | - Hongxia Li
- Department of Obstetrics and Gynecology, Beijing Shijitan Hospital, Capital Medical University, Haidian, Beijing 100038, P.R. China
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