101
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Structures of the Leishmania infantum polymerase beta. DNA Repair (Amst) 2014; 18:1-9. [PMID: 24666693 DOI: 10.1016/j.dnarep.2014.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 02/28/2014] [Accepted: 03/01/2014] [Indexed: 11/21/2022]
Abstract
Protozoans of the genus Leishmania, the pathogenic agent causing leishmaniasis, encode the family X DNA polymerase Li Pol β. Here, we report the first crystal structures of Li Pol β. Our pre- and post-catalytic structures show that the polymerase adopts the common family X DNA polymerase fold. However, in contrast to other family X DNA polymerases, the dNTP-induced conformational changes in Li Pol β are much more subtle. Moreover, pre- and post-catalytic structures reveal that Li Pol β interacts with the template strand through a nonconserved, variable region known as loop3. Li Pol β Δloop3 mutants display a higher catalytic rate, catalytic efficiency and overall error rates with respect to WT Li Pol β. These results further demonstrate the subtle structural variability that exists within this family of enzymes and provides insight into how this variability underlies the substantial functional differences among their members.
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102
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Waters CA, Strande NT, Wyatt DW, Pryor JM, Ramsden DA. Nonhomologous end joining: a good solution for bad ends. DNA Repair (Amst) 2014; 17:39-51. [PMID: 24630899 DOI: 10.1016/j.dnarep.2014.02.008] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 01/27/2014] [Accepted: 02/10/2014] [Indexed: 12/27/2022]
Abstract
Double strand breaks pose unique problems for DNA repair, especially when broken ends possess complex structures that interfere with standard DNA transactions. Nonhomologous end joining can use multiple strategies to solve these problems. It further uses sophisticated means to ensure the strategy chosen provides the ideal balance of flexibility and accuracy.
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Affiliation(s)
- Crystal A Waters
- Department of Biochemistry and Biophysics and Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Natasha T Strande
- Department of Biochemistry and Biophysics and Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - David W Wyatt
- Department of Biochemistry and Biophysics and Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - John M Pryor
- Department of Biochemistry and Biophysics and Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Dale A Ramsden
- Department of Biochemistry and Biophysics and Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.
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103
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Frit P, Barboule N, Yuan Y, Gomez D, Calsou P. Alternative end-joining pathway(s): bricolage at DNA breaks. DNA Repair (Amst) 2014; 17:81-97. [PMID: 24613763 DOI: 10.1016/j.dnarep.2014.02.007] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 02/01/2014] [Accepted: 02/10/2014] [Indexed: 10/25/2022]
Abstract
To cope with DNA double strand break (DSB) genotoxicity, cells have evolved two main repair pathways: homologous recombination which uses homologous DNA sequences as repair templates, and non-homologous Ku-dependent end-joining involving direct sealing of DSB ends by DNA ligase IV (Lig4). During the last two decades a third player most commonly named alternative end-joining (A-EJ) has emerged, which is defined as any Ku- or Lig4-independent end-joining process. A-EJ increasingly appears as a highly error-prone bricolage on DSBs and despite expanding exploration, it still escapes full characterization. In the present review, we discuss the mechanism and regulation of A-EJ as well as its biological relevance under physiological and pathological situations, with a particular emphasis on chromosomal instability and cancer. Whether or not it is a genuine DSB repair pathway, A-EJ is emerging as an important cellular process and understanding A-EJ will certainly be a major challenge for the coming years.
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Affiliation(s)
- Philippe Frit
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Nadia Barboule
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Ying Yuan
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Dennis Gomez
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Patrick Calsou
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France.
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104
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Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC. Sustained active site rigidity during synthesis by human DNA polymerase μ. Nat Struct Mol Biol 2014; 21:253-60. [PMID: 24487959 PMCID: PMC4164209 DOI: 10.1038/nsmb.2766] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 12/26/2013] [Indexed: 01/09/2023]
Abstract
DNA polymerase μ (Pol μ) is the only template-dependent human DNA polymerase capable of repairing double-strand DNA breaks (DSBs) with unpaired 3' ends in nonhomologous end joining (NHEJ). To probe this function, we structurally characterized Pol μ's catalytic cycle for single-nucleotide incorporation. These structures indicate that, unlike other template-dependent DNA polymerases, Pol μ shows no large-scale conformational changes in protein subdomains, amino acid side chains or DNA upon dNTP binding or catalysis. Instead, the only major conformational change is seen earlier in the catalytic cycle, when the flexible loop 1 region repositions upon DNA binding. Pol μ variants with changes in loop 1 have altered catalytic properties and are partially defective in NHEJ. The results indicate that specific loop 1 residues contribute to Pol μ's unique ability to catalyze template-dependent NHEJ of DSBs with unpaired 3' ends.
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Affiliation(s)
- Andrea F Moon
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - John M Pryor
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Dale A Ramsden
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Thomas A Kunkel
- 1] Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA. [2] Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Katarzyna Bebenek
- 1] Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA. [2] Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Lars C Pedersen
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
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105
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Hermetz KE, Newman S, Conneely KN, Martin CL, Ballif BC, Shaffer LG, Cody JD, Rudd MK. Large inverted duplications in the human genome form via a fold-back mechanism. PLoS Genet 2014; 10:e1004139. [PMID: 24497845 PMCID: PMC3907307 DOI: 10.1371/journal.pgen.1004139] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 12/09/2013] [Indexed: 11/27/2022] Open
Abstract
Inverted duplications are a common type of copy number variation (CNV) in germline and somatic genomes. Large duplications that include many genes can lead to both neurodevelopmental phenotypes in children and gene amplifications in tumors. There are several models for inverted duplication formation, most of which include a dicentric chromosome intermediate followed by breakage-fusion-bridge (BFB) cycles, but the mechanisms that give rise to the inverted dicentric chromosome in most inverted duplications remain unknown. Here we have combined high-resolution array CGH, custom sequence capture, next-generation sequencing, and long-range PCR to analyze the breakpoints of 50 nonrecurrent inverted duplications in patients with intellectual disability, autism, and congenital anomalies. For half of the rearrangements in our study, we sequenced at least one breakpoint junction. Sequence analysis of breakpoint junctions reveals a normal-copy disomic spacer between inverted and non-inverted copies of the duplication. Further, short inverted sequences are present at the boundary of the disomic spacer and the inverted duplication. These data support a mechanism of inverted duplication formation whereby a chromosome with a double-strand break intrastrand pairs with itself to form a “fold-back” intermediate that, after DNA replication, produces a dicentric inverted chromosome with a disomic spacer corresponding to the site of the fold-back loop. This process can lead to inverted duplications adjacent to terminal deletions, inverted duplications juxtaposed to translocations, and inverted duplication ring chromosomes. Chromosomes with large inverted duplications and terminal deletions cause neurodevelopmental disorders in children. These chromosome rearrangements typically involve hundreds of genes, leading to significant changes in gene dosage. Though inverted duplications adjacent to terminal deletions are a relatively common type of chromosomal imbalance, the DNA repair mechanism responsible for their formation is not known. In this study, we analyze the genomic organization of the largest collection of human inverted duplications. We find a common inverted duplication structure, consistent with a model that requires DNA to fold back and form a dicentric chromosome intermediate. These data provide insight into the formation of nonrecurrent inverted duplications in the human genome.
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Affiliation(s)
- Karen E Hermetz
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Scott Newman
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Karen N Conneely
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America ; Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, Georgia, United States of America
| | - Christa L Martin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Blake C Ballif
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, Washington, United States of America
| | - Lisa G Shaffer
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, Washington, United States of America
| | - Jannine D Cody
- Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America ; The Chromosome 18 Registry and Research Society, San Antonio, Texas, United States of America
| | - M Katharine Rudd
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
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106
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Strittmatter T, Brockmann A, Pott M, Hantusch A, Brunner T, Marx A. Expanding the scope of human DNA polymerase λ and β inhibitors. ACS Chem Biol 2014; 9:282-90. [PMID: 24171552 DOI: 10.1021/cb4007562] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The exact biological functions of individual DNA polymerases still await clarification, and therefore appropriate reagents to probe their respective functions are required. In the present study, we report the development of a highly potent series of human DNA polymerase λ and β (pol λ and β) inhibitors based on the rhodanine scaffold. Both enzymes are involved in DNA repair and are thus considered as future drug targets. We expanded the chemical diversity of the small-molecule inhibitors arising from a high content screening and designed and synthesized 30 novel analogues. By biochemical evaluation, we discovered 23 highly active compounds against pol λ. Importantly, 10 of these small-molecules selectively inhibited pol λ and not the homologous pol β. We discovered 14 small-molecules that target pol β and found out that they are more potent than known inhibitors. We also investigated whether the discovered compounds sensitize cancer cells toward DNA-damaging reagents. Thus, we cotreated human colorectal cancer cells (Caco-2) with the small-molecule inhibitors and hydrogen peroxide or the approved drug temozolomide. Interestingly, the tested compounds sensitized Caco-2 cells to both genotoxic agents in a DNA repair pathway-dependent manner.
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Affiliation(s)
- Tobias Strittmatter
- Departments of Chemistry
and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Anette Brockmann
- Departments of Chemistry
and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Moritz Pott
- Departments of Chemistry
and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Annika Hantusch
- Departments of Chemistry
and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Thomas Brunner
- Departments of Chemistry
and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Andreas Marx
- Departments of Chemistry
and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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107
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Mizushina Y, Onodera T, Kuriyama I, Nakayama H, Sugimoto K, Lee E. Screening of Mammalian DNA Polymerase Inhibitors from Rosemary Leaves and Analysis of the Anti-inflammatory and Antiallergic Effects of the Isolated Compounds. FOOD SCIENCE AND TECHNOLOGY RESEARCH 2014. [DOI: 10.3136/fstr.20.829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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108
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Berdis AJ. DNA Polymerases That Perform Template-Independent DNA Synthesis. NUCLEIC ACID POLYMERASES 2014. [DOI: 10.1007/978-3-642-39796-7_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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109
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Abstract
DNA transfer from chloroplasts and mitochondria to the nucleus is ongoing in eukaryotes but the mechanisms involved are poorly understood. Mitochondrial DNA was observed to integrate into the nuclear genome through DNA double-strand break repair in Nicotiana tabacum. Here, 14 nuclear insertions of chloroplast DNA (nupts) that are unique to Oryza sativa subsp. indica were identified. Comparisons with the preinsertion nuclear loci identified in the related subspecies, O. sativa subsp. japonica, which lacked these nupts, indicated that chloroplast DNA had integrated by nonhomologous end joining. Analyzing public DNase-seq data revealed that nupts were significantly more frequent in open chromatin regions of the nucleus. This preference was tested further in the chimpanzee genome by comparing nuclear loci containing integrants of mitochondrial DNA (numts) with their corresponding numt-lacking preinsertion sites in the human genome. Mitochondrial DNAs also tended to insert more frequently into regions of open chromatin revealed by human DNase-seq and Formaldehyde-Assisted Isolation of Regulatory Elements-seq databases.
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Affiliation(s)
- Dong Wang
- School of Molecular and Biomedical Science, The University of Adelaide, South Australia, Australia
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110
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The BRCT domain and the specific loop 1 of human Polμ are targets of Cdk2/cyclin A phosphorylation. DNA Repair (Amst) 2013; 12:824-34. [DOI: 10.1016/j.dnarep.2013.07.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 07/01/2013] [Accepted: 07/18/2013] [Indexed: 12/18/2022]
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111
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Costi R, Crucitti GC, Pescatori L, Messore A, Scipione L, Tortorella S, Amoroso A, Crespan E, Campiglia P, Maresca B, Porta A, Granata I, Novellino E, Gouge J, Delarue M, Maga G, Di Santo R. New nucleotide-competitive non-nucleoside inhibitors of terminal deoxynucleotidyl transferase: discovery, characterization, and crystal structure in complex with the target. J Med Chem 2013; 56:7431-41. [PMID: 23968551 DOI: 10.1021/jm4010187] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Terminal deoxynucletidyl transferase (TdT) is overexpressed in some cancer types, where it might compete with pol μ during the mutagenic repair of double strand breaks (DSBs) through the nonhomologous end joining (NHEJ) pathway. Here we report the discovery and characterization of pyrrolyl and indolyl diketo acids that specifically target TdT and behave as nucleotide-competitive inhibitors. These compounds show a selective toxicity toward MOLT-4 compared to HeLa cells that correlate well with in vitro selectivity for TdT. The binding site of two of these inhibitors was determined by cocrystallization with TdT, explaining why these compounds are competitive inhibitors of the deoxynucleotide triphosphate (dNTP). In addition, because of the observed dual localization of the phenyl substituent, these studies open the possibility of rationally designing more potent compounds.
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Affiliation(s)
- Roberta Costi
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma , P.le Aldo Moro 5, I-00185 Roma, Italy
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112
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Martin MJ, Garcia-Ortiz MV, Gomez-Bedoya A, Esteban V, Guerra S, Blanco L. A specific N-terminal extension of the 8 kDa domain is required for DNA end-bridging by human Polμ and Polλ. Nucleic Acids Res 2013; 41:9105-16. [PMID: 23935073 PMCID: PMC3799444 DOI: 10.1093/nar/gkt681] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Human DNA polymerases mu (Polµ) and lambda (Polλ) are X family members involved in the repair of double-strand breaks in DNA during non-homologous end joining. Crucial abilities of these enzymes include bridging of the two 3′ single-stranded overhangs and trans-polymerization using one 3′ end as primer and the other as template, to minimize sequence loss. In this context, we have studied the importance of a previously uncharacterised sequence (‘brooch’), located at the N-terminal boundary of the Polß-like polymerase core, and formed by Tyr141, Ala142, Cys143, Gln144 and Arg145 in Polµ, and by Trp239, Val240, Cys241, Ala242 and Gln243 in Polλ. The brooch is potentially implicated in the maintenance of a closed conformation throughout the catalytic cycle, and our studies indicate that it could be a target of Cdk phosphorylation in Polµ. The brooch is irrelevant for 1 nt gap filling, but of specific importance during end joining: single mutations in the conserved residues reduced the formation of two ended synapses and strongly diminished the ability of Polµ and polymerase lambda to perform non-homologous end joining reactions in vitro.
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Affiliation(s)
- Maria Jose Martin
- Centro de Biologia Molecular Severo Ochoa (CSIC-UAM), 28049 Madrid, Spain
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113
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Schenten V, Guéguinou N, Baatout S, Frippiat JP. Modulation of Pleurodeles waltl DNA polymerase mu expression by extreme conditions encountered during spaceflight. PLoS One 2013; 8:e69647. [PMID: 23936065 PMCID: PMC3729694 DOI: 10.1371/journal.pone.0069647] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 06/12/2013] [Indexed: 11/29/2022] Open
Abstract
DNA polymerase µ is involved in DNA repair, V(D)J recombination and likely somatic hypermutation of immunoglobulin genes. Our previous studies demonstrated that spaceflight conditions affect immunoglobulin gene expression and somatic hypermutation frequency. Consequently, we questioned whether Polμ expression could also be affected. To address this question, we characterized Polμ of the Iberian ribbed newt Pleurodeles waltl and exposed embryos of that species to spaceflight conditions or to environmental modifications corresponding to those encountered in the International Space Station. We noted a robust expression of Polμ mRNA during early ontogenesis and in the testis, suggesting that Polμ is involved in genomic stability. Full-length Polμ transcripts are 8–9 times more abundant in P. waltl than in humans and mice, thereby providing an explanation for the somatic hypermutation predilection of G and C bases in amphibians. Polμ transcription decreases after 10 days of development in space and radiation seem primarily involved in this down-regulation. However, space radiation, alone or in combination with a perturbation of the circadian rhythm, did not affect Polμ protein levels and did not induce protein oxidation, showing the limited impact of radiation encountered during a 10-day stay in the International Space Station.
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Affiliation(s)
- Véronique Schenten
- Stress Immunity Pathogens Laboratory, EA7300, Lorraine University, Vandœuvre-lès-Nancy, France
| | - Nathan Guéguinou
- Stress Immunity Pathogens Laboratory, EA7300, Lorraine University, Vandœuvre-lès-Nancy, France
| | - Sarah Baatout
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK•CEN, Mol, Belgium
- Department of Molecular Biotechnology, Ghent University, Ghent, Belgium
| | - Jean-Pol Frippiat
- Stress Immunity Pathogens Laboratory, EA7300, Lorraine University, Vandœuvre-lès-Nancy, France
- * E-mail:
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114
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Yeast pol4 promotes tel1-regulated chromosomal translocations. PLoS Genet 2013; 9:e1003656. [PMID: 23874240 PMCID: PMC3715435 DOI: 10.1371/journal.pgen.1003656] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 06/05/2013] [Indexed: 01/09/2023] Open
Abstract
DNA double-strand breaks (DSBs) are one of the most dangerous DNA lesions, since their erroneous repair by nonhomologous end-joining (NHEJ) can generate harmful chromosomal rearrangements. PolX DNA polymerases are well suited to extend DSB ends that cannot be directly ligated due to their particular ability to bind to and insert nucleotides at the imperfect template-primer structures formed during NHEJ. Herein, we have devised genetic assays in yeast to induce simultaneous DSBs in different chromosomes in vivo. The repair of these breaks in trans could result in reciprocal chromosomal translocations that were dependent on classical Ku-dependent NHEJ. End-joining events leading to translocations were mainly based on the formation of short base pairing between 3′-overhanging DNA ends coupled to gap-filling DNA synthesis. A major proportion of these events were specifically dependent on yeast DNA polymerase Pol4 activity. In addition, we have discovered that Pol4-Thr540 amino acid residue can be phosphorylated by Tel1/ATM kinase, which could modulate Pol4 activity during NHEJ. Our data suggest that the role of Tel1 in preventing break-induced chromosomal translocations can, to some extent, be due to its stimulating effect on gap-filling activity of Pol4 to repair DSBs in cis. Overall, this work provides further insight to the molecular mechanisms of DSB repair by NHEJ and presents a new perspective to the understanding of how chromosomal translocations are formed in eukaryotic cells. Chromosomal translocations are one of the most common types of genomic rearrangements, which may have a relevant impact on cell development. They are often generated from DNA double-strand breaks that are inaccurately repaired by DNA repair machinery. In this study, we have developed genetic assays in yeast to analyze the molecular mechanisms by which these translocations can arise. We found evidence showing that the classical nonhomologous end-joining repair pathway can be a source of chromosomal translocations, with a relevant role for yeast DNA polymerase Pol4 in such processes. The involvement of Pol4 is based on its efficient gap-filling DNA synthesis activity during the joining of overhanging DNA ends with short sequence complementarity. In addition, we discovered that DNA polymerase Pol4 can be modified during the repair of the breaks via phosphorylation by Tel1 kinase. This phosphorylation seems to have important structural and functional implications in the action of Pol4, which can finally influence the formation of translocations. This work provides a useful tool for deciphering factors and mechanisms involved in DNA double-strand break repair and identifying the molecular pathways leading to chromosomal translocations in eukaryotic cells.
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115
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Gouge J, Rosario S, Romain F, Beguin P, Delarue M. Structures of intermediates along the catalytic cycle of terminal deoxynucleotidyltransferase: dynamical aspects of the two-metal ion mechanism. J Mol Biol 2013; 425:4334-52. [PMID: 23856622 DOI: 10.1016/j.jmb.2013.07.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 06/28/2013] [Accepted: 07/03/2013] [Indexed: 11/19/2022]
Abstract
Terminal deoxynucleotidyltransferase (Tdt) is a non-templated eukaryotic DNA polymerase of the polX family that is responsible for the random addition of nucleotides at the V(D)J junctions of immunoglobulins and T-cell receptors. Here we describe a series of high-resolution X-ray structures that mimic the pre-catalytic state, the post-catalytic state and a competent state that can be transformed into the two other ones in crystallo via the addition of dAMPcPP and Zn(2+), respectively. We examined the effect of Mn(2+), Co(2+) and Zn(2+) because they all have a marked influence on the kinetics of the reaction. We demonstrate a dynamic role of divalent transition metal ions bound to site A: (i) Zn(2+) (or Co(2+)) in Metal A site changes coordination from octahedral to tetrahedral after the chemical step, which explains the known higher affinity of Tdt for the primer strand when these ions are present, and (ii) metal A has to leave to allow the translocation of the primer strand and to clear the active site, a typical feature for a ratchet-like mechanism. Except for Zn(2+), the sugar puckering of the primer strand 3' terminus changes from C2'-endo to C3'-endo during catalysis. In addition, our data are compatible with a scheme where metal A is the last component that binds to the active site to complete its productive assembly, as already inferred in human pol beta. The new structures have potential implications for modeling pol mu, a closely related polX implicated in the repair of DNA double-strand breaks, in a complex with a DNA synapsis.
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Affiliation(s)
- Jérôme Gouge
- Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528 du CNRS, 25 rue du Dr Roux, 75015 Paris, France
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116
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Kavanagh JN, Redmond KM, Schettino G, Prise KM. DNA double strand break repair: a radiation perspective. Antioxid Redox Signal 2013; 18:2458-72. [PMID: 23311752 DOI: 10.1089/ars.2012.5151] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
SIGNIFICANCE Ionizing radiation (IR) can induce a wide range of unique deoxyribonucleic acid (DNA) lesions due to the spatiotemporal correlation of the ionization produced. Of these, DNA double strand breaks (DSBs) play a key role. Complex mechanisms and sophisticated pathways are available within cells to restore the integrity and sequence of the damaged DNA molecules. RECENT ADVANCES Here we review the main aspects of the DNA DSB repair mechanisms with emphasis on the molecular pathways, radiation-induced lesions, and their significance for cellular processes. CRITICAL ISSUES Although the main characteristics and proteins involved in the two DNA DSB repair processes present in eukaryotic cells (homologous recombination and nonhomologous end-joining) are reasonably well established, there are still uncertainties regarding the primary sensing event and their dependency on the complexity, location, and time of the damage. Interactions and overlaps between the different pathways play a critical role in defining the repair efficiency and determining the cellular functional behavior due to unrepaired/miss-repaired DNA lesions. The repair pathways involved in repairing lesions induced by soluble factors released from directly irradiated cells may also differ from the established response mechanisms. FUTURE DIRECTIONS An improved understanding of the molecular pathways involved in sensing and repairing damaged DNA molecules and the role of DSBs is crucial for the development of novel classes of drugs to treat human diseases and to exploit characteristics of IR and alterations in tumor cells for successful radiotherapy applications.
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Affiliation(s)
- Joy N Kavanagh
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, Belfast, United Kingdom
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117
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"Gate-keeper" residues and active-site rearrangements in DNA polymerase μ help discriminate non-cognate nucleotides. PLoS Comput Biol 2013; 9:e1003074. [PMID: 23717197 PMCID: PMC3662701 DOI: 10.1371/journal.pcbi.1003074] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 04/11/2013] [Indexed: 11/19/2022] Open
Abstract
Incorporating the cognate instead of non-cognate substrates is crucial for DNA polymerase function. Here we analyze molecular dynamics simulations of DNA polymerase μ (pol μ) bound to different non-cognate incoming nucleotides including A:dCTP, A:dGTP, A(syn):dGTP, A:dATP, A(syn):dATP, T:dCTP, and T:dGTP to study the structure-function relationships involved with aberrant base pairs in the conformational pathway; while a pol μ complex with the A:dTTP base pair is available, no solved non-cognate structures are available. We observe distinct differences of the non-cognate systems compared to the cognate system. Specifically, the motions of active-site residue His329 and Asp330 distort the active site, and Trp436, Gln440, Glu443 and Arg444 tend to tighten the nucleotide-binding pocket when non-cognate nucleotides are bound; the latter effect may further lead to an altered electrostatic potential within the active site. That most of these “gate-keeper” residues are located farther apart from the upstream primer in pol μ, compared to other X family members, also suggests an interesting relation to pol μ's ability to incorporate nucleotides when the upstream primer is not paired. By examining the correlated motions within pol μ complexes, we also observe different patterns of correlations between non-cognate systems and the cognate system, especially decreased interactions between the incoming nucleotides and the nucleotide-binding pocket. Altered correlated motions in non-cognate systems agree with our recently proposed hybrid conformational selection/induced-fit models. Taken together, our studies propose the following order for difficulty of non-cognate system insertions by pol μ: T:dGTP<A(syn):dATP<T:dCTP<A:dGTP<A(syn):dGTP<A:dCTP<A:dATP. This sequence agrees with available kinetic data for non-cognate nucleotide insertions, with the exception of A:dGTP, which may be more sensitive to the template sequence. The structures and conformational aspects predicted here are experimentally testable. DNA polymerase μ (pol μ) is an enzyme that participates in DNA repair and thus has a central role in maintaining the integrity of genetic information. To efficiently repair the DNA, discriminating the cognate instead of non-cognate nucleotides (“fidelity-checking”) is required. Here we analyze molecular dynamics simulations of pol μ bound to different non-cognate nucleotides to study the structure-function relationships involved in the fidelity-checking mechanism of pol μ on the atomic level. Our results suggest that His329, Asp330, Trp436, Gln440, Glu443, and Arg444 are of great importance for pol μ's fidelity-checking mechanism. We also observe altered patterns of correlated motions within pol μ complex when non-cognate instead of cognate nucleotides are bound, which agrees with our recently proposed hybrid conformational selection/induced-fit models. Taken together, our studies help interpret the available kinetic data of various non-cognate nucleotide insertions by pol μ. We also suggest experimentally testable predictions; for example, a point mutation like E443M may reduce the ability of pol μ to insert the cognate more than of non-cognate nucleotides. Our studies suggest an interesting relation to pol μ's unique ability to incorporate nucleotides when the upstream primer is not paired.
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118
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Ribonucleolytic resection is required for repair of strand displaced nonhomologous end-joining intermediates. Proc Natl Acad Sci U S A 2013; 110:E1984-91. [PMID: 23671117 DOI: 10.1073/pnas.1302616110] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Nonhomologous end-joining (NHEJ) pathways repair DNA double-strand breaks (DSBs) in eukaryotes and many prokaryotes, although it is not reported to operate in the third domain of life, archaea. Here, we describe a complete NHEJ complex, consisting of DNA ligase (Lig), polymerase (Pol), phosphoesterase (PE), and Ku from a mesophillic archaeon, Methanocella paludicola (Mpa). Mpa Lig has limited DNA nick-sealing activity but is efficient in ligating nicks containing a 3' ribonucleotide. Mpa Pol preferentially incorporates nucleoside triphosphates onto a DNA primer strand, filling DNA gaps in annealed breaks. Mpa PE sequentially removes 3' phosphates and ribonucleotides from primer strands, leaving a ligatable terminal 3' monoribonucleotide. These proteins, together with the DNA end-binding protein Ku, form a functional NHEJ break-repair apparatus that is highly homologous to the bacterial complex. Although the major roles of Pol and Lig in break repair have been reported, PE's function in NHEJ has remained obscure. We establish that PE is required for ribonucleolytic resection of RNA intermediates at annealed DSBs. Polymerase-catalyzed strand-displacement synthesis on DNA gaps can result in the formation of nonligatable NHEJ intermediates. The function of PE in NHEJ repair is to detect and remove inappropriately incorporated ribonucleotides or phosphates from 3' ends of annealed DSBs to configure the termini for ligation. Thus, PE prevents the accumulation of abortive genotoxic DNA intermediates arising from strand displacement synthesis that otherwise would be refractory to repair.
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119
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Chiruvella KK, Liang Z, Wilson TE. Repair of double-strand breaks by end joining. Cold Spring Harb Perspect Biol 2013; 5:a012757. [PMID: 23637284 DOI: 10.1101/cshperspect.a012757] [Citation(s) in RCA: 279] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nonhomologous end joining (NHEJ) refers to a set of genome maintenance pathways in which two DNA double-strand break (DSB) ends are (re)joined by apposition, processing, and ligation without the use of extended homology to guide repair. Canonical NHEJ (c-NHEJ) is a well-defined pathway with clear roles in protecting the integrity of chromosomes when DSBs arise. Recent advances have revealed much about the identity, structure, and function of c-NHEJ proteins, but many questions exist regarding their concerted action in the context of chromatin. Alternative NHEJ (alt-NHEJ) refers to more recently described mechanism(s) that repair DSBs in less-efficient backup reactions. There is great interest in defining alt-NHEJ more precisely, including its regulation relative to c-NHEJ, in light of evidence that alt-NHEJ can execute chromosome rearrangements. Progress toward these goals is reviewed.
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120
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Malu S, Malshetty V, Francis D, Cortes P. Role of non-homologous end joining in V(D)J recombination. Immunol Res 2013; 54:233-46. [PMID: 22569912 DOI: 10.1007/s12026-012-8329-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The pathway of V(D)J recombination was discovered almost three decades ago. Yet it continues to baffle scientists because of its inherent complexity and the multiple layers of regulation that are required to efficiently generate a diverse repertoire of T and B cells. The non-homologous end-joining (NHEJ) DNA repair pathway is an integral part of the V(D)J reaction, and its numerous players perform critical functions in generating this vast diversity, while ensuring genomic stability. In this review, we summarize the efforts of a number of laboratories including ours in providing the mechanisms of V(D)J regulation with a focus on the NHEJ pathway. This involves discovering new players, unraveling unknown roles for known components, and understanding how deregulation of these pathways contributes to generation of primary immunodeficiencies. A long-standing interest of our laboratory has been to elucidate various mechanisms that control RAG activity. Our recent work has focused on understanding the multiple protein-protein interactions and protein-DNA interactions during V(D)J recombination, which allow efficient and regulated generation of the antigen receptors. Exploring how deregulation of this process contributes to immunodeficiencies also continues to be an important area of research for our group.
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Affiliation(s)
- Shruti Malu
- Department of Medicine, Immunology Institute, Mount Sinai School of Medicine, 1425 Madison Avenue, New York, NY 10029, USA
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121
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Nishana M, Raghavan SC. Role of recombination activating genes in the generation of antigen receptor diversity and beyond. Immunology 2013; 137:271-81. [PMID: 23039142 DOI: 10.1111/imm.12009] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2012] [Revised: 08/19/2012] [Accepted: 08/21/2012] [Indexed: 01/18/2023] Open
Abstract
V(D)J recombination is the process by which antibody and T-cell receptor diversity is attained. During this process, antigen receptor gene segments are cleaved and rejoined by non-homologous DNA end joining for the generation of combinatorial diversity. The major players of the initial process of cleavage are the proteins known as RAG1 (recombination activating gene 1) and RAG2. In this review, we discuss the physiological function of RAGs as a sequence-specific nuclease and its pathological role as a structure-specific nuclease. The first part of the review discusses the basic mechanism of V(D)J recombination, and the last part focuses on how the RAG complex functions as a sequence-specific and structure-specific nuclease. It also deals with the off-target cleavage of RAGs and its implications in genomic instability.
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122
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Lucas D, Delgado-García JM, Escudero B, Albo C, Aza A, Acín-Pérez R, Torres Y, Moreno P, Enríquez JA, Samper E, Blanco L, Fairén A, Bernad A, Gruart A. Increased learning and brain long-term potentiation in aged mice lacking DNA polymerase μ. PLoS One 2013; 8:e53243. [PMID: 23301049 PMCID: PMC3536760 DOI: 10.1371/journal.pone.0053243] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 11/27/2012] [Indexed: 01/14/2023] Open
Abstract
A definitive consequence of the aging process is the progressive deterioration of higher cognitive functions. Defects in DNA repair mechanisms mostly result in accelerated aging and reduced brain function. DNA polymerase µ is a novel accessory partner for the non-homologous end-joining DNA repair pathway for double-strand breaks, and its deficiency causes reduced DNA repair. Using associative learning and long-term potentiation experiments, we demonstrate that Polµ−/− mice, however, maintain the ability to learn at ages when wild-type mice do not. Expression and biochemical analyses suggest that brain aging is delayed in Polµ−/− mice, being associated with a reduced error-prone DNA oxidative repair activity and a more efficient mitochondrial function. This is the first example in which the genetic ablation of a DNA-repair function results in a substantially better maintenance of learning abilities, together with fewer signs of brain aging, in old mice.
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Affiliation(s)
- Daniel Lucas
- Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, Madrid, Spain
| | | | - Beatriz Escudero
- Department of Regenerative Cardiology, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
- Development and Cardiac Repair Department, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Carmen Albo
- Department of Regenerative Cardiology, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
- Development and Cardiac Repair Department, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Ana Aza
- Centro de Biología Molecular Severo Ochoa, Campus de Cantoblanco, Madrid, Spain
| | - Rebeca Acín-Pérez
- Department of Regenerative Cardiology, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
- Development and Cardiac Repair Department, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Yaima Torres
- Department of Regenerative Cardiology, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
- Development and Cardiac Repair Department, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Paz Moreno
- Department of Regenerative Cardiology, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - José Antonio Enríquez
- Department of Regenerative Cardiology, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
- Development and Cardiac Repair Department, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Enrique Samper
- Department of Regenerative Cardiology, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
- Development and Cardiac Repair Department, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Luis Blanco
- Centro de Biología Molecular Severo Ochoa, Campus de Cantoblanco, Madrid, Spain
| | - Alfonso Fairén
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas - Universidad Miguel Hernández, San Juan de Alicante, Spain
| | - Antonio Bernad
- Department of Regenerative Cardiology, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
- Development and Cardiac Repair Department, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
- Translational Research Platform, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
- * E-mail: (AB); (AG)
| | - Agnès Gruart
- División de Neurociencias, Universidad Pablo de Olavide, Sevilla, Spain
- * E-mail: (AB); (AG)
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123
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Strande NT, Waters CA, Ramsden DA. Resolution of complex ends by Nonhomologous end joining - better to be lucky than good? Genome Integr 2012; 3:10. [PMID: 23276302 PMCID: PMC3547747 DOI: 10.1186/2041-9414-3-10] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 12/16/2012] [Indexed: 12/03/2022] Open
Abstract
The Nonhomologous end joining pathway is essential for efficient repair of chromosome double strand breaks. This pathway consequently plays a key role in cellular resistance to break-inducing exogenous agents, as well as in the developmentally-programmed recombinations that are required for adaptive immunity. Chromosome breaks often have complex or “dirty” end structures that can interfere with the critical ligation step in this pathway; we review here how Nonhomologous end joining resolves such breaks.
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Affiliation(s)
- Natasha Tiffany Strande
- Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics and Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
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124
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Martin MJ, Garcia-Ortiz MV, Esteban V, Blanco L. Ribonucleotides and manganese ions improve non-homologous end joining by human Polμ. Nucleic Acids Res 2012; 41:2428-36. [PMID: 23275568 PMCID: PMC3575841 DOI: 10.1093/nar/gks1444] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Human DNA polymerase mu (Polμ), a family X member involved in DNA repair, has both template-directed and terminal transferase (template-independent) activities. In addition to their ability to incorporate untemplated nucleotides, another similarity between Polµ and terminal deoxynucleotidyl transferase (TdT) is their promiscuity in using ribonucleotides (NTPs), whose physiological significance is presently unknown. As shown here, Polµ can use NTPs instead of deoxynucleotides (dNTPs) during non-homologous end joining (NHEJ) of non-complementary ends, a Polµ-specific task. Moreover, a physiological concentration of Mn2+ ions did benefit Polµ-mediated NHEJ by improving the efficiency and accuracy of nucleotide insertion. Analysis of different mutations in the ‘steric gate’ of the active site indicated that Polµ is taking advantage of an open active site, valid for selecting alternative activating metal ions and nucleotides as substrates. This versatility would allow ad hoc selection of the most appropriate nucleotide/metal ion combination for individual NHEJ events to gain efficiency without a cost in terms of fidelity, thus widening the spectrum of available solutions to position a discontinuous template strand in proper register for connection.
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Affiliation(s)
- Maria Jose Martin
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), 28049 Madrid, Spain
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125
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Ramsden DA, Asagoshi K. DNA polymerases in nonhomologous end joining: are there any benefits to standing out from the crowd? ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2012; 53:741-751. [PMID: 22987211 DOI: 10.1002/em.21725] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 07/17/2012] [Accepted: 07/17/2012] [Indexed: 06/01/2023]
Abstract
Chromosome breaks, often with damaged or missing DNA flanking the break site, are an important threat to genome stability. They are repaired in vertebrates primarily by nonhomologous end joining (NHEJ). NHEJ is unique among the major DNA repair pathways in that a continuous template cannot be used by DNA polymerases to instruct replacement of damaged or lost DNA. Nevertheless, at least 3 out of the 17 mammalian DNA polymerases are specifically employed by NHEJ. Biochemical and structural studies are further revealing how each of the polymerases employed by NHEJ possesses distinct and sophisticated means to overcome the barriers this pathway presents to polymerase activity. Still unclear, though, is how the resulting network of overlapping and nonoverlapping polymerase activities contributes to repair in cells.
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Affiliation(s)
- Dale A Ramsden
- Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA.
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126
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Menezes MR, Sweasy JB. Mouse models of DNA polymerases. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2012; 53:645-665. [PMID: 23001998 DOI: 10.1002/em.21731] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 08/01/2012] [Accepted: 08/07/2012] [Indexed: 06/01/2023]
Abstract
In 1956, Arthur Kornberg discovered the mechanism of the biological synthesis of DNA and was awarded the Nobel Prize in Physiology or Medicine in 1959 for this contribution, which included the isolation and characterization of Escherichia coli DNA polymerase I. Now there are 15 known DNA polymerases in mammalian cells that belong to four different families. These DNA polymerases function in many different cellular processes including DNA replication, DNA repair, and damage tolerance. Several biochemical and cell biological studies have provoked a further investigation of DNA polymerase function using mouse models in which polymerase genes have been altered using gene-targeting techniques. The phenotypes of mice harboring mutant alleles reveal the prominent role of DNA polymerases in embryogenesis, prevention of premature aging, and cancer suppression.
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Affiliation(s)
- Miriam R Menezes
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
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127
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Aza A, Martin MJ, Juarez R, Blanco L, Terrados G. DNA expansions generated by human Polμ on iterative sequences. Nucleic Acids Res 2012; 41:253-63. [PMID: 23143108 PMCID: PMC3592450 DOI: 10.1093/nar/gks1054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Polµ is the only DNA polymerase equipped with template-directed and terminal transferase activities. Polµ is also able to accept distortions in both primer and template strands, resulting in misinsertions and extension of realigned mismatched primer terminus. In this study, we propose a model for human Polµ-mediated dinucleotide expansion as a function of the sequence context. In this model, Polµ requires an initial dislocation, that must be subsequently stabilized, to generate large sequence expansions at different 5′-P-containing DNA substrates, including those that mimic non-homologous end-joining (NHEJ) intermediates. Our mechanistic studies point at human Polµ residues His329 and Arg387 as responsible for regulating nucleotide expansions occurring during DNA repair transactions, either promoting or blocking, respectively, iterative polymerization. This is reminiscent of the role of both residues in the mechanism of terminal transferase activity. The iterative synthesis performed by Polµ at various contexts may lead to frameshift mutations producing DNA damage and instability, which may end in different human disorders, including cancer or congenital abnormalities.
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Affiliation(s)
- Ana Aza
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, 28049 Madrid, Spain
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128
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Zucca E, Bertoletti F, Wimmer U, Ferrari E, Mazzini G, Khoronenkova S, Grosse N, van Loon B, Dianov G, Hübscher U, Maga G. Silencing of human DNA polymerase λ causes replication stress and is synthetically lethal with an impaired S phase checkpoint. Nucleic Acids Res 2012; 41:229-41. [PMID: 23118481 PMCID: PMC3592438 DOI: 10.1093/nar/gks1016] [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: 12/21/2022] Open
Abstract
Human DNA polymerase (pol) λ functions in base excision repair and non-homologous end joining. We have previously shown that DNA pol λ is involved in accurate bypass of the two frequent oxidative lesions, 7,8-dihydro-8-oxoguanine and 1,2-dihydro-2-oxoadenine during the S phase. However, nothing is known so far about the relationship of DNA pol λ with the S phase DNA damage response checkpoint. Here, we show that a knockdown of DNA pol λ, but not of its close homologue DNA pol β, results in replication fork stress and activates the S phase checkpoint, slowing S phase progression in different human cancer cell lines. We furthermore show that DNA pol λ protects cells from oxidative DNA damage and also functions in rescuing stalled replication forks. Its absence becomes lethal for a cell when a functional checkpoint is missing, suggesting a DNA synthesis deficiency. Our results provide the first evidence, to our knowledge, that DNA pol λ is required for cell cycle progression and is functionally connected to the S phase DNA damage response machinery in cancer cells.
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Affiliation(s)
- Elisa Zucca
- Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, I-27100 Pavia, Italy
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129
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Martin MJ, Juarez R, Blanco L. DNA-binding determinants promoting NHEJ by human Polμ. Nucleic Acids Res 2012; 40:11389-403. [PMID: 23034807 PMCID: PMC3526283 DOI: 10.1093/nar/gks896] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Non-homologous end-joining (NHEJ), the preferred pathway to repair double-strand breaks (DSBs) in higher eukaryotes, relies on a collection of molecular tools to process the broken ends, including specific DNA polymerases. Among them, Polµ is unique as it can catalyze DNA synthesis upon connection of two non-complementary ends. Here, we demonstrate that this capacity is intrinsic to Polµ, not conferred by other NHEJ factors. To understand the molecular determinants of its specific function in NHEJ, the interaction of human Polµ with DNA has been directly visualized by electromobility shift assay and footprinting assays. Stable interaction with a DNA gap requires the presence of a recessive 5′-P, thus orienting the catalytic domain for primer and nucleotide binding. Accordingly, recognition of the 5′-P is crucial to align the two DNA substrates of the NHEJ reaction. Site-directed mutagenesis demonstrates the relevance of three specific residues (Lys249, Arg253 and Arg416) in stabilizing the primer strand during end synapsis, allowing a range of microhomology-induced distortions beneficial for NHEJ. Moreover, our results suggest that the Polµ BRCT domain, thought to be exclusively involved in interaction with NHEJ core factors, has a direct role in binding the DNA region neighbor to the 5′-P, thus boosting Polµ-mediated NHEJ reactions.
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Affiliation(s)
- Maria Jose Martin
- Department of Genome Dynamics and Function, Centro de Biologia Molecular Severo Ochoa (CSIC-UAM), 28049 Madrid, Spain
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130
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Matsumoto T, Go K, Hyodo M, Koiwai K, Maezawa S, Hayano T, Suzuki M, Koiwai O. BRCT domain of DNA polymerase μ has DNA-binding activity and promotes the DNA polymerization activity. Genes Cells 2012; 17:790-806. [DOI: 10.1111/j.1365-2443.2012.01628.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 06/14/2012] [Indexed: 11/30/2022]
Affiliation(s)
- Takuro Matsumoto
- Department of Applied Biological Science; Faculty of Science and Technology; Tokyo University of Science; Noda; Chiba; 278-8510; Japan
| | - Kaori Go
- Department of Applied Biological Science; Faculty of Science and Technology; Tokyo University of Science; Noda; Chiba; 278-8510; Japan
| | - Mariko Hyodo
- Department of Applied Biological Science; Faculty of Science and Technology; Tokyo University of Science; Noda; Chiba; 278-8510; Japan
| | - Kotaro Koiwai
- Department of Applied Biological Science; Faculty of Science and Technology; Tokyo University of Science; Noda; Chiba; 278-8510; Japan
| | - So Maezawa
- Department of Applied Biological Science; Faculty of Science and Technology; Tokyo University of Science; Noda; Chiba; 278-8510; Japan
| | - Takahide Hayano
- Department of Applied Biological Science; Faculty of Science and Technology; Tokyo University of Science; Noda; Chiba; 278-8510; Japan
| | - Masahiro Suzuki
- Department of Applied Biological Science; Faculty of Science and Technology; Tokyo University of Science; Noda; Chiba; 278-8510; Japan
| | - Osamu Koiwai
- Department of Applied Biological Science; Faculty of Science and Technology; Tokyo University of Science; Noda; Chiba; 278-8510; Japan
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131
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Baños B, Villar L, Salas M, de Vega M. DNA stabilization at the Bacillus subtilis PolX core--a binding model to coordinate polymerase, AP-endonuclease and 3'-5' exonuclease activities. Nucleic Acids Res 2012; 40:9750-62. [PMID: 22844091 PMCID: PMC3479172 DOI: 10.1093/nar/gks702] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Family X DNA polymerases (PolXs) are involved in DNA repair. Their binding to gapped DNAs relies on two conserved helix-hairpin-helix motifs, one located at the 8-kDa domain and the other at the fingers subdomain. Bacterial/archaeal PolXs have a specifically conserved third helix-hairpin-helix motif (GFGxK) at the fingers subdomain whose putative role in DNA binding had not been established. Here, mutagenesis at the corresponding residues of Bacillus subtilis PolX (PolXBs), Gly130, Gly132 and Lys134 produced enzymes with altered DNA binding properties affecting the three enzymatic activities of the protein: polymerization, located at the PolX core, 3'-5' exonucleolysis and apurinic/apyrimidinic (AP)-endonucleolysis, placed at the so-called polymerase and histidinol phosphatase domain. Furthermore, we have changed Lys192 of PolXBs, a residue moderately conserved in the palm subdomain of bacterial PolXs and immediately preceding two catalytic aspartates of the polymerization reaction. The results point to a function of residue Lys192 in guaranteeing the right orientation of the DNA substrates at the polymerization and histidinol phosphatase active sites. The results presented here and the recently solved structures of other bacterial PolX ternary complexes lead us to propose a structural model to account for the appropriate coordination of the different catalytic activities of bacterial PolXs.
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Affiliation(s)
- Benito Baños
- Instituto de Biología Molecular Eladio Viñuela (CSIC), Centro de Biología Molecular Severo Ochoa (CSIC-UAM), C/Nicolás Cabrera 1, Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain
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132
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Thompson LH. Recognition, signaling, and repair of DNA double-strand breaks produced by ionizing radiation in mammalian cells: the molecular choreography. Mutat Res 2012; 751:158-246. [PMID: 22743550 DOI: 10.1016/j.mrrev.2012.06.002] [Citation(s) in RCA: 261] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 06/09/2012] [Accepted: 06/16/2012] [Indexed: 12/15/2022]
Abstract
The faithful maintenance of chromosome continuity in human cells during DNA replication and repair is critical for preventing the conversion of normal diploid cells to an oncogenic state. The evolution of higher eukaryotic cells endowed them with a large genetic investment in the molecular machinery that ensures chromosome stability. In mammalian and other vertebrate cells, the elimination of double-strand breaks with minimal nucleotide sequence change involves the spatiotemporal orchestration of a seemingly endless number of proteins ranging in their action from the nucleotide level to nucleosome organization and chromosome architecture. DNA DSBs trigger a myriad of post-translational modifications that alter catalytic activities and the specificity of protein interactions: phosphorylation, acetylation, methylation, ubiquitylation, and SUMOylation, followed by the reversal of these changes as repair is completed. "Superfluous" protein recruitment to damage sites, functional redundancy, and alternative pathways ensure that DSB repair is extremely efficient, both quantitatively and qualitatively. This review strives to integrate the information about the molecular mechanisms of DSB repair that has emerged over the last two decades with a focus on DSBs produced by the prototype agent ionizing radiation (IR). The exponential growth of molecular studies, heavily driven by RNA knockdown technology, now reveals an outline of how many key protein players in genome stability and cancer biology perform their interwoven tasks, e.g. ATM, ATR, DNA-PK, Chk1, Chk2, PARP1/2/3, 53BP1, BRCA1, BRCA2, BLM, RAD51, and the MRE11-RAD50-NBS1 complex. Thus, the nature of the intricate coordination of repair processes with cell cycle progression is becoming apparent. This review also links molecular abnormalities to cellular pathology as much a possible and provides a framework of temporal relationships.
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Affiliation(s)
- Larry H Thompson
- Biology & Biotechnology Division, L452, Lawrence Livermore National Laboratory, P.O. Box 808, Livermore, CA 94551-0808, United States.
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133
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Chen H, Bernstein H, Ranganathan P, Schluter SF. Somatic hypermutation of TCR γ V genes in the sandbar shark. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2012; 37:176-83. [PMID: 21925537 DOI: 10.1016/j.dci.2011.08.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 08/29/2011] [Accepted: 08/31/2011] [Indexed: 05/05/2023]
Abstract
In a recent publication we demonstrated that somatic hypermutation occurs in the V region of the TCR γ gene of the sandbar shark (Carcharhinus plumbeus). We hypothesize that similar mechanisms are used to generate somatic mutations in both immunoglobulin and TCR γ genes of the sharks. Two distinct patterns of mutation occur, single nucleotide mutations (point mutations) and mutations comprising 2-5 consecutive bases (tandem mutations). Our data indicates that point mutations occur by a mechanism similar to that of somatic hypermutation in immunoglobulin genes of mammals, whereas tandem mutations may be generated by an error-prone DNA polymerase with terminal deoxynucleotidyl transferase (TdT)-like activity. Shark hotspot motifs identical to those of higher vertebrates were identified. We confirm that, as in immunoglobulin of sharks and higher vertebrates, highly significant targeting of AID activity to the classical DGYW/WRCH motif occurs in somatic hypermutation of sandbar shark TCR γ V genes. Our analysis suggests that the purpose of somatic mutations in shark TCR γ V-regions is to generate a more diverse repertoire in γ/δ receptors, rather than receptors with higher affinity.
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Affiliation(s)
- Hao Chen
- Department of Immunobiology, College of Medicine, University of Arizona, Tucson, AZ 85724, USA
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134
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Hogg M, Sauer-Eriksson AE, Johansson E. Promiscuous DNA synthesis by human DNA polymerase θ. Nucleic Acids Res 2012; 40:2611-22. [PMID: 22135286 PMCID: PMC3315306 DOI: 10.1093/nar/gkr1102] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 11/03/2011] [Accepted: 11/04/2011] [Indexed: 12/15/2022] Open
Abstract
The biological role of human DNA polymerase θ (POLQ) is not yet clearly defined, but it has been proposed to participate in several cellular processes based on its translesion synthesis capabilities. POLQ is a low-fidelity polymerase capable of efficient bypass of blocking lesions such as abasic sites and thymine glycols as well as extension of mismatched primer termini. Here, we show that POLQ possesses a DNA polymerase activity that appears to be template independent and allows efficient extension of single-stranded DNA as well as duplex DNA with either protruding or multiply mismatched 3'-OH termini. We hypothesize that this DNA synthesis activity is related to the proposed role for POLQ in the repair or tolerance of double-strand breaks.
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Affiliation(s)
- Matthew Hogg
- Department of Medical Biochemistry and Biophysics and Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
| | - A. Elisabeth Sauer-Eriksson
- Department of Medical Biochemistry and Biophysics and Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
| | - Erik Johansson
- Department of Medical Biochemistry and Biophysics and Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
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135
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Crespan E, Czabany T, Maga G, Hübscher U. Microhomology-mediated DNA strand annealing and elongation by human DNA polymerases λ and β on normal and repetitive DNA sequences. Nucleic Acids Res 2012; 40:5577-90. [PMID: 22373917 PMCID: PMC3384310 DOI: 10.1093/nar/gks186] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
'Classical' non-homologous end joining (NHEJ), dependent on the Ku70/80 and the DNA ligase IV/XRCC4 complexes, is essential for the repair of DNA double-strand breaks. Eukaryotic cells possess also an alternative microhomology-mediated end-joining (MMEJ) mechanism, which is independent from Ku and DNA ligase 4/XRCC4. The components of the MMEJ machinery are still largely unknown. Family X DNA polymerases (pols) are involved in the classical NHEJ pathway. We have compared in this work, the ability of human family X DNA pols β, λ and μ, to promote the MMEJ of different model templates with terminal microhomology regions. Our results reveal that DNA pol λ and DNA ligase I are sufficient to promote efficient MMEJ repair of broken DNA ends in vitro, and this in the absence of auxiliary factors. However, DNA pol β, not λ, was more efficient in promoting MMEJ of DNA ends containing the (CAG)n triplet repeat sequence of the human Huntingtin gene, leading to triplet expansion. The checkpoint complex Rad9/Hus1/Rad1 promoted end joining by DNA pol λ on non-repetitive sequences, while it limited triplet expansion by DNA pol β. We propose a possible novel role of DNA pol β in MMEJ, promoting (CAG)n triplet repeats instability.
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Affiliation(s)
- Emmanuele Crespan
- Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
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136
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Andres SN, Vergnes A, Ristic D, Wyman C, Modesti M, Junop M. A human XRCC4-XLF complex bridges DNA. Nucleic Acids Res 2012; 40:1868-78. [PMID: 22287571 PMCID: PMC3287209 DOI: 10.1093/nar/gks022] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
DNA double-strand breaks pose a significant threat to cell survival and must be repaired. In higher eukaryotes, such damage is repaired efficiently by non-homologous end joining (NHEJ). Within this pathway, XRCC4 and XLF fulfill key roles required for end joining. Using DNA-binding and -bridging assays, combined with direct visualization, we present evidence for how XRCC4-XLF complexes robustly bridge DNA molecules. This unanticipated, DNA Ligase IV-independent bridging activity by XRCC4-XLF suggests an early role for this complex during end joining, in addition to its more well-established later functions. Mutational analysis of the XRCC4-XLF C-terminal tail regions further identifies specialized functions in complex formation and interaction with DNA and DNA Ligase IV. Based on these data and the crystal structure of an extended protein filament of XRCC4-XLF at 3.94 Å, a model for XRCC4-XLF complex function in NHEJ is presented.
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Affiliation(s)
- Sara N Andres
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
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137
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Chayot R, Montagne B, Ricchetti M. DNA polymerase μ is a global player in the repair of non-homologous end-joining substrates. DNA Repair (Amst) 2012; 11:22-34. [DOI: 10.1016/j.dnarep.2011.09.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 09/23/2011] [Accepted: 09/27/2011] [Indexed: 12/25/2022]
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138
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Li P, Li J, Li M, Dou K, Zhang MJ, Suo F, Du LL. Multiple end joining mechanisms repair a chromosomal DNA break in fission yeast. DNA Repair (Amst) 2011; 11:120-30. [PMID: 22093869 DOI: 10.1016/j.dnarep.2011.10.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Non-homologous end joining (NHEJ) is an important mechanism for repairing DNA double-strand breaks (DSBs). The fission yeast Schizosaccharomyces pombe has a conserved set of NHEJ factors including Ku, DNA ligase IV, Xlf1, and Pol4. Their roles in chromosomal DSB repair have not been directly characterized before. Here we used HO endonuclease to create a specific chromosomal DSB in fission yeast and examined the imprecise end joining events allowing cells to survive the continuous expression of HO. Our analysis showed that cell survival was significantly reduced in mutants defective for Ku, ligase IV, or Xlf1. Using Sanger sequencing and Illumina sequencing, we have characterized in depth the repair junction sequences in HO survivors. In wild type cells the majority of repair events were one-nucleotide insertions dependent on Ku, ligase IV, and Pol4. Our data suggest that fission yeast Pol4 is important for gap filling during NHEJ repair and can extend primers in the absence of terminal base pairing with the templates. In Ku and ligase IV mutants, the survivors mainly resulted from two types of alternative end joining events: one used microhomology flanking the HO site to delete sequences of hundreds to thousands of base pairs, the other rejoined the break using the HO-generated overhangs but also introduced one- or two-nucleotide base substitutions. The chromosomal repair assay we describe here should provide a useful tool for further exploration of the end joining repair mechanisms in fission yeast.
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Affiliation(s)
- Peng Li
- National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing, China
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139
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Huefner ND, Mizuno Y, Weil CF, Korf I, Britt AB. Breadth by depth: expanding our understanding of the repair of transposon-induced DNA double strand breaks via deep-sequencing. DNA Repair (Amst) 2011; 10:1023-33. [PMID: 21889425 DOI: 10.1016/j.dnarep.2011.07.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Accepted: 07/26/2011] [Indexed: 01/20/2023]
Abstract
The transposases of DNA transposable elements catalyze the excision of the element from the host genome, but are not involved in the repair of the resulting double-strand break. To elucidate the role of various host DNA repair and damage response proteins in the repair of the hairpin-ended double strand breaks (DSBs) generated during excision of the maize Ac element in Arabidopsis thaliana, we deep-sequenced hundreds of thousands of somatic excision products from a variety of repair- or response-defective mutants. We find that each of these repair/response defects negatively affects the preservation of the ends, resulting in an enhanced frequency of deletions, insertions, and inversions at the excision site. The spectra of the resulting repair products demonstrate, not unexpectedly, that the canonical nonhomologous end joining (NHEJ) proteins DNA ligase IV and KU70 play an important role in the repair of the lesion generated by Ac excision. Our data also indicate that auxiliary NHEJ repair proteins such as DNA ligase VI and DNA polymerase lambda are routinely involved in the repair of these lesions. Roles for the damage response kinases ATM and ATR in the repair of transposition-induced DSBs are also discussed.
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Affiliation(s)
- Neil D Huefner
- Department of Plant Biology, University of California, Davis, CA 95616, USA
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140
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Oberle C, Blattner C. Regulation of the DNA Damage Response to DSBs by Post-Translational Modifications. Curr Genomics 2011; 11:184-98. [PMID: 21037856 PMCID: PMC2878983 DOI: 10.2174/138920210791110979] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Revised: 02/22/2010] [Accepted: 02/23/2010] [Indexed: 11/22/2022] Open
Abstract
Damage to the genetic material can affect cellular function in many ways. Therefore, maintenance of the genetic integrity is of primary importance for all cells. Upon DNA damage, cells respond immediately with proliferation arrest and repair of the lesion or apoptosis. All these consequences require recognition of the lesion and transduction of the information to effector systems. The accomplishment of DNA repair, but also of cell cycle arrest and apoptosis furthermore requires protein-protein interactions and the formation of larger protein complexes. More recent research shows that the formation of many of these aggregates depends on post-translational modifications. In this article, we have summarized the different cellular events in response to a DNA double strand break, the most severe lesion of the DNA.
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Affiliation(s)
- C Oberle
- Karlsruher Institute of Technology, Institute of Toxicology and Genetics, Karlsruhe PO-Box 3640, 76021 Karlsruhe, Germany
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141
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Ramsden DA. Polymerases in nonhomologous end joining: building a bridge over broken chromosomes. Antioxid Redox Signal 2011; 14:2509-19. [PMID: 20649463 PMCID: PMC3113452 DOI: 10.1089/ars.2010.3429] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Repair of double-strand breaks in chromosomal DNA is essential. Unfortunately, a paradigm central to most DNA repair pathways--damaged DNA is replaced by polymerases, by using an intact, undamaged complementary strand as a template--no longer works. The nonhomologous end joining (NHEJ) pathway nevertheless still uses DNA polymerases to help repair double-strand breaks. Bacteria use a member of the archaeo-eukaryal primase superfamily, whereas eukaryotes use multiple members of the polymerase X family. These polymerases can, depending on the biologic context, accurately replace break-associated damage, mitigate loss of flanking DNA, or diversify products of repair. Polymerases specifically implicated in NHEJ are uniquely effective in these roles: relative to canonic polymerases, NHEJ polymerases have been engineered to do more with less.
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Affiliation(s)
- Dale A Ramsden
- Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, and Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, NC 27599, USA.
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142
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Zuo Z, Lin HK, Trakselis MA. Strand annealing and terminal transferase activities of a B-family DNA polymerase. Biochemistry 2011; 50:5379-90. [PMID: 21545141 DOI: 10.1021/bi200421g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA replication polymerases have the inherent ability to faithfully and rapidly copy a DNA template according to precise Watson-Crick base pairing. The primary B-family DNA replication polymerase (Dpo1) in the hyperthermophilic archaeon, Sulfolobus solfataricus, is shown here to possess a remarkable DNA stabilizing ability for maintaining weak base pairing interactions to facilitate primer extension. This thermal stabilization by Dpo1 allowed for template-directed synthesis at temperatures more than 30 °C above the melting temperature of naked DNA. Surprisingly, Dpo1 also displays a competing terminal deoxynucleotide transferase (TdT) activity unlike any other B-family DNA polymerase. Dpo1 is shown to elongate single-stranded DNA in template-dependent and template-independent manners. Experiments with different homopolymeric templates indicate that initial deoxyribonucleotide incorporation is complementary to the template. Rate-limiting steps that include looping back and annealing to the template allow for a unique template-dependent terminal transferase activity. The multiple activities of this unique B-family DNA polymerase make this enzyme an essential component for DNA replication and DNA repair for the maintenance of the archaeal genome at high temperatures.
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Affiliation(s)
- Zhongfeng Zuo
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
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143
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Strittmatter T, Bareth B, Immel TA, Huhn T, Mayer TU, Marx A. Small Molecule Inhibitors of Human DNA Polymerase λ. ACS Chem Biol 2011; 6:314-9. [PMID: 21194240 DOI: 10.1021/cb100382m] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
To discover chemical probes to further under-stand the function of individual DNA polymerases, we established a generally applicable high-throughput screening. By applying this technique we discovered three novel inhibitor classes of human DNA polymerase λ (DNA Pol λ), a key enzyme to maintain the genetic integrity of the genome. The rhodanines, classified as an excellent drug scaffold, were found to be the most potent inhibitors for DNA Pol λ. Importantly, they are up to 10 times less active against the highly similar DNA polymerase β. We investigated basic structure activity relationships. Furthermore, the rhodanines showed pharmacological activity in two human cancer cell lines. So the here reported small molecules could serve as useful DNA Pol λ probes and might serve as starting point to develop novel therapeutic agents.
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Affiliation(s)
- Tobias Strittmatter
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Bettina Bareth
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Timo A. Immel
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Thomas Huhn
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Thomas U. Mayer
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Andreas Marx
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
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144
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Markkanen E, van Loon B, Ferrari E, Hübscher U. Ubiquitylation of DNA polymerase λ. FEBS Lett 2011; 585:2826-30. [PMID: 21486570 DOI: 10.1016/j.febslet.2011.03.069] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 03/31/2011] [Accepted: 03/31/2011] [Indexed: 12/26/2022]
Abstract
DNA polymerase (pol) λ, one of the 15 cellular pols, belongs to the X family. It is a small 575 amino-acid protein containing a polymerase, a dRP-lyase, a proline/serine rich and a BRCT domain. Pol λ shows various enzymatic activities including DNA polymerization, terminal transferase and dRP-lyase. It has been implicated to play a role in several DNA repair pathways, particularly base excision repair (BER), non-homologous end-joining (NHEJ) and translesion DNA synthesis (TLS). Similarly to other DNA repair enzymes, pol λ undergoes posttranslational modifications during the cell cycle that regulate its stability and possibly its subcellular localization. Here we describe our knowledge about ubiquitylation of pol λ and the impact of this modification on its regulation.
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Affiliation(s)
- Enni Markkanen
- Institute for Veterinary Biochemistry and Molecular Biology, University of Zürich-Irchel, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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145
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Xie P. A model for the dynamics of mammalian family X DNA polymerases. J Theor Biol 2011; 277:111-22. [PMID: 21377475 DOI: 10.1016/j.jtbi.2011.02.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2010] [Revised: 12/22/2010] [Accepted: 02/22/2011] [Indexed: 11/28/2022]
Abstract
Based on available structural studies, a model is presented for polymerization dynamics of mammalian family X DNA polymerases, including polymerases β, λ, μ, and terminal deoxynucleotidyl transferase (TdT). Using the model, distinct polymerization activities and processivities of the four polymerases acting on different forms of DNA substrate are analyzed and studied theoretically. A "gradient" of template dependence of polymerases β, λ, μ, and TdT is well explained. The much higher occurrence frequencies of the -1 frameshift DNA synthesis by pols λ and μ than that by pol β are well explained. The theoretical results on the polymerization processivities are also in agreement with the available experimental data.
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Affiliation(s)
- Ping Xie
- Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
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146
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Brissett NC, Martin MJ, Pitcher RS, Bianchi J, Juarez R, Green AJ, Fox GC, Blanco L, Doherty AJ. Structure of a preternary complex involving a prokaryotic NHEJ DNA polymerase. Mol Cell 2011; 41:221-31. [PMID: 21255731 DOI: 10.1016/j.molcel.2010.12.026] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Revised: 07/09/2010] [Accepted: 12/10/2010] [Indexed: 01/02/2023]
Abstract
In many prokaryotes, a specific DNA primase/polymerase (PolDom) is required for nonhomologous end joining (NHEJ) repair of DNA double-strand breaks (DSBs). Here, we report the crystal structure of a catalytically active conformation of Mycobacterium tuberculosis PolDom, consisting of a polymerase bound to a DNA end with a 3' overhang, two metal ions, and an incoming nucleotide but, significantly, lacking a primer strand. This structure represents a polymerase:DNA complex in a preternary intermediate state. This polymerase complex occurs in solution, stabilizing the enzyme on DNA ends and promoting nucleotide extension of short incoming termini. We also demonstrate that the invariant Arg(220), contained in a conserved loop (loop 2), plays an essential role in catalysis by regulating binding of a second metal ion in the active site. We propose that this NHEJ intermediate facilitates extension reactions involving critically short or noncomplementary DNA ends, thus promoting break repair and minimizing sequence loss during DSB repair.
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Affiliation(s)
- Nigel C Brissett
- Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
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147
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Li Y, Schlick T. Modeling DNA polymerase μ motions: subtle transitions before chemistry. Biophys J 2011; 99:3463-72. [PMID: 21081096 DOI: 10.1016/j.bpj.2010.09.056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 09/24/2010] [Accepted: 09/28/2010] [Indexed: 11/29/2022] Open
Abstract
To investigate whether an open-to-closed transition before the chemical step and induced-fit mechanism exist in DNA polymerase μ (pol μ), we analyze a series of molecular-dynamics simulations with and without the incoming nucleotide in various forms, including mutant systems, based on pol μ's crystal ternary structure. Our simulations capture no significant large-scale motion in either the DNA or the protein domains of pol μ. However, subtle residue motions can be distinguished, specifically of His(329) and Asp(330) to assemble in pol μ's active site, and of Gln(440) and Glu(443) to help accommodate the incoming nucleotide. Mutant simulations capture a DNA frameshift pairing and indicate the importance of Arg(444) and Arg(447) in stacking with the DNA template, and of Arg(448) and Gln(440) in helping to stabilize the position of both the DNA template and the incoming nucleotide. Although limited sampling in the molecular-dynamics simulations cannot be ruled out, our studies suggest an absence of a large-scale motion in pol μ. Together with the known crystallization difficulties of capturing the open form of pol μ, our studies also raise the possibility that a well-defined open form may not exist. Moreover, we suggest that residues Arg(448) and Gln(440) may be crucial for preventing insertion frameshift errors in pol μ.
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Affiliation(s)
- Yunlang Li
- Department of Chemistry, New York University, New York, NY, USA
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148
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Foley MC, Padow VA, Schlick T. DNA pol λ's extraordinary ability to stabilize misaligned DNA. J Am Chem Soc 2010; 132:13403-16. [PMID: 20822183 DOI: 10.1021/ja1049687] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
DNA polymerases have the venerable task of maintaining genome stability during DNA replication and repair. Errors, nonetheless, occur with error propensities that are polymerase specific. For example, DNA polymerase λ (pol λ) generates single-base deletions through template-strand slippage within short repetitive DNA regions much more readily than does the closely related polymerase β (pol β). Here we present in silico evidence to help interpret pol λ's greater tendency for deletion errors than pol β by its more favorable protein/DNA electrostatic interactions immediately around the extrahelical nucleotide on the template strand. Our molecular dynamics and free energy analyses suggest that pol λ provides greater stabilization to misaligned DNA than aligned DNA. Our study of several pol λ mutants of Lys544 (Ala, Phe, Glu) probes the interactions between the extrahelical nucleotide and the adjacent Lys544 to show that the charge of the 544 residue controls stabilization of the DNA misalignment. In addition, we identify other thumb residues (Arg538, Lys521, Arg517, and Arg514) that play coordinating roles in stabilizing pol λ's interactions with misaligned DNA. Interestingly, their aggregate stabilization effect is more important than that of any one component residue, in contrast to aligned DNA systems, as we determined from mutations of these key residues and energetic analyses. No such comparable network of stabilizing misaligned DNA exists in pol β. Evolutionary needs for DNA repair on substrates with minimal base-pairing, such as those encountered by pol λ in the non-homologous end-joining pathway, may have been solved by a greater tolerance to deletion errors. Other base-flipping proteins share similar binding properties and motions for extrahelical nucleotides.
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Affiliation(s)
- Meredith C Foley
- Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, New York 10012, USA
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149
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Rastogi RP, Richa, Kumar A, Tyagi MB, Sinha RP. Molecular mechanisms of ultraviolet radiation-induced DNA damage and repair. J Nucleic Acids 2010; 2010:592980. [PMID: 21209706 PMCID: PMC3010660 DOI: 10.4061/2010/592980] [Citation(s) in RCA: 603] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Revised: 08/15/2010] [Accepted: 09/28/2010] [Indexed: 11/20/2022] Open
Abstract
DNA is one of the prime molecules, and its stability is of utmost importance for proper functioning and existence of all living systems. Genotoxic chemicals and radiations exert adverse effects on genome stability. Ultraviolet radiation (UVR) (mainly UV-B: 280-315 nm) is one of the powerful agents that can alter the normal state of life by inducing a variety of mutagenic and cytotoxic DNA lesions such as cyclobutane-pyrimidine dimers (CPDs), 6-4 photoproducts (6-4PPs), and their Dewar valence isomers as well as DNA strand breaks by interfering the genome integrity. To counteract these lesions, organisms have developed a number of highly conserved repair mechanisms such as photoreactivation, base excision repair (BER), nucleotide excision repair (NER), and mismatch repair (MMR). Additionally, double-strand break repair (by homologous recombination and nonhomologous end joining), SOS response, cell-cycle checkpoints, and programmed cell death (apoptosis) are also operative in various organisms with the expense of specific gene products. This review deals with UV-induced alterations in DNA and its maintenance by various repair mechanisms.
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Affiliation(s)
- Rajesh P Rastogi
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
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Belousova EA, Lavrik OI. DNA polymerases β and λ and their roles in DNA replication and repair. Mol Biol 2010. [DOI: 10.1134/s0026893310060014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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