151
|
Abstract
During DNA repair by HR (homologous recombination), the ends of a DNA DSB (double-strand break) must be resected to generate single-stranded tails, which are required for strand invasion and exchange with homologous chromosomes. This 5'-3' end-resection of the DNA duplex is an essential process, conserved across all three domains of life: the bacteria, eukaryota and archaea. In the present review, we examine the numerous and redundant helicase and nuclease systems that function as the enzymatic analogues for this crucial process in the three major phylogenetic divisions.
Collapse
|
152
|
Ibanes S, Kremer EJ. Canine adenovirus type 2 vector generation via I-Sce1-mediated intracellular genome release. PLoS One 2013; 8:e71032. [PMID: 23936483 PMCID: PMC3731271 DOI: 10.1371/journal.pone.0071032] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 06/24/2013] [Indexed: 02/06/2023] Open
Abstract
When canine adenovirus type 2 (CAdV-2, or also commonly referred to as CAV-2) vectors are injected into the brain parenchyma they preferentially transduce neurons, are capable of efficient axonal transport to afferent regions, and allow transgene expression for at last >1 yr. Yet, translating these data into a user-friendly vector platform has been limited because CAV-2 vector generation is challenging. Generation of E1-deleted adenovirus vectors often requires transfection of linear DNA fragments of >30 kb containing the vector genome into an E1-transcomplementing cell line. In contrast to human adenovirus type 5 vector generation, CAV-2 vector generation is less efficient due, in part, to a reduced ability to initiate replication and poor transfectibility of canine cells with large, linear DNA fragments. To improve CAV-2 vector generation, we generated an E1-transcomplementing cell line expressing the estrogen receptor (ER) fused to I-SceI, a yeast meganuclease, and plasmids containing the I-SceI recognition sites flanking the CAV-2 vector genome. Using transfection of supercoiled plasmid and intracellular genome release via 4-OH-tamoxifen-induced nuclear translocation of I-SceI, we improved CAV-2 vector titers 1,000 fold, and in turn increased the efficacy of CAV-2 vector generation.
Collapse
Affiliation(s)
- Sandy Ibanes
- Institut de Génétique Moléculaire de Montpellier, CNRS, Montpellier, France
- Université de Montpellier I, Montpellier, France
- Université Montpellier II, Montpellier, France
| | - Eric J. Kremer
- Institut de Génétique Moléculaire de Montpellier, CNRS, Montpellier, France
- Université de Montpellier I, Montpellier, France
- Université Montpellier II, Montpellier, France
- * E-mail:
| |
Collapse
|
153
|
Mishra M, Sharma A, Shukla AK, Pragya P, Murthy RC, de Pomerai D, Dwivedi UN, Chowdhuri DK. Transcriptomic analysis provides insights on hexavalent chromium induced DNA double strand breaks and their possible repair in midgut cells of Drosophila melanogaster larvae. Mutat Res 2013; 747-748:28-39. [PMID: 23628323 DOI: 10.1016/j.mrfmmm.2013.04.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 04/16/2013] [Accepted: 04/19/2013] [Indexed: 06/02/2023]
Abstract
Hexavalent chromium [Cr(VI)] is a well known mutagen and carcinogen. Since genomic instability due to generation of double strand breaks (DSBs) is causally linked to carcinogenesis, we tested a hypothesis that Cr(VI) causes in vivo generation of DSBs and elicits DNA damage response. We fed repair proficient Drosophila melanogaster (Oregon R(+)) larvae Cr(VI) (20.0μg/ml) mixed food for 24 and 48h and observed a significant (p<0.05) induction of DSBs in their midgut cells after 48h using neutral Comet assay. Global gene expression profiling in Cr(VI)-exposed Oregon R(+) larvae unveiled mis-regulation of DSBs responsive repair genes both after 24 and 48h. In vivo generation of DSBs in exposed Drosophila was confirmed by an increased pH2Av immunostaining along with the activation of cell cycle regulation genes. Analysis of mis-regulated genes grouped under DSB response by GOEAST indicated the participation of non-homologous end joining (NHEJ) DSB repair pathway. We selected two strains, one mutant (ligIV) and another ku80-RNAi (knockdown of ku80), whose functions are essentially linked to NHEJ-DSB repair pathway. As a proof of principle, we compared the DSBs generation in larvae of these two strains with that of repair proficient Oregon R(+). Along with this, DSBs generation in spn-A and okr [essential genes in homologous recombination repair (HR) pathway] mutants was also tested for the possible involvement of HR-DSB repair. A significantly increased DSBs generation in the exposed ku80-RNAi and ligIV (mutant) larvae because of impaired repair, concomitant with an insignificant DSBs generation in okr and spn-A mutant larvae indicates an active participation of NHEJ repair pathway. The study, first of its kind to our knowledge, while providing evidences for in vivo generation of DSBs in Cr(VI) exposed Drosophila larvae, assumes significance for its relevance to higher organisms due to causal link between DSB generation and Cr(VI)-induced carcinogenesis.
Collapse
Affiliation(s)
- Manish Mishra
- Embryotoxicology Section and Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research CSIR-IITR, Lucknow 226001, Uttar Pradesh, India
| | | | | | | | | | | | | | | |
Collapse
|
154
|
Ji J, Tang D, Wang M, Li Y, Zhang L, Wang K, Li M, Cheng Z. MRE11 is required for homologous synapsis and DSB processing in rice meiosis. Chromosoma 2013; 122:363-76. [PMID: 23793712 DOI: 10.1007/s00412-013-0421-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 05/23/2013] [Accepted: 06/07/2013] [Indexed: 11/26/2022]
Abstract
Mre11, a conserved protein found in organisms ranging from yeast to multicellular organisms, is required for normal meiotic recombination. Mre11 interacts with Rad50 and Nbs1/Xrs2 to form a complex (MRN/X) that participates in double-strand break (DSB) ends processing. In this study, we silenced the MRE11 gene in rice and detailed its function using molecular and cytological methods. The OsMRE11-deficient plants exhibited normal vegetative growth but could not set seed. Cytological analysis indicated that in the OsMRE11-deficient plants, homologous pairing was totally inhibited, and the chromosomes were completely entangled as a formation of multivalents at metaphase I, leading to the consequence of serious chromosome fragmentation during anaphase I. Immunofluorescence studies further demonstrated that OsMRE11 is required for homologous synapsis and DSB processing but is dispensable for meiotic DSB formation. We found that OsMRE11 protein was located on meiotic chromosomes from interphase to late pachytene. This protein showed normal localization in zep1, Oscom1 and Osmer3, as well as in OsSPO11-1(RNAi) plants, but not in pair2 and pair3 mutants. Taken together, our results provide evidence that OsMRE11 performs a function essential for maintaining the normal HR process and inhibiting non-homologous recombination during meiosis.
Collapse
Affiliation(s)
- Jianhui Ji
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | | | | | | | | | | | | | | |
Collapse
|
155
|
Tang LL, Chen FY, Wang H, Hu XL, Dai X, Mao J, Shen ZT, Wu YH, Wang SM, Hai J, Yan GJ, Li H, Huang J. Haplotype analysis of eight genes of the monoubiquitinated FANCD2–DNA damage–repair pathway in breast cancer patients. Cancer Epidemiol 2013; 37:311-7. [DOI: 10.1016/j.canep.2012.12.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 11/20/2012] [Accepted: 12/30/2012] [Indexed: 11/28/2022]
|
156
|
Vissers JHA, van Lohuizen M, Citterio E. The emerging role of Polycomb repressors in the response to DNA damage. J Cell Sci 2013; 125:3939-48. [PMID: 23104738 DOI: 10.1242/jcs.107375] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Polycomb group (PcG) genes encode chromatin modifiers that are involved in the maintenance of cell identity and in proliferation, processes that are often deregulated in cancer. Interestingly, besides a role in epigenetic gene silencing, recent studies have begun to uncover a function for PcG proteins in the cellular response to DNA damage. In particular, PcG proteins have been shown to accumulate at sites of DNA double-strand breaks (DSBs). Several signaling pathways contribute to the recruitment of PcG proteins to DSBs, where they catalyze the ubiquitylation of histone H2A. The relevance of these findings is supported by the fact that loss of PcG genes decreases the efficiency of cells to repair DSBs and renders them sensitive to ionizing radiation. The recruitment of PcG proteins to DNA breaks suggests that they have a function in coordinating gene silencing and DNA repair at the chromatin flanking DNA lesions. In this Commentary, we discuss the current knowledge of the mechanisms that allow PcG proteins to exert their positive functions in genome maintenance.
Collapse
Affiliation(s)
- Joseph H A Vissers
- Division of Molecular Genetics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | | | | |
Collapse
|
157
|
Lee JH, Mand MR, Deshpande RA, Kinoshita E, Yang SH, Wyman C, Paull TT. Ataxia telangiectasia-mutated (ATM) kinase activity is regulated by ATP-driven conformational changes in the Mre11/Rad50/Nbs1 (MRN) complex. J Biol Chem 2013; 288:12840-51. [PMID: 23525106 PMCID: PMC3642328 DOI: 10.1074/jbc.m113.460378] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 03/22/2013] [Indexed: 11/23/2022] Open
Abstract
The Ataxia Telangiectasia-Mutated (ATM) protein kinase is recruited to sites of double-strand DNA breaks by the Mre11/Rad50/Nbs1 (MRN) complex, which also facilitates ATM monomerization and activation. MRN exists in at least two distinct conformational states, dependent on ATP binding and hydrolysis by the Rad50 protein. Here we use an ATP analog-sensitive form of ATM to determine that ATP binding, but not hydrolysis, by Rad50 is essential for MRN stimulation of ATM. Mre11 nuclease activity is dispensable, although some mutations in the Mre11 catalytic domain block ATM activation independent of nuclease function, as does the mirin compound. The coiled-coil domains of Rad50 are important for the DNA binding ability of MRN and are essential for ATM activation, but loss of the zinc hook connection can be substituted by higher levels of the complex. Nbs1 binds to the "closed" form of the MR complex, promoted by the zinc hook and by ATP binding. Thus the primary role of the hook is to tether Rad50 monomers together, promoting the association of the Rad50 catalytic domains into a form that binds ATP and also binds Nbs1. Collectively, these results show that the ATP-bound form of MRN is the critical conformation for ATM activation.
Collapse
Affiliation(s)
- Ji-Hoon Lee
- From the Howard Hughes Medical Institute and the Department of Molecular Genetics and Microbiology, the Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712 and
| | - Michael R. Mand
- From the Howard Hughes Medical Institute and the Department of Molecular Genetics and Microbiology, the Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712 and
| | - Rajashree A. Deshpande
- From the Howard Hughes Medical Institute and the Department of Molecular Genetics and Microbiology, the Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712 and
| | | | - Soo-Hyun Yang
- From the Howard Hughes Medical Institute and the Department of Molecular Genetics and Microbiology, the Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712 and
| | - Claire Wyman
- Radiation Oncology, Erasmus University Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Tanya T. Paull
- From the Howard Hughes Medical Institute and the Department of Molecular Genetics and Microbiology, the Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712 and
| |
Collapse
|
158
|
|
159
|
Rozier L, Guo Y, Peterson S, Sato M, Baer R, Gautier J, Mao Y. The MRN-CtIP pathway is required for metaphase chromosome alignment. Mol Cell 2013; 49:1097-107. [PMID: 23434370 PMCID: PMC3615147 DOI: 10.1016/j.molcel.2013.01.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Revised: 10/30/2012] [Accepted: 01/17/2013] [Indexed: 02/01/2023]
Abstract
Faithful duplication of the genome in S phase followed by its accurate segregation in mitosis is essential to maintain genomic integrity. Recent studies have suggested that proteins involved in DNA transactions are also required for whole-chromosome stability. Here we demonstrate that the MRN (Mre11, Rad50, and Nbs1) complex and CtIP are required for accurate chromosome segregation. Depletion of Mre11 or CtIP, antibody-mediated inhibition of Mre11, or small-molecule inhibition of MRN using mirin results in metaphase chromosome alignment defects in Xenopus egg extracts. Similarly, loss of MRN function adversely affects spindle assembly around DNA-coated beads in egg extracts. Inhibition of MRN function in mammalian cells triggers a metaphase delay and disrupts the RCC1-dependent RanGTP gradient. Addition of the Mre11 inhibitor mirin to egg extracts and mammalian cells reduces RCC1 association with mitotic chromosomes. Thus, the MRN-CtIP pathway contributes to Ran-dependent mitotic spindle assembly by modulating RCC1 chromosome association.
Collapse
Affiliation(s)
- Lorene Rozier
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, 630 W 168Street, New York, NY 10032
| | - Yige Guo
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, 630 W 168Street, New York, NY 10032
| | - Shaun Peterson
- Institute for Cancer Genetics, Irving Cancer Research Center, 1130 St. Nicholas Avenue, New York, NY 10032
| | - Mai Sato
- Institute for Cancer Genetics, Irving Cancer Research Center, 1130 St. Nicholas Avenue, New York, NY 10032
| | - Richard Baer
- Institute for Cancer Genetics, Irving Cancer Research Center, 1130 St. Nicholas Avenue, New York, NY 10032
| | - Jean Gautier
- Institute for Cancer Genetics, Irving Cancer Research Center, 1130 St. Nicholas Avenue, New York, NY 10032
| | - Yinghui Mao
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, 630 W 168Street, New York, NY 10032
| |
Collapse
|
160
|
Williams JS, Smith DJ, Marjavaara L, Lujan SA, Chabes A, Kunkel TA. Topoisomerase 1-mediated removal of ribonucleotides from nascent leading-strand DNA. Mol Cell 2013; 49:1010-5. [PMID: 23375499 DOI: 10.1016/j.molcel.2012.12.021] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 11/06/2012] [Accepted: 12/20/2012] [Indexed: 10/27/2022]
Abstract
RNase H2-dependent ribonucleotide excision repair (RER) removes ribonucleotides incorporated during DNA replication. When RER is defective, ribonucleotides in the nascent leading strand of the yeast genome are associated with replication stress and genome instability. Here, we provide evidence that topoisomerase 1 (Top1) initiates an independent form of repair to remove ribonucleotides from genomic DNA. This Top1-dependent process activates the S phase checkpoint. Deleting TOP1 reverses this checkpoint activation and also relieves replication stress and genome instability in RER-defective cells. The results reveal an additional removal pathway for a very common lesion in DNA, and they imply that the "dirty" DNA ends created when Top1 incises ribonucleotides in DNA are responsible for the adverse consequences of ribonucleotides in RNase H2-defective cells.
Collapse
Affiliation(s)
- Jessica S Williams
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA
| | | | | | | | | | | |
Collapse
|
161
|
Kumala S, Fujarewicz K, Jayaraju D, Rzeszowska-Wolny J, Hancock R. Repair of DNA strand breaks in a minichromosome in vivo: kinetics, modeling, and effects of inhibitors. PLoS One 2013; 8:e52966. [PMID: 23382828 PMCID: PMC3559499 DOI: 10.1371/journal.pone.0052966] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 11/26/2012] [Indexed: 11/23/2022] Open
Abstract
To obtain an overall picture of the repair of DNA single and double strand breaks in a defined region of chromatin in vivo, we studied their repair in a ∼170 kb circular minichromosome whose length and topology are analogous to those of the closed loops in genomic chromatin. The rate of repair of single strand breaks in cells irradiated with γ photons was quantitated by determining the sensitivity of the minichromosome DNA to nuclease S1, and that of double strand breaks by assaying the reformation of supercoiled DNA using pulsed field electrophoresis. Reformation of supercoiled DNA, which requires that all single strand breaks have been repaired, was not slowed detectably by the inhibitors of poly(ADP-ribose) polymerase-1 NU1025 or 1,5-IQD. Repair of double strand breaks was slowed by 20–30% when homologous recombination was supressed by KU55933, caffeine, or siRNA-mediated depletion of Rad51 but was completely arrested by the inhibitors of nonhomologous end-joining wortmannin or NU7441, responses interpreted as reflecting competition between these repair pathways similar to that seen in genomic DNA. The reformation of supercoiled DNA was unaffected when topoisomerases I or II, whose participation in repair of strand breaks has been controversial, were inhibited by the catalytic inhibitors ICRF-193 or F11782. Modeling of the kinetics of repair provided rate constants and showed that repair of single strand breaks in minichromosome DNA proceeded independently of repair of double strand breaks. The simplicity of quantitating strand breaks in this minichromosome provides a usefull system for testing the efficiency of new inhibitors of their repair, and since the sequence and structural features of its DNA and its transcription pattern have been studied extensively it offers a good model for examining other aspects of DNA breakage and repair.
Collapse
Affiliation(s)
- Slawomir Kumala
- Laval University Cancer Research Centre, Hôtel-Dieu Hospital, Québec, Canada
| | - Krzysztof Fujarewicz
- Bioinformatics Group, Institute of Automatic Control, Silesian University of Technology, Gliwice, Poland
| | - Dheekollu Jayaraju
- Laval University Cancer Research Centre, Hôtel-Dieu Hospital, Québec, Canada
| | - Joanna Rzeszowska-Wolny
- Biosystems Group, Institute of Automatic Control, Silesian University of Technology, Gliwice, Poland
| | - Ronald Hancock
- Laval University Cancer Research Centre, Hôtel-Dieu Hospital, Québec, Canada
- * E-mail:
| |
Collapse
|
162
|
Mechanism of repair of 5'-topoisomerase II-DNA adducts by mammalian tyrosyl-DNA phosphodiesterase 2. Nat Struct Mol Biol 2012; 19:1363-71. [PMID: 23104055 PMCID: PMC3529160 DOI: 10.1038/nsmb.2418] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 09/18/2012] [Indexed: 01/07/2023]
Abstract
The topoisomerase II (topo II) DNA incision-and-ligation cycle can be poisoned (for example following treatment with cancer chemotherapeutics) to generate cytotoxic DNA double-strand breaks (DSBs) with topo II covalently conjugated to DNA. Tyrosyl-DNA phosphodiesterase 2 (Tdp2) protects genomic integrity by reversing 5'-phosphotyrosyl-linked topo II-DNA adducts. Here, X-ray structures of mouse Tdp2-DNA complexes reveal that Tdp2 β-2-helix-β DNA damage-binding 'grasp', helical 'cap' and DNA lesion-binding elements fuse to form an elongated protein-DNA conjugate substrate-interaction groove. The Tdp2 DNA-binding surface is highly tailored for engagement of 5'-adducted single-stranded DNA ends and restricts nonspecific endonucleolytic or exonucleolytic processing. Structural, mutational and functional analyses support a single-metal ion catalytic mechanism for the exonuclease-endonuclease-phosphatase (EEP) nuclease superfamily and establish a molecular framework for targeted small-molecule blockade of Tdp2-mediated resistance to anticancer topoisomerase drugs.
Collapse
|
163
|
Delmas S, Duggin IG, Allers T. DNA damage induces nucleoid compaction via the Mre11-Rad50 complex in the archaeon Haloferax volcanii. Mol Microbiol 2012; 87:168-79. [PMID: 23145964 PMCID: PMC3565448 DOI: 10.1111/mmi.12091] [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] [Accepted: 11/05/2012] [Indexed: 11/30/2022]
Abstract
In prokaryotes the genome is organized in a dynamic structure called the nucleoid, which is embedded in the cytoplasm. We show here that in the archaeon Haloferax volcanii, compaction and reorganization of the nucleoid is induced by stresses that damage the genome or interfere with its replication. The fraction of cells exhibiting nucleoid compaction was proportional to the dose of the DNA damaging agent, and results obtained in cells defective for nucleotide excision repair suggest that breakage of DNA strands triggers reorganization of the nucleoid. We observed that compaction depends on the Mre11-Rad50 complex, suggesting a link to DNA double-strand break repair. However, compaction was observed in a radA mutant, indicating that the role of Mre11-Rad50 in nucleoid reorganisation is independent of homologous recombination. We therefore propose that nucleoid compaction is part of a DNA damage response that accelerates cell recovery by helping DNA repair proteins to locate their targets, and facilitating the search for intact DNA sequences during homologous recombination.
Collapse
Affiliation(s)
- Stéphane Delmas
- School of Biology, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK.
| | | | | |
Collapse
|
164
|
Pathways for genome integrity in G2 phase of the cell cycle. Biomolecules 2012; 2:579-607. [PMID: 24970150 PMCID: PMC4030857 DOI: 10.3390/biom2040579] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 11/17/2012] [Accepted: 11/23/2012] [Indexed: 12/31/2022] Open
Abstract
The maintenance of genome integrity is important for normal cellular functions, organism development and the prevention of diseases, such as cancer. Cellular pathways respond immediately to DNA breaks leading to the initiation of a multi-facetted DNA damage response, which leads to DNA repair and cell cycle arrest. Cell cycle checkpoints provide the cell time to complete replication and repair the DNA damage before it can continue to the next cell cycle phase. The G2/M checkpoint plays an especially important role in ensuring the propagation of error-free copies of the genome to each daughter cell. Here, we review recent progress in our understanding of DNA repair and checkpoint pathways in late S and G2 phases. This review will first describe the current understanding of normal cell cycle progression through G2 phase to mitosis. It will also discuss the DNA damage response including cell cycle checkpoint control and DNA double-strand break repair. Finally, we discuss the emerging concept that DNA repair pathways play a major role in the G2/M checkpoint pathway thereby blocking cell division as long as DNA lesions are present.
Collapse
|
165
|
Abstract
The histone variant H2AX is a principal component of chromatin involved in the detection, signaling, and repair of DNA double-strand breaks (DSBs). H2AX is thought to operate primarily through its C-terminal S139 phosphorylation, which mediates the recruitment of DNA damage response (DDR) factors to chromatin at DSB sites. Here, we describe a comprehensive screen of 67 residues in H2AX to determine their contributions to H2AX functions. Our analysis revealed that H2AX is both sumoylated and ubiquitylated. Individual residues defective for sumoylation, ubiquitylation, and S139 phosphorylation in untreated and damaged cells were identified. Specifically, we identified an acidic triad region in both H2A and H2AX that is required in cis for their ubiquitylation. We also report the characterization of a human H2AX knockout cell line, which exhibits DDR defects, including p53 activation, following DNA damage. Collectively, this work constitutes the first genetic complementation system for a histone in human cells. Finally, our data reveal new roles for several residues in H2AX and define distinct functions for H2AX in human cells.
Collapse
|
166
|
Oplustilova L, Wolanin K, Mistrik M, Korinkova G, Simkova D, Bouchal J, Lenobel R, Bartkova J, Lau A, O’Connor MJ, Lukas J, Bartek J. Evaluation of candidate biomarkers to predict cancer cell sensitivity or resistance to PARP-1 inhibitor treatment. Cell Cycle 2012; 11:3837-50. [PMID: 22983061 PMCID: PMC3495826 DOI: 10.4161/cc.22026] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Impaired DNA damage response pathways may create vulnerabilities of cancer cells that can be exploited therapeutically. One such selective vulnerability is the sensitivity of BRCA1- or BRCA2-defective tumors (hence defective in DNA repair by homologous recombination, HR) to inhibitors of the poly(ADP-ribose) polymerase-1 (PARP-1), an enzyme critical for repair pathways alternative to HR. While promising, treatment with PARP-1 inhibitors (PARP-1i) faces some hurdles, including (1) acquired resistance, (2) search for other sensitizing, non-BRCA1/2 cancer defects and (3) lack of biomarkers to predict response to PARP-1i. Here we addressed these issues using PARP-1i on 20 human cell lines from carcinomas of the breast, prostate, colon, pancreas and ovary. Aberrations of the Mre11-Rad50-Nbs1 (MRN) complex sensitized cancer cells to PARP-1i, while p53 status was less predictive, even in response to PARP-1i combinations with camptothecin or ionizing radiation. Furthermore, monitoring PARsylation and Rad51 foci formation as surrogate markers for PARP activity and HR, respectively, supported their candidacy for biomarkers of PARP-1i responses. As to resistance mechanisms, we confirmed the role of the multidrug resistance efflux transporters and its reversibility. More importantly, we demonstrated that shRNA lentivirus-mediated depletion of 53BP1 in human BRCA1-mutant breast cancer cells increased their resistance to PARP-1i. Given the preferential loss of 53BP1 in BRCA-defective and triple-negative breast carcinomas, our findings warrant assessment of 53BP1 among candidate predictive biomarkers of response to PARPi. Overall, this study helps characterize genetic and functional determinants of cellular responses to PARP-1i and contributes to the search for biomarkers to exploit PARP inhibitors in cancer therapy.
Collapse
Affiliation(s)
- Lenka Oplustilova
- Danish Cancer Society Research Center; Copenhagen, Denmark
- AstraZeneca; iMed Oncology; Macclesfield, Cheshire, UK
| | - Kamila Wolanin
- Danish Cancer Society Research Center; Copenhagen, Denmark
| | - Martin Mistrik
- Institute of Molecular and Translational Medicine; Faculty of Medicine and Dentistry; Palacky University; Olomouc, Czech Republic
| | - Gabriela Korinkova
- Institute of Molecular and Translational Medicine; Faculty of Medicine and Dentistry; Palacky University; Olomouc, Czech Republic
| | - Dana Simkova
- Institute of Molecular and Translational Medicine; Faculty of Medicine and Dentistry; Palacky University; Olomouc, Czech Republic
| | - Jan Bouchal
- Institute of Molecular and Translational Medicine; Faculty of Medicine and Dentistry; Palacky University; Olomouc, Czech Republic
| | - Rene Lenobel
- Laboratory of Growth Regulators; Palacky University Olomouc; Olomouc, Czech Republic
| | | | - Alan Lau
- AstraZeneca; iMed Oncology; Macclesfield, Cheshire, UK
| | | | - Jiri Lukas
- Danish Cancer Society Research Center; Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research; Faculty of Health and Medical Sciences; University of Copenhagen; Copenhagen, Denmark
| | - Jiri Bartek
- Danish Cancer Society Research Center; Copenhagen, Denmark
- Institute of Molecular and Translational Medicine; Faculty of Medicine and Dentistry; Palacky University; Olomouc, Czech Republic
| |
Collapse
|
167
|
Tittel-Elmer M, Lengronne A, Davidson MB, Bacal J, François P, Hohl M, Petrini JHJ, Pasero P, Cobb JA. Cohesin association to replication sites depends on rad50 and promotes fork restart. Mol Cell 2012; 48:98-108. [PMID: 22885006 PMCID: PMC3904740 DOI: 10.1016/j.molcel.2012.07.004] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 05/21/2012] [Accepted: 07/05/2012] [Indexed: 01/19/2023]
Abstract
The cohesin complex holds together newly replicated chromatids and is involved in diverse pathways that preserve genome integrity. We show that in budding yeast, cohesin is transiently recruited to active replication origins, and it spreads along DNA as forks progress. When DNA synthesis is impeded, cohesin accumulates at replication sites and is critical for the recovery of stalled forks. Cohesin enrichment at replication forks does not depend on γH2A(X) formation, which differs from its loading requirements at DNA double-strand breaks (DSBs). However, cohesin localization is largely reduced in rad50Δ mutants and in cells lacking both Mec1 and Tel1 checkpoint kinases. Interestingly, cohesin loading at replication sites depends on the structural features of Rad50 that are important for bridging sister chromatids, including the CXXC hook domain and the length of the coiled-coil extensions. Together, these data reveal a function for cohesin in the maintenance of genome integrity during S phase.
Collapse
Affiliation(s)
- Mireille Tittel-Elmer
- Department of Biochemistry and Molecular Biology, Southern Alberta Cancer Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB Canada T2N 4N1
- Institute of Human Genetics, Centre National de la Recherche Scientifique, Unité Propre de Recherche 1142, Montpellier, France
| | - Armelle Lengronne
- Institute of Human Genetics, Centre National de la Recherche Scientifique, Unité Propre de Recherche 1142, Montpellier, France
| | - Marta B Davidson
- Department of Biochemistry and Molecular Biology, Southern Alberta Cancer Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB Canada T2N 4N1
| | - Julien Bacal
- Institute of Human Genetics, Centre National de la Recherche Scientifique, Unité Propre de Recherche 1142, Montpellier, France
| | - Philippe François
- Institute of Human Genetics, Centre National de la Recherche Scientifique, Unité Propre de Recherche 1142, Montpellier, France
| | - Marcel Hohl
- Laboratory of Chromosome Biology, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA
| | - John H J Petrini
- Laboratory of Chromosome Biology, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA
| | - Philippe Pasero
- Institute of Human Genetics, Centre National de la Recherche Scientifique, Unité Propre de Recherche 1142, Montpellier, France
| | - Jennifer A Cobb
- Department of Biochemistry and Molecular Biology, Southern Alberta Cancer Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB Canada T2N 4N1
| |
Collapse
|
168
|
He J, Shi LZ, Truong LN, Lu CS, Razavian N, Li Y, Negrete A, Shiloach J, Berns MW, Wu X. Rad50 zinc hook is important for the Mre11 complex to bind chromosomal DNA double-stranded breaks and initiate various DNA damage responses. J Biol Chem 2012; 287:31747-56. [PMID: 22833675 PMCID: PMC3442509 DOI: 10.1074/jbc.m112.384750] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 07/24/2012] [Indexed: 11/06/2022] Open
Abstract
The Mre11-Rad50-Nbs1 (MRN) complex plays critical roles in checkpoint activation and double-stranded break (DSB) repair. The Rad50 zinc hook domain mediates zinc-dependent intercomplex associations of MRN, which is important for DNA tethering. Studies in yeast suggest that the Rad50 zinc hook domain is essential for MRN functions, but its role in mammalian cells is not clear. We demonstrated that the human Rad50 hook mutants are severely defective in various DNA damage responses including ATM (Ataxia telangiectasia mutated) activation, homologous recombination, sensitivity to IR, and activation of the ATR pathway. By using live cell imaging, we observed that the Rad50 hook mutants fail to be recruited to chromosomal DSBs, suggesting a novel mechanism underlying the severe defects observed for the Rad50 hook mutants. In vitro analysis showed that Zn(2+) promotes wild type but not the hook mutant of MR to bind double-stranded DNA. In vivo, the Rad50 hook mutants are defective in being recruited to chromosomal DSBs in both H2AX-proficient and -deficient cells, suggesting that the Rad50 hook mutants are impaired in direct binding to chromosomal DSB ends. We propose that the Rad50 zinc hook domain is important for the initial binding of MRN to DSBs, leading to ATM activation to phosphorylate H2AX, which recruits more MRN to the DSB-flanking chromosomal regions. Our studies reveal a critical role for the Rad50 zinc hook domain in establishing and maintaining MRN recruitment to chromosomal DSBs and suggest an important mechanism of how the Rad50 zinc hook domain contributes to DNA repair and checkpoint activation.
Collapse
Affiliation(s)
- Jing He
- From the Department of Molecular and Experimental Medicine, The Scripps Research Institute, La, Jolla, California 92037
| | - Linda Z. Shi
- the Institute of Engineering in Medicine, University of California San Diego, La Jolla, California 92093, and
| | - Lan N. Truong
- From the Department of Molecular and Experimental Medicine, The Scripps Research Institute, La, Jolla, California 92037
| | - Chi-Sheng Lu
- From the Department of Molecular and Experimental Medicine, The Scripps Research Institute, La, Jolla, California 92037
| | - Niema Razavian
- From the Department of Molecular and Experimental Medicine, The Scripps Research Institute, La, Jolla, California 92037
| | - Yongjiang Li
- From the Department of Molecular and Experimental Medicine, The Scripps Research Institute, La, Jolla, California 92037
| | - Alejandro Negrete
- the Biotechnology Core Laboratory, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Joseph Shiloach
- the Biotechnology Core Laboratory, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Michael W. Berns
- the Institute of Engineering in Medicine, University of California San Diego, La Jolla, California 92093, and
| | - Xiaohua Wu
- From the Department of Molecular and Experimental Medicine, The Scripps Research Institute, La, Jolla, California 92037
| |
Collapse
|
169
|
Yuan SSF, Hou MF, Hsieh YC, Huang CY, Lee YC, Chen YJ, Lo S. Role of MRE11 in cell proliferation, tumor invasion, and DNA repair in breast cancer. J Natl Cancer Inst 2012; 104:1485-502. [PMID: 22914783 DOI: 10.1093/jnci/djs355] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Previous studies have shown that altered forms of MRE11, a protein known to play a vital role in DNA double-strand break repair, DNA replication, and telomere maintenance are associated with cancer outcomes. We investigated the role of MRE11 in breast cancer in both clinical and in vitro settings. METHODS We examined MRE11 expression in tumor tissues from invasive ductal carcinoma breast cancer patients (n = 254) by immunohistochemistry, and associations with clinicopathological characteristics and overall survival were assessed using Cox proportional hazards regression models and Kaplan-Meier survival curves. Effect of MRE11 overexpression and knockdown on cell proliferation, invasion, and radioresistance was assessed in vitro using breast cancer cell lines (MCF-7 and MDA-MB-231). We also investigated the mechanisms involved. Effect of MRE11 overexpression on tumor growth was assessed in an orthotopic xenograft model (n = 8 mice per group). All statistical tests were two-sided. RESULTS Of the 254 tissue samples, 69.3% and 30.7% showed high and low MRE11 expression, respectively. High MRE11 expression was statistically significantly associated with malignant cancer behavior compared with low MRE11 expression (eg, stages III and IV vs stage I, P = .004; poor overall survival, P = .005). MRE11 overexpression in breast cancer cell lines promoted cell proliferation through STAT3, cell cycle entry, invasion and migration, and radioresistance via enhanced DNA repair activity and also inhibited apoptosis; knockdown of MRE11 had the opposite effect. In xenograft tumor-bearing mice (n = 8 per group), increased tumor growth was observed in the MRE11-overexpressing group compared with the control group (tumor volume at week 8, control vs MRE11-overexpressing tumor originating from MCF-7 cells, mean = 280.4 mm(3), 95% confidence interval [CI] = 62.4 to 498.4 mm(3) vs mean = 631.0 mm(3), 95% CI = 296.9 to 965.0 mm(3), P = .043). CONCLUSION High MRE11 expression was associated with a more malignant behavior in breast cancer. MRE11 may be a novel oncoprotein and may therefore serve as a new therapeutic intervention against breast cancer.
Collapse
|
170
|
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.
Collapse
Affiliation(s)
- Larry H Thompson
- Biology & Biotechnology Division, L452, Lawrence Livermore National Laboratory, P.O. Box 808, Livermore, CA 94551-0808, United States.
| |
Collapse
|
171
|
Andrin C, McDonald D, Attwood KM, Rodrigue A, Ghosh S, Mirzayans R, Masson JY, Dellaire G, Hendzel MJ. A requirement for polymerized actin in DNA double-strand break repair. Nucleus 2012; 3:384-95. [PMID: 22688650 DOI: 10.4161/nucl.21055] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Nuclear actin is involved in several nuclear processes from chromatin remodeling to transcription. Here we examined the requirement for actin polymerization in DNA double-strand break repair. Double-strand breaks are considered the most dangerous type of DNA lesion. Double-strand break repair consists of a complex set of events that are tightly regulated. Failure at any step can have catastrophic consequences such as genomic instability, oncogenesis or cell death. Many proteins involved in this repair process have been identified and their roles characterized. We discovered that some DNA double-strand break repair factors are capable of associating with polymeric actin in vitro and specifically, that purified Ku70/80 interacts with polymerized actin under these conditions. We find that the disruption of polymeric actin inhibits DNA double strand break repair both in vitro and in vivo. Introduction of nuclear targeted mutant actin that cannot polymerize, or the depolymerization of endogenous actin filaments by the addition of cytochalasin D, alters the retention of Ku80 at sites of DNA damage in live cells. Our results suggest that polymeric actin is required for proper DNA double-strand break repair and may function through the stabilization of the Ku heterodimer at the DNA damage site.
Collapse
Affiliation(s)
- Christi Andrin
- Department of Oncology, University of Alberta, Edmonton, AB Canada
| | | | | | | | | | | | | | | | | |
Collapse
|
172
|
Schreiner S, Wimmer P, Dobner T. Adenovirus degradation of cellular proteins. Future Microbiol 2012; 7:211-25. [PMID: 22324991 DOI: 10.2217/fmb.11.153] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Eukaryotic cells orchestrate constant synthesis and degradation of intracellular components, including soluble proteins and organelles. The two major intracellular degradation pathways are the ubiquitin/proteasome system and autophagy. Whereas ubiquitin/proteasome system is involved in rapid degradation of proteins, autophagy selectively removes protein aggregates and damaged organelles. Failure of these highly adjusted proteolytic systems to maintain basal turnover leads to altered cellular homeostasis. During evolution, certain viruses have developed mechanisms to exploit their functions to facilitate their own replication, prevent viral clearance and promote the outcome of infection. In this article, we summarize the current opinion on adenoviruses (Ad) and molecular host cell targets, extending on recent evidences for protein degradation pathways in infected cells. We describe recently identified connections between Ad-mediated proteolysis and viral replication with main emphasis on the function of certain Ad proteins.
Collapse
Affiliation(s)
- Sabrina Schreiner
- Heinrich-Pette-Institute, Leibniz-Institute for Experimental Virology, Martinistrasse 52, 20251 Hamburg, Germany. sabrina.schreiner@hpi. uni-hamburg.de
| | | | | |
Collapse
|
173
|
Sinha M, Peterson CL. Chromatin dynamics during repair of chromosomal DNA double-strand breaks. Epigenomics 2012; 1:371-85. [PMID: 20495614 DOI: 10.2217/epi.09.22] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The integrity of a eukaryotic genome is often challenged by DNA double-strand breaks (DSBs). Even a single, unrepaired DSB can be a lethal event, or such unrepaired damage can result in chromosomal instability and loss of genetic information. Furthermore, defects in the pathways that respond to and repair DSBs can lead to the onset of several human pathologic disorders with pleiotropic clinical features, including age-related diseases and cancer. For decades, studies have focused on elucidating the enzymatic mechanisms involved in recognizing, signaling and repairing DSBs within eukaryotic cells. The majority of biochemical and genetic studies have used simple, DNA substrates, whereas only recently efforts have been geared towards understanding how the repair machinery deals with DSBs within chromatin fibers, the nucleoprotein complex that packages DNA within the eukaryotic nucleus. The aim of this review is to discuss our recent understanding of the relationship between chromatin structure and the repair of DSBs by homologous recombination. In particular, we discuss recent studies implicating specialized roles for several, distinct ATP-dependent chromatin remodeling enzymes in facilitating multiple steps within the homologous recombination process.
Collapse
Affiliation(s)
- Manisha Sinha
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA.
| | | |
Collapse
|
174
|
Wu J, Zhang X, Zhang L, Wu CY, Rezaeian AH, Chan CH, Li JM, Wang J, Gao Y, Han F, Jeong YS, Yuan X, Khanna KK, Jin J, Zeng YX, Lin HK. Skp2 E3 ligase integrates ATM activation and homologous recombination repair by ubiquitinating NBS1. Mol Cell 2012; 46:351-61. [PMID: 22464731 DOI: 10.1016/j.molcel.2012.02.018] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 12/16/2011] [Accepted: 02/28/2012] [Indexed: 11/28/2022]
Abstract
The Mre11/Rad50/NBS1 (MRN) complex is thought to be a critical sensor that detects damaged DNA and recruits ATM to DNA foci for activation. However, it remains to be established how the MRN complex regulates ATM recruitment to the DNA foci during DNA double-strand breaks (DSBs). Here we show that Skp2 E3 ligase is a key component for the MRN complex-mediated ATM activation in response to DSBs. Skp2 interacts with NBS1 and triggers K63-linked ubiquitination of NBS1 upon DSBs, which is critical for the interaction of NBS1 with ATM, thereby facilitating ATM recruitment to the DNA foci for activation. Finally, we show that Skp2 deficiency exhibits a defect in homologous recombination (HR) repair, thereby increasing IR sensitivity. Our results provide molecular insights into how Skp2 and the MRN complex coordinate to activate ATM, and identify Skp2-mediatetd NBS1 ubiquitination as a vital event for ATM activation in response to DNA damage.
Collapse
Affiliation(s)
- Juan Wu
- State Key Laboratory of Oncology in South China and Department of Experimental Research, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
175
|
Savina NV, Smal MP, Kuzhir TD, Egorova TM, Khurs OM, Polityko AD, Goncharova RI. Biomarkers for genome instability in some genetic disorders: a pilot study. Biomarkers 2012; 17:201-8. [DOI: 10.3109/1354750x.2011.651157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
176
|
Molecular nature of radiation injury and DNA repair disorders associated with radiosensitivity. Int J Hematol 2012; 95:239-45. [DOI: 10.1007/s12185-012-1008-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 01/09/2012] [Accepted: 01/09/2012] [Indexed: 12/29/2022]
|
177
|
Errico A, Costanzo V. Mechanisms of replication fork protection: a safeguard for genome stability. Crit Rev Biochem Mol Biol 2012; 47:222-35. [DOI: 10.3109/10409238.2012.655374] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
178
|
Abstract
In recent years, our understanding of the functioning of ABC (ATP-binding cassette) systems has been boosted by the combination of biochemical and structural approaches. However, the origin and the distribution of ABC proteins among living organisms are difficult to understand in a phylogenetic perspective, because it is hard to discriminate orthology and paralogy, due to the existence of horizontal gene transfer. In this chapter, I present an update of the classification of ABC systems and discuss a hypothetical scenario of their evolution. The hypothetical presence of ABC ATPases in the last common ancestor of modern organisms is discussed, as well as the additional possibility that ABC systems might have been transmitted to eukaryotes, after the two endosymbiosis events that led to the constitution of eukaryotic organelles. I update the functional information of selected ABC systems and introduce new families of ABC proteins that have been included recently into this vast superfamily, thanks to the availability of high-resolution three-dimensional structures.
Collapse
|
179
|
Liu J, Luo S, Zhao H, Liao J, Li J, Yang C, Xu B, Stern DF, Xu X, Ye K. Structural mechanism of the phosphorylation-dependent dimerization of the MDC1 forkhead-associated domain. Nucleic Acids Res 2012; 40:3898-912. [PMID: 22234877 PMCID: PMC3351156 DOI: 10.1093/nar/gkr1296] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
MDC1 is a key mediator of the DNA-damage response in mammals with several phosphorylation-dependent protein interaction domains. The function of its N-terminal forkhead-associated (FHA) domain remains elusive. Here, we show with structural, biochemical and cellular data that the FHA domain mediates phosphorylation-dependent dimerization of MDC1 in response to DNA damage. Crystal structures of the FHA domain reveal a face-to-face dimer with pseudo-dyad symmetry. We found that the FHA domain recognizes phosphothreonine 4 (pT4) at the N-terminus of MDC1 and determined its crystal structure in complex with a pT4 peptide. Biochemical analysis further revealed that in the dimer, the FHA domain binds in trans to pT4 from the other subunit, which greatly stabilizes the otherwise unstable dimer. We show that T4 is phosphorylated primarily by ATM upon DNA damage. MDC1 mutants with the FHA domain deleted or impaired in its ability to dimerize formed fewer foci at DNA-damage sites, but the localization defect was largely rescued by an artificial dimerization module, suggesting that dimerization is the primary function of the MDC1 FHA domain. Our results suggest a novel mechanism for the regulation of MDC1 function through T4 phosphorylation and FHA-mediated dimerization.
Collapse
Affiliation(s)
- Jinping Liu
- Beijing Key Laboratory of DNA Damage Response and College of Life Science, Capital Normal University, Beijing 100048, China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
180
|
Brooks JD, Teraoka SN, Reiner AS, Satagopan JM, Bernstein L, Thomas DC, Capanu M, Stovall M, Smith SA, Wei S, Shore RE, Boice JD, Lynch CF, Mellemkjaer L, Malone KE, Liang X, Haile RW, Concannon P, Bernstein JL. Variants in activators and downstream targets of ATM, radiation exposure, and contralateral breast cancer risk in the WECARE study. Hum Mutat 2012; 33:158-64. [PMID: 21898661 PMCID: PMC3240722 DOI: 10.1002/humu.21604] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 08/25/2011] [Indexed: 11/07/2022]
Abstract
Ionizing radiation (IR) is a breast carcinogen that induces DNA double-strand breaks (DSBs), and variation in genes involved in the DNA DSB response has been implicated in radiation-induced breast cancer. The Women's Environmental, Cancer, and Radiation Epidemiology (WECARE) study is a population-based study of cases with contralateral breast cancer (CBC) and matched controls with unilateral breast cancer. The location-specific radiation dose received by the contralateral breast was estimated from radiotherapy records and mathematical models. One hundred fifty-two SNPs in six genes (CHEK2, MRE11A, MDC1, NBN, RAD50, TP53BP1) involved in the DNA DSBs response were genotyped. No variants or haplotypes were associated with CBC risk (649 cases and 1,284 controls) and no variants were found to interact with radiation dose. Carriers of a RAD50 haplotype exposed to ≥1 gray (Gy) had an increased risk of CBC compared with unexposed carriers (Rate ratios [RR] = 4.31 [95% confidence intervals [CI] 1.93-9.62]); with an excess relative risk (ERR) per Gy = 2.13 [95% CI 0.61-5.33]). Although the results of this study were largely null, carriers of a haplotype in RAD50 treated with radiation had a greater CBC risk than unexposed carriers. This suggests that carriers of this haplotype may be susceptible to the DNA-damaging effects of radiation therapy associated with radiation-induced breast cancer.
Collapse
Affiliation(s)
- Jennifer D Brooks
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
181
|
Golla RM, Li M, Shen Y, Ji M, Yan Y, Fu K, Greiner TC, McKeithan TW, Chan WC. Inhibition of poly(ADP-ribose) polymerase (PARP) and ataxia telangiectasia mutated (ATM) on the chemosensitivity of mantle cell lymphoma to agents that induce DNA strand breaks. Hematol Oncol 2011; 30:175-9. [PMID: 22170260 DOI: 10.1002/hon.1020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 09/29/2011] [Accepted: 10/03/2011] [Indexed: 02/02/2023]
Abstract
There is a high incidence of genomic aberration of ataxia telangiectasia mutated (ATM) and genes encoding proteins involved in the ATM pathway in mantle cell lymphoma (MCL). It has been shown that poly(ADP-ribose) polymerase inhibitor (PARPi) strongly enhances the cytotoxicity of agents, causing single-strand DNA breaks in cells with impaired homologous recombination repair. Here, we show that PARPi AG14361 potentiates the cytotoxicity induced by topotecan treatment in MCL cell lines, which was not dependent on either TP53 or CHEK2 status. Inhibition and/or knockdown of ATM and BRCA2 did not potentiate the cytotoxic effect of treatment with PARPi and topotecan. With loss of function of ATM, other kinases can still mediate activation of ATM substrates as demonstrated by continued phosphorylation of CHEK2 (Thr-68), although attenuated and delayed. These results suggest that PARPi may enhance the therapeutic efficacy of DNA damaging agents on MCL through TP53-independent mechanisms without requiring the inhibition of either ATM or BRCA2.
Collapse
Affiliation(s)
- Radha M Golla
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
182
|
Abstract
Generation of the 3′ overhang is a critical event during homologous recombination (HR) repair of DNA double strand breaks. A 5′–3′ nuclease, NurA, plays an important role in generating 3′ single-stranded DNA during archaeal HR, together with Mre11–Rad50 and HerA. We have determined the crystal structures of apo- and dAMP-Mn2+-bound NurA from Pyrococcus furiousus (Pf NurA) to provide the basis for its cleavage mechanism. Pf NurA forms a pyramid-shaped dimer containing a large central channel on one side, which becomes narrower towards the peak of the pyramid. The structure contains a PIWI domain with high similarity to argonaute, endoV nuclease and RNase H. The two active sites, each of which contains Mn2+ ion(s) and dAMP, are at the corners of the elliptical channel near the flat face of the dimer. The 3′ OH group of the ribose ring is directed toward the channel entrance, explaining the 5′–3′ nuclease activity of Pf NurA. We provide a DNA binding and cleavage model for Pf NurA.
Collapse
Affiliation(s)
- Jina Chae
- Department of Life Science, Pohang University of Science and Technology, Pohang 790-784, South Korea
| | | | | |
Collapse
|
183
|
Weitzel CS, Waldman VM, Graham TA, Oakley MG. A repeated coiled-coil interruption in the Escherichia coli condensin MukB. J Mol Biol 2011; 414:578-95. [PMID: 22041452 DOI: 10.1016/j.jmb.2011.10.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 10/17/2011] [Accepted: 10/18/2011] [Indexed: 01/18/2023]
Abstract
MukB, a divergent structural maintenance of chromosomes (SMC) protein, is important for chromosome segregation and condensation in Escherichia coli and other γ-proteobacteria. MukB and canonical SMC proteins share a common five-domain structure in which globular N- and C-terminal regions combine to form an ATP-binding-cassette-like ATPase domain. This ATPase domain is connected to a central, globular dimerization domain by a long antiparallel coiled coil. The structures of both globular domains have been solved recently. In contrast, little is known about the coiled coil, in spite of its clear importance for SMC function. Recently, we identified interacting regions on the N- and C-terminal halves of the MukB coiled coil through photoaffinity cross-linking experiments. On the basis of these low-resolution experimental constraints, phylogenetic data, and coiled-coil prediction analysis, we proposed a preliminary model in which the MukB coiled coil is divided into multiple segments. Here, we use a disulfide cross-linking assay to detect paired residues on opposite strands of MukB's coiled coil. This method provides accurate register data and demonstrates the presence of at least five coiled-coil segments in this domain. Moreover, these studies show that the segments are interrupted by a repeated, unprecedented deviation from canonical coiled-coil structure. These experiments provide a sufficiently detailed view of the MukB coiled coil to allow rational manipulation of this region for the first time, opening the door for structure-function studies of this domain.
Collapse
|
184
|
Höglund A, Strömvall K, Li Y, Forshell LP, Nilsson JA. Chk2 deficiency in Myc overexpressing lymphoma cells elicits a synergistic lethal response in combination with PARP inhibition. Cell Cycle 2011; 10:3598-607. [PMID: 22030621 DOI: 10.4161/cc.10.20.17887] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Myc is a transcription factor frequently found deregulated in human cancer. The Myc-mediated cellular transformation process is associated with fast proliferative cells and inherent genomic instability, giving rise to malignant, invasive neoplasms with poor prognosis for survival. Transcription-independent functions of Myc include stimulation of replication. Excessive Myc expression stimulates a replication-associated DNA damage response that signals via the phosphoinositide-3-kinase (PI3K)-related protein kinases (PIKKs) ATM and ATR. These, in turn, activate the DNA damage transducers Chk1 and Chk2. Here, we show that Myc can stimulate Chek2 transcript indirectly in vitro as well as in B cells of λ-Myc transgenic mice or in the intestine of Apc (Min) mice. However, Chk2 is dispensable for Myc's ability to transform cells in vitro and for the survival of established lymphoma cells from λ-Myc transgenic mice. Chk2 deficiency induces polyploidy and slow growth, but the cells are viable and protected against DNA damage. Furthermore, inhibition of both Chk1/Chk2 with AZD7762 induces cell death and significantly delays disease progression of transplanted lymphoma cells in vivo. DNA damage recruits PARP family members to sites of DNA breaks that, in turn, facilitate the induction of DNA repair. Strikingly, combining Chk2 and PARP inhibition elicits a synergistic lethal response in the context of Myc overexpression. Our data indicates that only certain types of chemotherapy would give rise to a synergistic lethal response in combination with specific Chk2 inhibitors, which will be important if Chk2 inhibitors enter the clinic.
Collapse
Affiliation(s)
- Andreas Höglund
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | | | | | | | | |
Collapse
|
185
|
Möckel C, Lammens K, Schele A, Hopfner KP. ATP driven structural changes of the bacterial Mre11:Rad50 catalytic head complex. Nucleic Acids Res 2011; 40:914-27. [PMID: 21937514 PMCID: PMC3258140 DOI: 10.1093/nar/gkr749] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
DNA double-strand breaks (DSBs) threaten genome stability in all kingdoms of life and are linked to cancerogenic chromosome aberrations in humans. The Mre11:Rad50 (MR) complex is an evolutionarily conserved complex of two Rad50 ATPases and a dimer of the Mre11 nuclease that senses and processes DSBs and tethers DNA for repair. ATP binding and hydrolysis by Rad50 is functionally coupled to DNA-binding and tethering, but also regulates Mre11's nuclease in processing DNA ends. To understand how ATP controls the interaction between Mre11 and Rad50, we determined the crystal structure of Thermotoga maritima (Tm) MR trapped in an ATP/ADP state. ATP binding to Rad50 induces a large structural change from an open form with accessible Mre11 nuclease sites into a closed form. Remarkably, the NBD dimer binds in the Mre11 DNA-binding cleft blocking Mre11's dsDNA-binding sites. An accompanying large swivel of the Rad50 coiled coil domains appears to prepare the coiled coils for DNA tethering. DNA-binding studies show that within the complex, Rad50 likely forms a dsDNA-binding site in response to ATP, while the Mre11 nuclease module retains a ssDNA-binding site. Our results suggest a possible mechanism for ATP-dependent DNA tethering and DSB processing by MR.
Collapse
Affiliation(s)
- Carolin Möckel
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-University Munich, Feodor-Lynen-Strasse 25, 81377, Munich, Germany
| | | | | | | |
Collapse
|
186
|
The Rad50 coiled-coil domain is indispensable for Mre11 complex functions. Nat Struct Mol Biol 2011; 18:1124-31. [PMID: 21892167 PMCID: PMC3190017 DOI: 10.1038/nsmb.2116] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Accepted: 06/27/2011] [Indexed: 01/09/2023]
Abstract
The Mre11 complex (Mre11, Rad50 and Xrs2 in Saccharomyces cerevisiae) influences diverse functions in the DNA damage response. The complex comprises the globular DNA-binding domain and the Rad50 hook domain, which are linked by a long and extended Rad50 coiled-coil domain. In this study, we constructed rad50 alleles encoding truncations of the coiled-coil domain to determine which Mre11 complex functions required the full length of the coils. These mutations abolished telomere maintenance and meiotic double-strand break (DSB) formation, and severely impaired homologous recombination, indicating a requirement for long-range action. Nonhomologous end joining, which is probably mediated by the globular domain of the Mre11 complex, was also severely impaired by alteration of the coiled-coil and hook domains, providing the first evidence of their influence on this process. These data show that functions of Mre11 complex are integrated by the coiled coils of Rad50.
Collapse
|
187
|
Ricceri F, Porcedda P, Allione A, Turinetto V, Polidoro S, Guarrera S, Rosa F, Voglino F, Pezzotti A, Minieri V, Accomasso L, Cibrario Rocchietti E, Orlando L, Giachino C, Matullo G. Involvement of MRE11A and XPA gene polymorphisms in the modulation of DNA double-strand break repair activity: a genotype-phenotype correlation study. DNA Repair (Amst) 2011; 10:1044-50. [PMID: 21880556 DOI: 10.1016/j.dnarep.2011.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 07/25/2011] [Accepted: 08/07/2011] [Indexed: 10/17/2022]
Abstract
DNA double-strand breaks (DSB) are the most lethal form of ionizing radiation-induced DNA damage, and failure to repair them results in cell death. In order to see if any associations exist between DNA repair gene polymorphisms and phenotypic profiles of DSB repair (DSBR) we performed a genotype-phenotype correlation study in 118 young healthy subjects (mean age 25.8±6.7years). Subjects were genotyped for 768 single nucleotide polymorphisms (SNPs) with a custom Illumina Golden Gate Assay, and an H2AX histone phosphorylation assay was done to test DSBR capacity. We found that H2AX phosphorylation at 1h was significantly lower in subjects heterozygous (no variant homozygotes were observed) for the XPA gene SNP rs3176683 (p-value=0.005), while dephosphorylation was significantly higher in subjects carrying the variant allele in three MRE11A gene SNPs: rs1014666, rs476137 and rs2508784 (p-value=0.003, 0.003 and 0.008, respectively). An additive effect of low-activity DNA repair alleles was associated with altered DSBR activity, as demonstrated by both H2AX phosphorylation at 1 h (p-trend <0.0001) and γH2AX dephosphorylation at 3h (p-trend <0.0001). Our study revealed that in addition to SNPs of genes that are well-established players in DSBR, non-DSBR genes, such as the XPA gene that is mainly involved in the nucleotide excision repair pathway, can also influence DSBR in healthy subjects. This suggests that successful DSBR may require both DSBR and non-DSBR mechanisms.
Collapse
|
188
|
The MRE11 GAR motif regulates DNA double-strand break processing and ATR activation. Cell Res 2011; 22:305-20. [PMID: 21826105 DOI: 10.1038/cr.2011.128] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The MRE11/RAD50/NBS1 complex is the primary sensor rapidly recruited to DNA double-strand breaks (DSBs). MRE11 is known to be arginine methylated by PRMT1 within its glycine-arginine-rich (GAR) motif. In this study, we report a mouse knock-in allele of Mre11 that substitutes the arginines with lysines in the GAR motif and generates the MRE11(RK) protein devoid of methylated arginines. The Mre11(RK/RK) mice were hypersensitive to γ-irradiation (IR) and the cells from these mice displayed cell cycle checkpoint defects and chromosome instability. Moreover, the Mre11(RK/RK) MEFs exhibited ATR/CHK1 signaling defects and impairment in the recruitment of RPA and RAD51 to the damaged sites. The M(RK)RN complex formed and localized to the sites of DNA damage and normally activated the ATM pathway in response to IR. The M(RK)RN complex exhibited exonuclease and DNA-binding defects in vitro responsible for the impaired DNA end resection and ATR activation observed in vivo in response to IR. Our findings provide genetic evidence for the critical role of the MRE11 GAR motif in DSB repair, and demonstrate a mechanistic link between post-translational modifications at the MRE11 GAR motif and DSB processing, as well as the ATR/CHK1 checkpoint signaling.
Collapse
|
189
|
Dmitrieva NI, Malide D, Burg MB. Mre11 is expressed in mammalian mitochondria where it binds to mitochondrial DNA. Am J Physiol Regul Integr Comp Physiol 2011; 301:R632-40. [PMID: 21677273 DOI: 10.1152/ajpregu.00853.2010] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mre11 is a critical participant in upkeep of nuclear DNA, its repair, replication, meiosis, and maintenance of telomeres. The upkeep of mitochondrial DNA (mtDNA) is less well characterized, and whether Mre11 participates has been unknown. We previously found that high NaCl causes some of the Mre11 to leave the nucleus, but we did not then attempt to localize it within the cytoplasm. In the present studies, we find Mre11 in mitochondria isolated from primary renal cells and show that the amount of Mre11 in mitochondria increases with elevation of extracellular NaCl. We confirm the presence of Mre11 in the mitochondria of cells by confocal microscopy and show that some of the Mre11 colocalizes with mtDNA. Furthermore, crosslinking of Mre11 to DNA followed by Mre11 immunoprecipitation directly demonstrates that some Mre11 binds to mtDNA. Abundant Mre11 is also present in tissue sections from normal mouse kidneys, colocalized with mitochondria of proximal tubule and thick ascending limb cells. To explore whether distribution of Mre11 changes with cell differentiation, we used an experimental model of tubule formation by culturing primary kidney cells in Matrigel matrix. In nondifferentiated cells, Mre11 is mostly in the nucleus, but it becomes mostly cytoplasmic upon cell differentiation. We conclude that Mre11 is present in mitochondria where it binds to mtDNA and that the amount in mitochondria varies depending on cellular stress and differentiation. Our results suggest a role for Mre11 in the maintenance of genome integrity in mitochondria in addition to its previously known role in maintenance of nuclear DNA.
Collapse
Affiliation(s)
- Natalia I Dmitrieva
- Laboratory of Kidney and Electrolyte Metabolism,National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA.
| | | | | |
Collapse
|
190
|
Lammens K, Bemeleit DJ, Möckel C, Clausing E, Schele A, Hartung S, Schiller CB, Lucas M, Angermüller C, Söding J, Strässer K, Hopfner KP. The Mre11:Rad50 structure shows an ATP-dependent molecular clamp in DNA double-strand break repair. Cell 2011; 145:54-66. [PMID: 21458667 DOI: 10.1016/j.cell.2011.02.038] [Citation(s) in RCA: 163] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Revised: 12/22/2010] [Accepted: 02/18/2011] [Indexed: 11/16/2022]
Abstract
The MR (Mre11 nuclease and Rad50 ABC ATPase) complex is an evolutionarily conserved sensor for DNA double-strand breaks, highly genotoxic lesions linked to cancer development. MR can recognize and process DNA ends even if they are blocked and misfolded. To reveal its mechanism, we determined the crystal structure of the catalytic head of Thermotoga maritima MR and analyzed ATP-dependent conformational changes. MR adopts an open form with a central Mre11 nuclease dimer and two peripheral Rad50 molecules, a form suited for sensing obstructed breaks. The Mre11 C-terminal helix-loop-helix domain binds Rad50 and attaches flexibly to the nuclease domain, enabling large conformational changes. ATP binding to the two Rad50 subunits induces a rotation of the Mre11 helix-loop-helix and Rad50 coiled-coil domains, creating a clamp conformation with increased DNA-binding activity. The results suggest that MR is an ATP-controlled transient molecular clamp at DNA double-strand breaks.
Collapse
Affiliation(s)
- Katja Lammens
- Center for Integrated Protein Science Munich, Ludwig-Maximilians-University Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
191
|
Fuss JO, Tainer JA. XPB and XPD helicases in TFIIH orchestrate DNA duplex opening and damage verification to coordinate repair with transcription and cell cycle via CAK kinase. DNA Repair (Amst) 2011; 10:697-713. [PMID: 21571596 DOI: 10.1016/j.dnarep.2011.04.028] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Helicases must unwind DNA at the right place and time to maintain genomic integrity or gene expression. Biologically critical XPB and XPD helicases are key members of the human TFIIH complex; they anchor CAK kinase (cyclinH, MAT1, CDK7) to TFIIH and open DNA for transcription and for repair of duplex distorting damage by nucleotide excision repair (NER). NER is initiated by arrested RNA polymerase or damage recognition by XPC-RAD23B with or without DDB1/DDB2. XP helicases, named for their role in the extreme sun-mediated skin cancer predisposition xeroderma pigmentosum (XP), are then recruited to asymmetrically unwind dsDNA flanking the damage. XPB and XPD genetic defects can also cause premature aging with profound neurological defects without increased cancers: Cockayne syndrome (CS) and trichothiodystrophy (TTD). XP helicase patient phenotypes cannot be predicted from the mutation position along the linear gene sequence and adjacent mutations can cause different diseases. Here we consider the structural biology of DNA damage recognition by XPC-RAD23B, DDB1/DDB2, RNAPII, and ATL, and of helix unwinding by the XPB and XPD helicases plus the bacterial repair helicases UvrB and UvrD in complex with DNA. We then propose unified models for TFIIH assembly and roles in NER. Collective crystal structures with NMR and electron microscopy results reveal functional motifs, domains, and architectural elements that contribute to biological activities: damaged DNA binding, translocation, unwinding, and ATP driven changes plus TFIIH assembly and signaling. Coupled with mapping of patient mutations, these combined structural analyses provide a framework for integrating and unifying the rich biochemical and cellular information that has accumulated over forty years of study. This integration resolves puzzles regarding XP helicase functions and suggests that XP helicase positions and activities within TFIIH detect and verify damage, select the damaged strand for incision, and coordinate repair with transcription and cell cycle through CAK signaling.
Collapse
Affiliation(s)
- Jill O Fuss
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | | |
Collapse
|
192
|
SUMOylation and de-SUMOylation in response to DNA damage. FEBS Lett 2011; 585:2891-6. [PMID: 21486569 DOI: 10.1016/j.febslet.2011.04.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 04/01/2011] [Accepted: 04/01/2011] [Indexed: 11/22/2022]
Abstract
To maintain genomic integrity, a cell must utilize multiple mechanisms to protect its DNA from the damage generated by environmental agents or DNA metabolism. SUMO (small ubiquitin-like modifier) can regulate protein stability, protein cellular location, and protein-protein interactions. In this review, we summarize the current understanding of the roles of SUMOylation and de-SUMOylation in DNA damage response (DDR) and DNA repair with a specific focus on the role of RPA SUMOylation in homologous recombination (HR).
Collapse
|
193
|
Williams GJ, Williams RS, Williams JS, Moncalian G, Arvai AS, Limbo O, Guenther G, SilDas S, Hammel M, Russell P, Tainer JA. ABC ATPase signature helices in Rad50 link nucleotide state to Mre11 interface for DNA repair. Nat Struct Mol Biol 2011; 18:423-31. [PMID: 21441914 PMCID: PMC3118400 DOI: 10.1038/nsmb.2038] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Accepted: 02/15/2011] [Indexed: 01/05/2023]
Abstract
The Rad50 ABC-ATPase complex with Mre11 nuclease is essential for dsDNA break repair, telomere maintenance and ataxia telangiectasia-mutated kinase checkpoint signaling. How Rad50 affects Mre11 functions and how ABC-ATPases communicate nucleotide binding and ligand states across long distances and among protein partners are questions that have remained obscure. Here, structures of Mre11-Rad50 complexes define the Mre11 2-helix Rad50 binding domain (RBD) that forms a four-helix interface with Rad50 coiled coils adjoining the ATPase core. Newly identified effector and basic-switch helix motifs extend the ABC-ATPase signature motif to link ATP-driven Rad50 movements to coiled coils binding Mre11, implying an ~30-Å pull on the linker to the nuclease domain. Both RBD and basic-switch mutations cause clastogen sensitivity. Our new results characterize flexible ATP-dependent Mre11 regulation, defects in cancer-linked RBD mutations, conserved superfamily basic switches and motifs effecting ATP-driven conformational change, and they provide a unified comprehension of ABC-ATPase activities.
Collapse
Affiliation(s)
- Gareth J Williams
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
194
|
Human T-lymphotropic type 1 virus p30 inhibits homologous recombination and favors unfaithful DNA repair. Blood 2011; 117:5897-906. [PMID: 21427292 DOI: 10.1182/blood-2010-08-304600] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Whereas oncogenic retroviruses are common in animals, human T-lymphotropic virus 1 (HTLV-1) is the only transmissible retrovirus associated with cancer in humans and is etiologically linked to adult T-cell leukemia. The leukemogenesis process is still largely unknown, but relies on extended survival and clonal expansion of infected cells, which in turn accumulate genetic defects. A common feature of human tumor viruses is their ability to stimulate proliferation and survival of infected pretumoral cells and then hide by establishing latency in cells that have acquired a transformed phenotype. Whereas disruption of the DNA repair is one of the major processes responsible for the accumulation of genomic abnormalities and carcinogenesis, the absence of DNA repair also poses the threat of cell-cycle arrest or apoptosis of virus-infected cells. This study describes how the HTLV-1 p30 viral protein inhibits conservative homologous recombination (HR) DNA repair by targeting the MRE11/RAD50/NBS1 complex and favors the error-prone nonhomologous-end-joining (NHEJ) DNA-repair pathway instead. As a result, HTLV-1 p30 may facilitate the accumulation of mutations in the host genome and the cumulative risk of transformation. Our results provide new insights into how human tumor viruses may manipulate cellular DNA-damage responses to promote cancer.
Collapse
|
195
|
Cherubini G, Naim V, Caruso P, Burla R, Bogliolo M, Cundari E, Benihoud K, Saggio I, Rosselli F. The FANC pathway is activated by adenovirus infection and promotes viral replication-dependent recombination. Nucleic Acids Res 2011; 39:5459-73. [PMID: 21421559 PMCID: PMC3141233 DOI: 10.1093/nar/gkr084] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Deciphering the crosstalk between a host cell and a virus during infection is important not only to better define viral biology but also to improve our understanding of cellular processes. We identified the FANC pathway as a helper of viral replication and recombination by searching for cellular targets that are modified by adenovirus (Ad) infection and are involved in its outcome. This pathway, which is involved in the DNA damage response and checkpoint control, is altered in Fanconi anaemia, a rare cancer predisposition syndrome. We show here that Ad5 infection activates the FANC pathway independent of the classical DNA damage response. Infection with a non-replicating Ad shows that the presence of viral DNA is not sufficient to induce the monoubiquitination of FANCD2 but still activates the DNA damage response coordinated by phospho-NBS1 and phospho-CHK1. E1A expression alone fails to induce FANCD2 monoubiquitination, indicating that a productive viral infection and/or replication is required for FANC pathway activation. Our data indicate that Ad5 infection induces FANCD2 activation to promote its own replication. Specifically, we show that FANCD2 is involved in the recombination process that accompanies viral DNA replication. This study provides evidence of a DNA damage-independent function of the FANC pathway and identifies a cellular system involved in Ad5 recombination.
Collapse
Affiliation(s)
- Gioia Cherubini
- University Paris-Sud, UMR8200 CNRS, Institute Gustave Roussy, Villejuif, France
| | | | | | | | | | | | | | | | | |
Collapse
|
196
|
Colado E, Paíno T, Maiso P, Ocio EM, Chen X, Alvarez-Fernández S, Gutiérrez NC, Martín-Sánchez J, Flores-Montero J, San Segundo L, Garayoa M, Fernández-Lázaro D, Vidriales MB, Galmarini CM, Avilés P, Cuevas C, Pandiella A, San-Miguel JF. Zalypsis has in vitro activity in acute myeloid blasts and leukemic progenitor cells through the induction of a DNA damage response. Haematologica 2011; 96:687-95. [PMID: 21330323 DOI: 10.3324/haematol.2010.036400] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Although the majority of patients with acute myeloid leukemia initially respond to conventional chemotherapy, relapse is still the leading cause of death, probably because of the presence of leukemic stem cells that are insensitive to current therapies. We investigated the antileukemic activity and mechanism of action of zalypsis, a novel alkaloid of marine origin. DESIGN AND METHODS The activity of zalypsis was studied in four acute myeloid leukemia cell lines and in freshly isolated blasts taken from patients with acute myeloid leukemia before they started therapy. Zalypsis-induced apoptosis of both malignant and normal cells was measured using flow cytometry techniques. Gene expression profiling and western blot studies were performed to assess the mechanism of action of the alkaloid. RESULTS Zalypsis showed a very potent antileukemic activity in all the cell lines tested and potentiated the effect of conventional antileukemic drugs such as cytarabine, fludarabine and daunorubicin. Interestingly, zalypsis showed remarkable ex vivo potency, including activity against the most immature blast cells (CD34(+) CD38(-) Lin(-)) which include leukemic stem cells. Zalypsis-induced apoptosis was the result of an important deregulation of genes involved in the recognition of double-strand DNA breaks, such as Fanconi anemia genes and BRCA1, but also genes implicated in the repair of double-strand DNA breaks, such as RAD51 and RAD54. These gene findings were confirmed by an increase in several proteins involved in the pathway (pCHK1, pCHK2 and pH2AX). CONCLUSIONS The potent and selective antileukemic effect of zalypsis on DNA damage response mechanisms observed in acute myeloid leukemia cell lines and in patients' samples provides the rationale for the investigation of this compound in clinical trials.
Collapse
Affiliation(s)
- Enrique Colado
- Centro de Investigación del Cáncer, IBMCC/CSIC-Universidad de Salamanca, Salamanca, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
197
|
Abstract
The maintenance of genome stability depends on the DNA damage response (DDR), which is a functional network comprising signal transduction, cell cycle regulation and DNA repair. The metabolism of DNA double-strand breaks governed by the DDR is important for preventing genomic alterations and sporadic cancers, and hereditary defects in this response cause debilitating human pathologies, including developmental defects and cancer. The MRE11 complex, composed of the meiotic recombination 11 (MRE11), RAD50 and Nijmegen breakage syndrome 1 (NBS1; also known as nibrin) proteins is central to the DDR, and recent insights into its structure and function have been gained from in vitro structural analysis and studies of animal models in which the DDR response is deficient.
Collapse
Affiliation(s)
- Travis H Stracker
- Institute for Research in Biomedicine Barcelona, C/ Baldiri Reixac 10, 08028 Barcelona, Spain.
| | | |
Collapse
|
198
|
Cheng L, Wu Q, Huang Z, Guryanova OA, Huang Q, Shou W, Rich JN, Bao S. L1CAM regulates DNA damage checkpoint response of glioblastoma stem cells through NBS1. EMBO J 2011; 30:800-13. [PMID: 21297581 DOI: 10.1038/emboj.2011.10] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Accepted: 01/11/2011] [Indexed: 12/21/2022] Open
Abstract
Glioblastomas (GBMs) are highly lethal brain tumours with current therapies limited to palliation due to therapeutic resistance. We previously demonstrated that GBM stem cells (GSCs) display a preferential activation of DNA damage checkpoint and are relatively resistant to radiation. However, the molecular mechanisms underlying the preferential checkpoint response in GSCs remain undefined. Here, we show that L1CAM (CD171) regulates DNA damage checkpoint responses and radiosensitivity of GSCs through nuclear translocation of L1CAM intracellular domain (L1-ICD). Targeting L1CAM by RNA interference attenuated DNA damage checkpoint activation and repair, and sensitized GSCs to radiation. L1CAM regulates expression of NBS1, a critical component of the MRE11-RAD50-NBS1 (MRN) complex that activates ataxia telangiectasia mutated (ATM) kinase and early checkpoint response. Ectopic expression of NBS1 in GSCs rescued the decreased checkpoint activation and radioresistance caused by L1CAM knockdown, demonstrating that L1CAM signals through NBS1 to regulate DNA damage checkpoint responses. Mechanistically, nuclear translocation of L1-ICD mediates NBS1 upregulation via c-Myc. These data demonstrate that L1CAM augments DNA damage checkpoint activation and radioresistance of GSCs through L1-ICD-mediated NBS1 upregulation and the enhanced MRN-ATM-Chk2 signalling.
Collapse
Affiliation(s)
- Lin Cheng
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | | | | | | | | | | | | |
Collapse
|
199
|
Pérez R, Cuadrado A, Chen IP, Puchta H, Jouve N, De Bustos A. The Rad50 genes of diploid and polyploid wheat species. Analysis of homologue and homoeologue expression and interactions with Mre11. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:251-262. [PMID: 20827456 DOI: 10.1007/s00122-010-1440-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Accepted: 08/25/2010] [Indexed: 05/29/2023]
Abstract
The MRN complex plays a central role in the DNA repair pathways of eukaryotic cells and takes part in many other processes, including cell cycle checkpoint signalling, meiosis, DNA replication and telomere maintenance. This complex is formed by the interaction of the products of the Mre11, Rad50 and Nbs1 genes. This paper reports the molecular characterization, expression and interactions of the Rad50 gene in several wheat species with different levels of ploidy. The homoeologous Rad50 wheat genes were found to show a high level of conservation. Most of the RAD50 domains and motifs previously described in other species were also present in wheat RAD50; these proteins are therefore likely to have similar functions. Interactions between the RAD50 wheat proteins and their MRE11 counterparts in the MRN complex were observed. The level of expression of Rad50 in each of the species examined was determined and compared with those previously reported for the Mre11 genes. In some cases similar levels of expression were seen, as expected. The expression of the RAD50 homoeologous genes was assessed in two polyploid wheat species using quantitative PCR. In both cases, an overexpression of the Rad50B gene was detected. Although the results indicate the maintenance of function of these species' three homoeologous Rad50 genes, the biased expression of Rad50B might indicate ongoing silencing of one or both other homoeologues in polyploid wheat. To assess the consequences of such silencing on the formation of the MRN complex, the interactions between individual homoeologues of Rad50 and their genomic counterpart Mre11 genes were examined. The results indicate the inexistence of genomic specificity in the interactions between these genes. This would guarantee the formation of an MRN complex in wheat.
Collapse
Affiliation(s)
- R Pérez
- Department of Cell Biology and Genetics, University of Alcalá, Alcalá de Henares, Spain
| | | | | | | | | | | |
Collapse
|
200
|
Cann KL, Dellaire G. Heterochromatin and the DNA damage response: the need to relaxThis paper is one of a selection of papers in a Special Issue entitled 31st Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process. Biochem Cell Biol 2011; 89:45-60. [DOI: 10.1139/o10-113] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Higher order chromatin structure has an impact on all nuclear functions, including the DNA damage response. Over the past several years, it has become increasingly clear that heterochromatin and euchromatin represent separate entities with respect to both damage sensitivity and repair. The chromatin compaction present in heterochromatin helps to protect this DNA from damage; however, when lesions do occur, the compaction restricts the ability of DNA damage response proteins to access the site, as evidenced by its ability to block the expansion of H2AX phosphorylation. As such, DNA damage in heterochromatin is refractory to repair, which requires the surrounding chromatin structure to be decondensed. In the case of DNA double-strand breaks, this relaxation is at least partially mediated by the ATM kinase phosphorylating and inhibiting the function of the transcriptional repressor KAP1. This review will focus on the functions of KAP1 and other proteins involved in the maintenance or restriction of heterochromatin, including HP1 and TIP60, in the DNA damage response. As heterochromatin is important for maintaining genomic stability, cells must maintain a delicate balance between allowing repair factors access to these regions and ensuring that these regions retain their organization to prevent increased DNA damage and chromosomal mutations.
Collapse
Affiliation(s)
- Kendra L. Cann
- Departments of Pathology and Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
| | - Graham Dellaire
- Departments of Pathology and Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
| |
Collapse
|