51
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Ibler AEM, ElGhazaly M, Naylor KL, Bulgakova NA, F El-Khamisy S, Humphreys D. Typhoid toxin exhausts the RPA response to DNA replication stress driving senescence and Salmonella infection. Nat Commun 2019; 10:4040. [PMID: 31492859 PMCID: PMC6731267 DOI: 10.1038/s41467-019-12064-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 08/15/2019] [Indexed: 01/10/2023] Open
Abstract
Salmonella Typhi activates the host DNA damage response through the typhoid toxin, facilitating typhoid symptoms and chronic infections. Here we reveal a non-canonical DNA damage response, which we call RING (response induced by a genotoxin), characterized by accumulation of phosphorylated histone H2AX (γH2AX) at the nuclear periphery. RING is the result of persistent DNA damage mediated by toxin nuclease activity and is characterized by hyperphosphorylation of RPA, a sensor of single-stranded DNA (ssDNA) and DNA replication stress. The toxin overloads the RPA pathway with ssDNA substrate, causing RPA exhaustion and senescence. Senescence is also induced by canonical γΗ2ΑΧ foci revealing distinct mechanisms. Senescence is transmitted to non-intoxicated bystander cells by an unidentified senescence-associated secreted factor that enhances Salmonella infections. Thus, our work uncovers a mechanism by which genotoxic Salmonella exhausts the RPA response by inducing ssDNA formation, driving host cell senescence and facilitating infection.
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Affiliation(s)
- Angela E M Ibler
- Department of Biomedical Science, University of Sheffield, Sheffield, S10 2TN, UK
- Department of Pathology, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Mohamed ElGhazaly
- Department of Biomedical Science, University of Sheffield, Sheffield, S10 2TN, UK
| | - Kathryn L Naylor
- Department of Biomedical Science, University of Sheffield, Sheffield, S10 2TN, UK
| | - Natalia A Bulgakova
- Department of Biomedical Science, University of Sheffield, Sheffield, S10 2TN, UK
| | - Sherif F El-Khamisy
- The Healthy Life Span Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
- Center of Genomics, Zewail City of Science and Technology, Giza, Egypt
| | - Daniel Humphreys
- Department of Biomedical Science, University of Sheffield, Sheffield, S10 2TN, UK.
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52
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FANCM limits ALT activity by restricting telomeric replication stress induced by deregulated BLM and R-loops. Nat Commun 2019; 10:2253. [PMID: 31138795 PMCID: PMC6538666 DOI: 10.1038/s41467-019-10179-z] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 04/23/2019] [Indexed: 12/13/2022] Open
Abstract
Telomerase negative immortal cancer cells elongate telomeres through the Alternative Lengthening of Telomeres (ALT) pathway. While sustained telomeric replicative stress is required to maintain ALT, it might also lead to cell death when excessive. Here, we show that the ATPase/translocase activity of FANCM keeps telomeric replicative stress in check specifically in ALT cells. When FANCM is depleted in ALT cells, telomeres become dysfunctional, and cells stop proliferating and die. FANCM depletion also increases ALT-associated marks and de novo synthesis of telomeric DNA. Depletion of the BLM helicase reduces the telomeric replication stress and cell proliferation defects induced by FANCM inactivation. Finally, FANCM unwinds telomeric R-loops in vitro and suppresses their accumulation in cells. Overexpression of RNaseH1 completely abolishes the replication stress remaining in cells codepleted for FANCM and BLM. Thus, FANCM allows controlled ALT activity and ALT cell proliferation by limiting the toxicity of uncontrolled BLM and telomeric R-loops. In cancer cells, telomeres can be elongated through homology directed-repair pathways in a process known as Alternative Lengthening of Telomeres (ALT). Here, the authors reveal that FANCM regulates ALT activity and ALT cell proliferation by limiting the activity of uncontrolled BLM and telomeric R-loops.
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53
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Xu L, Zhao J, Wang Z. Genotoxic response and damage recovery of macrophages to graphene quantum dots. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 664:536-545. [PMID: 30759415 DOI: 10.1016/j.scitotenv.2019.01.356] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 01/24/2019] [Accepted: 01/27/2019] [Indexed: 05/20/2023]
Abstract
The potential adverse effects of graphene quantum dots (GQDs) have increasingly attracted attention. Our present study revealed the genotoxic responses of rat alveolar macrophages (NR8383) to aminated graphene QDs (AG-QDs) and detected the cellular recovery after removing AG-QDs. Global gene expression analysis from RNA-sequencing showed that AG-QDs (100 μg/mL) caused significant alterations in expression of 2898 genes after exposure for 24 h. Among these, 1335 and 1563 genes were up-regulated and down-regulated, respectively. Based on the Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genomes (KEGG) analysis, we found that most of the down-regulated genes were responsive to "cell cycle", which correlated well with the cell cycle arrest data that AG-QDs triggered cell cycle arrest at S (synthesis) and G2/M (second gap/mitosis) phase. The percentages of cells in S and G2/M phase were increased by 4.5%, and 29.0%, respectively. In addition, the up-regulated genes related with "endocytosis" and "phagocytosis" were identified, which could regulate the internalization of AG-QDs by endocytosis and phagocytosis. After removing exposed AG-QDs and re-incubating the cells in fresh medium, the arrest of S and G2/M phase in NR8383 cells was reduced, and the cell cycle gradually recovered. This cellular recovery could be attributed to the cellular excretion of AG-QDs and the up-regulation of the DNA-repair-related genes (Rad51, Brca2, and Atm). The current work provides insights into the potential hazards of AG-QDs in transcriptional level and presented the long-term effects of AG-QDs on organisms in environment.
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Affiliation(s)
- Lina Xu
- Institute of Environmental Processes and Pollution Control, and School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China; Institute of Coastal Environmental Pollution Control, and College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Jian Zhao
- Institute of Coastal Environmental Pollution Control, and College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control, and School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China.
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54
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Byrne BM, Oakley GG. Replication protein A, the laxative that keeps DNA regular: The importance of RPA phosphorylation in maintaining genome stability. Semin Cell Dev Biol 2018; 86:112-120. [PMID: 29665433 DOI: 10.1016/j.semcdb.2018.04.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/30/2018] [Accepted: 04/06/2018] [Indexed: 11/25/2022]
Abstract
The eukaryotic ssDNA-binding protein, Replication protein A (RPA), was first discovered almost three decades ago. Since then, much progress has been made to elucidate the critical roles for RPA in DNA metabolic pathways that help promote genomic stability. The canonical RPA heterotrimer (RPA1-3) is an essential coordinator of DNA metabolism that interacts with ssDNA and numerous protein partners to coordinate its roles in DNA replication, repair, recombination and telomere maintenance. An alternative form of RPA, termed aRPA, is formed by a complex of RPA4 with RPA1 and RPA3. aRPA is expressed differentially in cells compared to canonical RPA and has been shown to inhibit canonical RPA function while allowing for regular maintenance of cell viability. Interestingly, while aRPA is defective in DNA replication and cell cycle progression, it was shown to play a supporting role in nucleotide excision repair and recombination. The binding domains of canonical RPA interact with a growing number of partners involved in numerous genome maintenance processes. The protein interactions of the RPA-ssDNA complex are not only governed by competition between the binding proteins but also by post-translation modifications such as phosphorylation. Phosphorylation of RPA2 is an important post-translational modification of the RPA complex, and is essential for directing context-specific functions of the RPA complex in the DNA damage response. Due to the importance of RPA in cellular metabolism, it was identified as an appealing target for chemotherapeutic drug development that could be used in future cancer treatment regimens.
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Affiliation(s)
- Brendan M Byrne
- University of Nebraska Medical Center Department of Oral Biology, Lincoln NE, USA.
| | - Gregory G Oakley
- University of Nebraska Medical Center Department of Oral Biology, Lincoln NE, USA; Eppley Cancer Center, Omaha NE, USA.
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55
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Weßbecher IM, Brieger A. Phosphorylation meets DNA mismatch repair. DNA Repair (Amst) 2018; 72:107-114. [PMID: 30249411 DOI: 10.1016/j.dnarep.2018.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 09/04/2018] [Indexed: 12/14/2022]
Abstract
DNA mismatch repair (MMR) is a highly conserved process and ensures the removal of mispaired DNA bases and insertion-deletion loops right after replication. For this, a MutSα or MutSβ protein complex recognizes the DNA damage, MutLα nicks the erroneous strand, exonuclease 1 removes the wrong nucleotides, DNA polymerase δ refills the gap and DNA ligase I joins the fragments to seal the nicks and complete the repair process. The failure to accomplish these functions is associated with higher mutation rates and may lead to cancer, which highlights the importance of MMR by the maintenance of genomic stability. The post-replicative MMR implies that involved proteins are regulated at several levels, including posttranslational modifications (PTMs). Phosphorylation is one of the most common and major PTMs. Suitable with its regulatory force phosphorylation was shown to influence MMR factors thereby adjusting eukaryotic MMR activity. In this review, we summarized the current knowledge of the role of phosphorylation of MMR process involved proteins and their functional relevance.
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Affiliation(s)
| | - Angela Brieger
- Medical Clinic I, Biomedical Research Laboratory, Goethe-University, Frankfurt a.M., Germany.
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56
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Romanova LY, Mushinski F, Kovalchuk AL. Transcriptional activation of p21 Waf1 contributes to suppression of HR by p53 in response to replication arrest induced by camptothecin. Oncotarget 2018; 9:25427-25440. [PMID: 29875999 PMCID: PMC5986631 DOI: 10.18632/oncotarget.25172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 03/21/2018] [Indexed: 11/25/2022] Open
Abstract
The inhibitory effect of p53 on homologous recombination (HR) is exerted through sequestration of replication protein A (RPA). Release of the p53/RPA complex in response to replication stress is crucially dependent on the phosphorylation status of both proteins and is required for efficient DNA repair by HR. Phosphorylation of RPA within its RPA2 subunit by cyclin-dependent kinases (CDK) is an early event in the replication stress response. Here we investigated the role of transcriptional activation of the p53 downstream target, p21Waf1, on RPA2 phosphorylation, the stability of the p53/RPA complex and HR in cells undergoing replication arrest induced by camptothecin (CPT). We show that in CPT-treated cells, activation of p53 and p21Waf1 impedes RPA2 phosphorylation, while their depletion by siRNA stimulates it. The p53/RPA complex is more stable in wild-type cells than in cells depleted of p21Waf1. We used nocodazole-synchronized cells treated with CPT at the entrance to S phase to assess rates of HR. Regardless of their p53 or p21Waf1 status, the cells proceed through S phase at a similar rate and enter G2. While HR is low in wild-type cells and high in p53-depleted cells, only partial inhibition of HR is observed in the p21Waf1-depleted cells. This correlates with the extent of RPA sequestration by p53. Thus, in CPT-treated cells, p53-induced transcriptional activation of p21Waf1 regulates RPA2 phosphorylation, the stability of the p53/RPA complex and HR.
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Affiliation(s)
- Larisa Y Romanova
- The Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA.,The Virology and Cellular Immunology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, NIH, Rockville, Maryland, USA
| | - Frederick Mushinski
- The Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Alexander L Kovalchuk
- The Virology and Cellular Immunology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, NIH, Rockville, Maryland, USA
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57
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Gupta D, Lin B, Cowan A, Heinen CD. ATR-Chk1 activation mitigates replication stress caused by mismatch repair-dependent processing of DNA damage. Proc Natl Acad Sci U S A 2018; 115:1523-1528. [PMID: 29378956 PMCID: PMC5816205 DOI: 10.1073/pnas.1720355115] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The mismatch repair pathway (MMR) is essential for removing DNA polymerase errors, thereby maintaining genomic stability. Loss of MMR function increases mutation frequency and is associated with tumorigenesis. However, how MMR is executed at active DNA replication forks is unclear. This has important implications for understanding how MMR repairs O6-methylguanine/thymidine (MeG/T) mismatches created upon exposure to DNA alkylating agents. If MeG/T lesion recognition by MMR initiates mismatch excision, the reinsertion of a mismatched thymidine during resynthesis could initiate futile repair cycles. One consequence of futile repair cycles might be a disruption of overall DNA replication in the affected cell. Herein, we show that in MMR-proficient HeLa cancer cells, treatment with a DNA alkylating agent slows S phase progression, yet cells still progress into the next cell cycle. In the first S phase following treatment, they activate ataxia telangiectasia and Rad3-related (ATR)-Checkpoint Kinase 1 (Chk1) signaling, which limits DNA damage, while inhibition of ATR kinase activity accelerates DNA damage accumulation and sensitivity to the DNA alkylating agent. We also observed that exposure of human embryonic stem cells to alkylation damage severely compromised DNA replication in a MMR-dependent manner. These cells fail to activate the ATR-Chk1 signaling axis, which may limit their ability to handle replication stress. Accordingly, they accumulate double-strand breaks and undergo immediate apoptosis. Our findings implicate the MMR-directed response to alkylation damage as a replication stress inducer, suggesting that repeated MMR processing of mismatches may occur that can disrupt S phase progression.
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Affiliation(s)
- Dipika Gupta
- Neag Comprehensive Cancer Center, UConn Health, Farmington, CT 06030-3101
- Center for Molecular Oncology, UConn Health, Farmington, CT 06030-3101
| | - Bo Lin
- Neag Comprehensive Cancer Center, UConn Health, Farmington, CT 06030-3101
- Center for Molecular Oncology, UConn Health, Farmington, CT 06030-3101
| | - Ann Cowan
- R. D. Berlin Center for Cell Analysis and Modeling, UConn Health, Farmington, CT 06030
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030
| | - Christopher D Heinen
- Neag Comprehensive Cancer Center, UConn Health, Farmington, CT 06030-3101;
- Center for Molecular Oncology, UConn Health, Farmington, CT 06030-3101
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58
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Valvezan AJ, Turner M, Belaid A, Lam HC, Miller SK, McNamara MC, Baglini C, Housden BE, Perrimon N, Kwiatkowski DJ, Asara JM, Henske EP, Manning BD. mTORC1 Couples Nucleotide Synthesis to Nucleotide Demand Resulting in a Targetable Metabolic Vulnerability. Cancer Cell 2017; 32:624-638.e5. [PMID: 29056426 PMCID: PMC5687294 DOI: 10.1016/j.ccell.2017.09.013] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 07/21/2017] [Accepted: 09/20/2017] [Indexed: 12/13/2022]
Abstract
The mechanistic target of rapamycin complex 1 (mTORC1) supports proliferation through parallel induction of key anabolic processes, including protein, lipid, and nucleotide synthesis. We hypothesized that these processes are coupled to maintain anabolic balance in cells with mTORC1 activation, a common event in human cancers. Loss of the tuberous sclerosis complex (TSC) tumor suppressors results in activation of mTORC1 and development of the tumor syndrome TSC. We find that pharmacological inhibitors of guanylate nucleotide synthesis have selective deleterious effects on TSC-deficient cells, including in mouse tumor models. This effect stems from replication stress and DNA damage caused by mTORC1-driven rRNA synthesis, which renders nucleotide pools limiting. These findings reveal a metabolic vulnerability downstream of mTORC1 triggered by anabolic imbalance.
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Affiliation(s)
- Alexander J Valvezan
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Marc Turner
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Amine Belaid
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hilaire C Lam
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Spencer K Miller
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Molly C McNamara
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Christian Baglini
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston, MA, USA
| | - David J Kwiatkowski
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - John M Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Elizabeth P Henske
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Brendan D Manning
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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59
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Kumar V, Fleming T, Terjung S, Gorzelanny C, Gebhardt C, Agrawal R, Mall MA, Ranzinger J, Zeier M, Madhusudhan T, Ranjan S, Isermann B, Liesz A, Deshpande D, Häring HU, Biswas SK, Reynolds PR, Hammes HP, Peperkok R, Angel P, Herzig S, Nawroth PP. Homeostatic nuclear RAGE-ATM interaction is essential for efficient DNA repair. Nucleic Acids Res 2017; 45:10595-10613. [PMID: 28977635 PMCID: PMC5737477 DOI: 10.1093/nar/gkx705] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 08/02/2017] [Indexed: 12/12/2022] Open
Abstract
The integrity of genome is a prerequisite for healthy life. Indeed, defects in DNA repair have been associated with several human diseases, including tissue-fibrosis, neurodegeneration and cancer. Despite decades of extensive research, the spatio-mechanical processes of double-strand break (DSB)-repair, especially the auxiliary factor(s) that can stimulate accurate and timely repair, have remained elusive. Here, we report an ATM-kinase dependent, unforeseen function of the nuclear isoform of the Receptor for Advanced Glycation End-products (nRAGE) in DSB-repair. RAGE is phosphorylated at Serine376 and Serine389 by the ATM kinase and is recruited to the site of DNA-DSBs via an early DNA damage response. nRAGE preferentially co-localized with the MRE11 nuclease subunit of the MRN complex and orchestrates its nucleolytic activity to the ATR kinase signaling. This promotes efficient RPA2S4-S8 and CHK1S345 phosphorylation and thereby prevents cellular senescence, IPF and carcinoma formation. Accordingly, loss of RAGE causatively linked to perpetual DSBs signaling, cellular senescence and fibrosis. Importantly, in a mouse model of idiopathic pulmonary fibrosis (RAGE−/−), reconstitution of RAGE efficiently restored DSB-repair and reversed pathological anomalies. Collectively, this study identifies nRAGE as a master regulator of DSB-repair, the absence of which orchestrates persistent DSB signaling to senescence, tissue-fibrosis and oncogenesis.
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Affiliation(s)
- Varun Kumar
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany.,German Center for Diabetes Research (DZD), Helmholtz-Zentrum, München, Germany
| | - Thomas Fleming
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany.,German Center for Diabetes Research (DZD), Helmholtz-Zentrum, München, Germany
| | - Stefan Terjung
- European Molecular Biology Laboratory, Advanced Light Microscopy Facility, Heidelberg, Germany
| | - Christian Gorzelanny
- Experimental Dermatology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Christoffer Gebhardt
- Division of Dermatooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Signal Transduction and Growth Control DKFZ DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Raman Agrawal
- Department of Translational Pulmonology, Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University of Heidelberg, INF 156, Heidelberg, Germany
| | - Marcus A Mall
- Department of Translational Pulmonology, Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University of Heidelberg, INF 156, Heidelberg, Germany
| | - Julia Ranzinger
- Department of Nephrology, University of Heidelberg, Heidelberg, INF 410, Heidelberg, Germany
| | - Martin Zeier
- Department of Nephrology, University of Heidelberg, Heidelberg, INF 410, Heidelberg, Germany
| | - Thati Madhusudhan
- Institute of Clinical Chemistry and Pathobiochemistry, Otto-von-Guericke-University, Magdeburg, Germany
| | - Satish Ranjan
- Institute of Clinical Chemistry and Pathobiochemistry, Otto-von-Guericke-University, Magdeburg, Germany
| | - Berend Isermann
- Institute of Clinical Chemistry and Pathobiochemistry, Otto-von-Guericke-University, Magdeburg, Germany
| | - Arthur Liesz
- Institute for Stroke and Dementia Research (ISD) University Hospital München, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Divija Deshpande
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany
| | - Hans-Ulrich Häring
- German Center for Diabetes Research (DZD), Helmholtz-Zentrum, München, Germany.,Department of Internal Medicine, University of Tübingen, Tübingen, Germany
| | - Subrata K Biswas
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Shahbag, Dhaka 1000, Bangladesh
| | - Paul R Reynolds
- Department of Physiology and Developmental Biology, Brigham Young University, 3054 Life Sciences Building, Provo, UT 84602, USA
| | - Hans-Peter Hammes
- 5th Medical Department, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Rainer Peperkok
- European Molecular Biology Laboratory, Advanced Light Microscopy Facility, Heidelberg, Germany
| | - Peter Angel
- Division of Signal Transduction and Growth Control DKFZ DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stephan Herzig
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany.,German Center for Diabetes Research (DZD), Helmholtz-Zentrum, München, Germany.,Institute for Diabetes and Cancer, Helmholtz Center Munich, Neuherberg, Germany.,Joint Heidelberg-IDC Translational Diabetes Program, Helmholtz-Zentrum, München, Germany
| | - Peter P Nawroth
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany.,German Center for Diabetes Research (DZD), Helmholtz-Zentrum, München, Germany.,Joint Heidelberg-IDC Translational Diabetes Program, Helmholtz-Zentrum, München, Germany
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60
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Dubois JC, Yates M, Gaudreau-Lapierre A, Clément G, Cappadocia L, Gaudreau L, Zou L, Maréchal A. A phosphorylation-and-ubiquitylation circuitry driving ATR activation and homologous recombination. Nucleic Acids Res 2017; 45:8859-8872. [PMID: 28666352 PMCID: PMC5587784 DOI: 10.1093/nar/gkx571] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/26/2017] [Indexed: 12/27/2022] Open
Abstract
RPA-coated single-stranded DNA (RPA–ssDNA), a nucleoprotein structure induced by DNA damage, promotes ATR activation and homologous recombination (HR). RPA is hyper-phosphorylated and ubiquitylated after DNA damage. The ubiquitylation of RPA by PRP19 and RFWD3 facilitates ATR activation and HR, but how it is stimulated by DNA damage is still unclear. Here, we show that RFWD3 binds RPA constitutively, whereas PRP19 recognizes RPA after DNA damage. The recruitment of PRP19 by RPA depends on PIKK-mediated RPA phosphorylation and a positively charged pocket in PRP19. An RPA32 mutant lacking phosphorylation sites fails to recruit PRP19 and support RPA ubiquitylation. PRP19 mutants unable to bind RPA or lacking ubiquitin ligase activity also fail to support RPA ubiquitylation and HR. These results suggest that RPA phosphorylation enhances the recruitment of PRP19 to RPA–ssDNA and stimulates RPA ubiquitylation through a process requiring both PRP19 and RFWD3, thereby triggering a phosphorylation-ubiquitylation circuitry that promotes ATR activation and HR.
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Affiliation(s)
| | - Maïlyn Yates
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | | | - Geneviève Clément
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Laurent Cappadocia
- Structural Biology Program, Sloan Kettering Institute, New York, NY 10021, USA
| | - Luc Gaudreau
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Alexandre Maréchal
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
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61
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Progerin-Induced Replication Stress Facilitates Premature Senescence in Hutchinson-Gilford Progeria Syndrome. Mol Cell Biol 2017; 37:MCB.00659-16. [PMID: 28483909 DOI: 10.1128/mcb.00659-16] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 04/28/2017] [Indexed: 12/12/2022] Open
Abstract
Hutchinson-Gilford progeria syndrome (HGPS) is caused by a mutation in LMNA that produces an aberrant lamin A protein, progerin. The accumulation of progerin in HGPS cells leads to an aberrant nuclear morphology, genetic instability, and p53-dependent premature senescence. How p53 is activated in response to progerin production is unknown. Here we show that young cycling HGPS fibroblasts exhibit chronic DNA damage, primarily in S phase, as well as delayed replication fork progression. We demonstrate that progerin binds to PCNA, altering its distribution away from replicating DNA in HGPS cells, leading to γH2AX formation, ATR activation, and RPA Ser33 phosphorylation. Unlike normal human cells that can be immortalized by enforced expression of telomerase alone, immortalization of HGPS cells requires telomerase expression and p53 repression. In addition, we show that the DNA damage response in HGPS cells does not originate from eroded telomeres. Together, these results establish that progerin interferes with the coordination of essential DNA replication factors, causing replication stress, and is the primary signal for p53 activation leading to premature senescence in HGPS. Furthermore, this damage response is shown to be independent of progerin farnesylation, implying that unprocessed lamin A alone causes replication stress.
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62
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Zanini IMY, Soneson C, Lorenzi LE, Azzalin CM. Human cactin interacts with DHX8 and SRRM2 to assure efficient pre-mRNA splicing and sister chromatid cohesion. J Cell Sci 2017; 130:767-778. [PMID: 28062851 DOI: 10.1242/jcs.194068] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 12/26/2016] [Indexed: 12/20/2022] Open
Abstract
Cactins constitute a family of eukaryotic proteins broadly conserved from yeast to human and required for fundamental processes such as cell proliferation, genome stability maintenance, organismal development and immune response. Cactin proteins have been found to associate with the spliceosome in several model organisms, nevertheless their molecular functions await elucidation. Here we show that depletion of human cactin leads to premature sister chromatid separation, genome instability and cell proliferation arrest. Moreover, cactin is essential for efficient splicing of thousands of pre-mRNAs, and incomplete splicing of the pre-mRNA of sororin (also known as CDCA5), a cohesin-associated factor, is largely responsible for the aberrant chromatid separation in cactin-depleted cells. Lastly, cactin physically and functionally interacts with the spliceosome-associated factors DHX8 and SRRM2. We propose that cellular complexes comprising cactin, DHX8 and SRRM2 sustain precise chromosome segregation, genome stability and cell proliferation by allowing faithful splicing of specific pre-mRNAs. Our data point to novel pathways of gene expression regulation dependent on cactin, and provide an explanation for the pleiotropic dysfunctions deriving from cactin inactivation in distant eukaryotes.
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Affiliation(s)
- Isabella M Y Zanini
- Institute of Biochemistry (IBC), Department of Biology, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
| | - Charlotte Soneson
- Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics, Lausanne CH-1015, Switzerland
| | - Luca E Lorenzi
- Institute of Biochemistry (IBC), Department of Biology, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
| | - Claus M Azzalin
- Institute of Biochemistry (IBC), Department of Biology, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
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63
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Krasikova YS, Rechkunova NI, Lavrik OI. Replication protein A as a major eukaryotic single-stranded DNA-binding protein and its role in DNA repair. Mol Biol 2016. [DOI: 10.1134/s0026893316030080] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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64
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Chiker S, Pennaneach V, Loew D, Dingli F, Biard D, Cordelières FP, Gemble S, Vacher S, Bieche I, Hall J, Fernet M. Cdk5 promotes DNA replication stress checkpoint activation through RPA-32 phosphorylation, and impacts on metastasis free survival in breast cancer patients. Cell Cycle 2016; 14:3066-78. [PMID: 26237679 DOI: 10.1080/15384101.2015.1078020] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Cyclin dependent kinase 5 (Cdk5) is a determinant of PARP inhibitor and ionizing radiation (IR) sensitivity. Here we show that Cdk5-depleted (Cdk5-shRNA) HeLa cells show higher sensitivity to S-phase irradiation, chronic hydroxyurea exposure, and 5-fluorouracil and 6-thioguanine treatment, with hydroxyurea and IR sensitivity also seen in Cdk5-depleted U2OS cells. As Cdk5 is not directly implicated in DNA strand break repair we investigated in detail its proposed role in the intra-S checkpoint activation. While Cdk5-shRNA HeLa cells showed altered basal S-phase dynamics with slower replication velocity and fewer active origins per DNA megabase, checkpoint activation was impaired after a hydroxyurea block. Cdk5 depletion was associated with reduced priming phosphorylations of RPA32 serines 29 and 33 and SMC1-Serine 966 phosphorylation, lower levels of RPA serine 4 and 8 phosphorylation and DNA damage measured using the alkaline Comet assay, gamma-H2AX signal intensity, RPA and Rad51 foci, and sister chromatid exchanges resulting in impaired intra-S checkpoint activation and subsequently higher numbers of chromatin bridges. In vitro kinase assays coupled with mass spectrometry demonstrated that Cdk5 can carry out the RPA32 priming phosphorylations on serines 23, 29, and 33 necessary for this checkpoint activation. In addition we found an association between lower Cdk5 levels and longer metastasis free survival in breast cancer patients and survival in Cdk5-depleted breast tumor cells after treatment with IR and a PARP inhibitor. Taken together, these results show that Cdk5 is necessary for basal replication and replication stress checkpoint activation and highlight clinical opportunities to enhance tumor cell killing.
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Affiliation(s)
- Sara Chiker
- a Institut Curie; Centre de Recherche; Centre Universitaire ; Orsay Cedex , France.,b Inserm; U612; Centre Universitaire ; Orsay Cedex , France.,c Université Paris-XI; Faculté de Médecine ; Le Kremlin Bicêtre , France
| | - Vincent Pennaneach
- a Institut Curie; Centre de Recherche; Centre Universitaire ; Orsay Cedex , France.,b Inserm; U612; Centre Universitaire ; Orsay Cedex , France
| | - Damarys Loew
- d Institut Curie; Centre de Recherche; Laboratoire de Spectrométrie de Masse Protéomique ; Paris , France
| | - Florent Dingli
- d Institut Curie; Centre de Recherche; Laboratoire de Spectrométrie de Masse Protéomique ; Paris , France
| | - Denis Biard
- e Commissariat à l'Energie Atomique; DSV; iMETI; SEPIA; Team Cellular Engineering and Human Syndromes ; Fontenay aux Roses , France
| | - Fabrice P Cordelières
- a Institut Curie; Centre de Recherche; Centre Universitaire ; Orsay Cedex , France.,f CNRS; UMR3348; Centre Universitaire ; Orsay Cedex , France.,g Plateforme IBiSA d'Imagerie Cellulaire et Tissulaire; Institut Curie; Centre Universitaire ; Orsay , France
| | - Simon Gemble
- a Institut Curie; Centre de Recherche; Centre Universitaire ; Orsay Cedex , France.,f CNRS; UMR3348; Centre Universitaire ; Orsay Cedex , France
| | - Sophie Vacher
- h Pharmacogenetics Unit; Genetics Service ; Department of Tumour Biology ; Institut Curie ; Paris , France
| | - Ivan Bieche
- h Pharmacogenetics Unit; Genetics Service ; Department of Tumour Biology ; Institut Curie ; Paris , France
| | - Janet Hall
- a Institut Curie; Centre de Recherche; Centre Universitaire ; Orsay Cedex , France.,b Inserm; U612; Centre Universitaire ; Orsay Cedex , France.,i Centre de Recherche en Cancérologie de Lyon -UMR Inserm 1052 - CNRS 5286 ; Lyon , France
| | - Marie Fernet
- a Institut Curie; Centre de Recherche; Centre Universitaire ; Orsay Cedex , France.,b Inserm; U612; Centre Universitaire ; Orsay Cedex , France
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Wu Y, Lu J, Kang T. Human single-stranded DNA binding proteins: guardians of genome stability. Acta Biochim Biophys Sin (Shanghai) 2016; 48:671-7. [PMID: 27217471 DOI: 10.1093/abbs/gmw044] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 04/15/2016] [Indexed: 01/03/2023] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) are essential for maintaining the integrity of the genome in all organisms. All processes related to DNA, such as replication, excision, repair, and recombination, require the participation of SSBs whose oligonucleotide/oligosaccharide-binding (OB)-fold domain is responsible for the interaction with single-stranded DNA (ssDNA). For a long time, the heterotrimeric replication protein A (RPA) complex was believed to be the only nuclear SSB in eukaryotes to participate in ssDNA processing, while mitochondrial SSBs that are conserved with prokaryotic SSBs were shown to be essential for maintaining genome stability in eukaryotic mitochondria. In recent years, two new proteins, hSSB1 and hSSB2 (human SSBs 1/2), were identified and have better sequence similarity to bacterial and archaeal SSBs than RPA. This review summarizes the current understanding of these human SSBs in DNA damage repair and in cell-cycle checkpoint activation following DNA damage, as well as their relationships with cancer.
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Affiliation(s)
- Yuanzhong Wu
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Jinping Lu
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Tiebang Kang
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
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Kaneko Y, Daitoku H, Komeno C, Fukamizu A. CTF18 interacts with replication protein A in response to replication stress. Mol Med Rep 2016; 14:367-72. [PMID: 27175616 DOI: 10.3892/mmr.2016.5262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 05/03/2016] [Indexed: 11/06/2022] Open
Abstract
Replication stress response is a protective mechanism against defects in chromosome replication for maintaining genome integrity in eukaryotic cells. An alternative clamp loader complex termed chromosome transmission fidelity protein 18 and replication factor C (CTF18‑RFC) has been shown to act as a positive regulator of two types of replication stress response: S‑phase checkpoint signaling and translesion DNA synthesis. However, it remains largely unknown how CTF18‑RFC responds to replication stress and is recruited to stalled replication forks. The present study demonstrated that endogenous CTF18 forms a physical complex with a single‑stranded DNA‑binding protein replication protein A (RPA) in mammalian cells. Using an in situ proximity ligation assay (PLA), it was demonstrated that the interaction between CTF18 and RPA occurs in chromatin when replication stress is elicited by treatment with hydroxyurea during S phase. Similar results were obtained after exposure to ultraviolet irradiation, which triggers translesion DNA synthesis. Furthermore, the PLA demonstrated that the kinetics of the interaction between CTF18 and RPA was positively correlated with that of checkpoint kinase 1 phosphorylation, which is an indicator of activation of the ATM and Rad3‑related pathway. These findings provide novel insights into the molecular mechanism underlying the participation of CTF18‑RFC in the regulation of replication stress response.
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Affiliation(s)
- Yuta Kaneko
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305‑8577, Japan
| | - Hiroaki Daitoku
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305‑8577, Japan
| | - Chihiro Komeno
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305‑8577, Japan
| | - Akiyoshi Fukamizu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305‑8577, Japan
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67
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Awate S, De Benedetti A. TLK1B mediated phosphorylation of Rad9 regulates its nuclear/cytoplasmic localization and cell cycle checkpoint. BMC Mol Biol 2016; 17:3. [PMID: 26860083 PMCID: PMC4746922 DOI: 10.1186/s12867-016-0056-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 01/26/2016] [Indexed: 01/09/2023] Open
Abstract
Background The Tousled like kinase 1B (TLK1B) is critical for DNA repair and survival of cells. Upon DNA damage, Chk1 phosphorylates TLK1B at S457 leading to its transient inhibition. Once TLK1B regains its kinase activity it phosphorylates Rad9 at S328. In this work we investigated the significance of this mechanism by overexpressing mutant TLK1B in which the inhibitory phosphorylation site was eliminated. Results and discussion These cells expressing TLK1B resistant to DNA damage showed constitutive phosphorylation of Rad9 S328 that occurred even in the presence of hydroxyurea (HU), and this resulted in a delayed checkpoint recovery. One possible explanation was that premature phosphorylation of Rad9 caused its dissociation from 9-1-1 at stalled replication forks, resulting in their collapse and prolonged activation of the S-phase checkpoint. We found that phosphorylation of Rad9 at S328 results in its dissociation from chromatin and redistribution to the cytoplasm. This results in double stranded breaks formation with concomitant activation of ATM and phosphorylation of H2AX. Furthermore, a Rad9 (S328D) phosphomimic mutant was exclusively localized to the cytoplasm and not the chromatin. Another Rad9 phosphomimic mutant (T355D), which is also a site phosphorylated by TLK1, localized normally. In cells expressing the mutant TLK1B treated with HU, Rad9 association with Hus1 and WRN was greatly reduced, suggesting again that its phosphorylation causes its premature release from stalled forks. Conclusions We propose that normally, the inactivation of TLK1B following replication arrest and genotoxic stress functions to allow the retention of 9-1-1 at the sites of damage or stalled forks. Following reactivation of TLK1B, whose synthesis is concomitantly induced by genotoxins, Rad9 is hyperphosphorylated at S328, resulting in its dissociation and inactivation of the checkpoint that occurs once repair is complete. Electronic supplementary material The online version of this article (doi:10.1186/s12867-016-0056-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sanket Awate
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, 1501 Kings Highway, Shreveport, LA, 71130, USA.
| | - Arrigo De Benedetti
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, 1501 Kings Highway, Shreveport, LA, 71130, USA.
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Li Z, Pearlman AH, Hsieh P. DNA mismatch repair and the DNA damage response. DNA Repair (Amst) 2016; 38:94-101. [PMID: 26704428 PMCID: PMC4740233 DOI: 10.1016/j.dnarep.2015.11.019] [Citation(s) in RCA: 204] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 09/17/2015] [Accepted: 11/30/2015] [Indexed: 12/12/2022]
Abstract
This review discusses the role of DNA mismatch repair (MMR) in the DNA damage response (DDR) that triggers cell cycle arrest and, in some cases, apoptosis. Although the focus is on findings from mammalian cells, much has been learned from studies in other organisms including bacteria and yeast [1,2]. MMR promotes a DDR mediated by a key signaling kinase, ATM and Rad3-related (ATR), in response to various types of DNA damage including some encountered in widely used chemotherapy regimes. An introduction to the DDR mediated by ATR reveals its immense complexity and highlights the many biological and mechanistic questions that remain. Recent findings and future directions are highlighted.
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Affiliation(s)
- Zhongdao Li
- Genetics & Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bldg. 5 Rm. 324, 5 Memorial Dr. MSC 0538, Bethesda, MD 20892-0538, USA
| | - Alexander H Pearlman
- Genetics & Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bldg. 5 Rm. 324, 5 Memorial Dr. MSC 0538, Bethesda, MD 20892-0538, USA
| | - Peggy Hsieh
- Genetics & Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bldg. 5 Rm. 324, 5 Memorial Dr. MSC 0538, Bethesda, MD 20892-0538, USA.
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69
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Yajima H, Xue L. DNA Repair Processes and Checkpoint Pathways in Human Cells Exposed to Heavy Ion Beams. Int J Part Ther 2016; 2:439-446. [PMID: 31772954 DOI: 10.14338/ijpt-15-00020.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 10/01/2015] [Indexed: 11/21/2022] Open
Abstract
The DNA double-strand break (DSB) is the most deleterious of the ionizing radiation-induced DNA damages. Two major repair pathways for DSBs have been well studied, nonhomologous end-joining and homologous recombination. It is known that high linear energy transfer radiation, such as heavy ion beams, induces complex DSBs with clustered damages at the end and that, as a result, the efficiency of nonhomologous end-joining in repairing these DSBs is diminished. We have shown that more than 80% of complex DSBs in S/G2 human cells are subjected to DNA end resection, an early step in homologous recombination to generate single-strand DNA. Furthermore, recent work, including ours, revealed that a subpopulation of human G1 cells exhibit resection activity following ionizing radiation, which is dependent on CtIP, as in other cell cycle phases, and also dependent on the complexity of the DSB. Collectively, this recent progress indicates that the complexity of the DSB structure drastically enhances end resection, with CtIP being a significant factor required for complex DSB repair throughout the cell cycle. We further revealed that the ATR pathway, which is activated by end resection, plays a pivotal role in regulating early G2/M arrest in ATM-deficient cells exposed to high linear energy transfer ion beams. This suggests that the complexity of the DSB also influences the choice of the signaling pathway via the enhanced resection. Additionally, we discuss a possibility that CtIP has an additional function (or functions) after the initiation of resection. In conclusion, new findings and insight are pivotal to allow innovative progress in heavy ion-particle therapy by shedding light on the whole response at the molecular level in cells exposed to heavy ion beams.
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Affiliation(s)
- Hirohiko Yajima
- Research Center for Charged Particle Therapy, National Institute of Radiological Sciences, Chiba, Japan
| | - Lian Xue
- School of Public Health, Medical College of Soochow University, Suzhou, China
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Xu Q, Wang F, Xiang Y, Zhang X, Zhao ZA, Gao Z, Liu W, Lu X, Liu Y, Yu XJ, Wang H, Huang J, Yi Z, Gao S, Li L. Maternal BCAS2 protects genomic integrity in mouse early embryonic development. Development 2015; 142:3943-53. [PMID: 26428007 DOI: 10.1242/dev.129841] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 09/24/2015] [Indexed: 11/20/2022]
Abstract
Mammalian early embryos maintain accurate genome integrity for proper development within a programmed timeline despite constant assaults on their DNA by replication, DNA demethylation and genetic defects transmitted from germ cells. However, how genome integrity is safeguarded during mammalian early embryonic development remains unclear. BCAS2 (breast carcinoma amplified sequence 2), a core component of the PRP19 complex involved in pre-mRNA splicing, plays an important role in the DNA damage response through the RPA complex, a key regulator in the maintenance of genome integrity. Currently, the physiological role of BCAS2 in mammals is unknown. We now report that BCAS2 responds to endogenous and exogenous DNA damage in mouse zygotes. Maternal depletion of BCAS2 compromises the DNA damage response in early embryos, leading to developmental arrest at the two- to four-cell stage accompanied by the accumulation of damaged DNA and micronuclei. Furthermore, BCAS2 mutants that are unable to bind RPA1 fail in DNA repair during the zygotic stage. In addition, phosphorylated RPA2 cannot localise to the DNA damage sites in mouse zygotes with disrupted maternal BCAS2. These data suggest that BCAS2 might function through the RPA complex during DNA repair in zygotes. Together, our results reveal that maternal BCAS2 maintains the genome integrity of early embryos and is essential for female mouse fertility.
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Affiliation(s)
- Qianhua Xu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fengchao Wang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yunlong Xiang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoxin Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhen-Ao Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zheng Gao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenbo Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xukun Lu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yusheng Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xing-Jiang Yu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Haibin Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun Huang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhenjiang 310058, China
| | - Zhaohong Yi
- College of Biological Science and Engineering, Beijing University of Agriculture, Beijing 102206, China
| | - Shaorong Gao
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Lei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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Managing Single-Stranded DNA during Replication Stress in Fission Yeast. Biomolecules 2015; 5:2123-39. [PMID: 26393661 PMCID: PMC4598791 DOI: 10.3390/biom5032123] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 08/28/2015] [Accepted: 09/01/2015] [Indexed: 01/27/2023] Open
Abstract
Replication fork stalling generates a variety of responses, most of which cause an increase in single-stranded DNA. ssDNA is a primary signal of replication distress that activates cellular checkpoints. It is also a potential source of genome instability and a substrate for mutation and recombination. Therefore, managing ssDNA levels is crucial to chromosome integrity. Limited ssDNA accumulation occurs in wild-type cells under stress. In contrast, cells lacking the replication checkpoint cannot arrest forks properly and accumulate large amounts of ssDNA. This likely occurs when the replication fork polymerase and helicase units are uncoupled. Some cells with mutations in the replication helicase (mcm-ts) mimic checkpoint-deficient cells, and accumulate extensive areas of ssDNA to trigger the G2-checkpoint. Another category of helicase mutant (mcm4-degron) causes fork stalling in early S-phase due to immediate loss of helicase function. Intriguingly, cells realize that ssDNA is present, but fail to detect that they accumulate ssDNA, and continue to divide. Thus, the cellular response to replication stalling depends on checkpoint activity and the time that replication stress occurs in S-phase. In this review we describe the signs, signals, and symptoms of replication arrest from an ssDNA perspective. We explore the possible mechanisms for these effects. We also advise the need for caution when detecting and interpreting data related to the accumulation of ssDNA.
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Zuazua-Villar P, Ganesh A, Phear G, Gagou ME, Meuth M. Extensive RPA2 hyperphosphorylation promotes apoptosis in response to DNA replication stress in CHK1 inhibited cells. Nucleic Acids Res 2015; 43:9776-87. [PMID: 26271993 PMCID: PMC4787776 DOI: 10.1093/nar/gkv835] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 08/06/2015] [Indexed: 11/14/2022] Open
Abstract
The replication protein A (RPA)-ssDNA complex formed at arrested replication forks recruits key proteins to activate the ATR-CHK1 signalling cascade. When CHK1 is inhibited during DNA replication stress, RPA2 is extensively hyperphosphorylated. Here, we investigated the role of RPA2 hyperphosphorylation in the fate of cells when CHK1 is inhibited. We show that proteins normally involved in DNA repair (RAD51) or control of RPA phosphorylation (the PP4 protein phosphatase complex) are not recruited to the genome after treatment with CHK1 and DNA synthesis inhibitors. This is not due to RPA2 hyperphosphorylation as suppression of this response does not restore loading suggesting that recruitment requires active CHK1. To determine whether RPA2 hyperphosphorylation protects stalled forks from collapse or induction of apoptosis in CHK1 inhibited cells during replication stress, cells expressing RPA2 genes mutated at key phosphorylation sites were characterized. Mutant RPA2 rescued cells from RPA2 depletion and reduced the level of apoptosis induced by treatment with CHK1 and replication inhibitors however the incidence of double strand breaks was not affected. Our data indicate that RPA2 hyperphosphorylation promotes cell death during replication stress when CHK1 function is compromised but does not appear to be essential for replication fork integrity.
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Affiliation(s)
- Pedro Zuazua-Villar
- Molecular Oncology Unit, Department of Oncology, School of Medicine and Biomedical Sciences, University of Sheffield, Sheffield S10 2RX, UK
| | - Anil Ganesh
- Molecular Oncology Unit, Department of Oncology, School of Medicine and Biomedical Sciences, University of Sheffield, Sheffield S10 2RX, UK
| | - Geraldine Phear
- Molecular Oncology Unit, Department of Oncology, School of Medicine and Biomedical Sciences, University of Sheffield, Sheffield S10 2RX, UK
| | - Mary E Gagou
- Molecular Oncology Unit, Department of Oncology, School of Medicine and Biomedical Sciences, University of Sheffield, Sheffield S10 2RX, UK
| | - Mark Meuth
- Molecular Oncology Unit, Department of Oncology, School of Medicine and Biomedical Sciences, University of Sheffield, Sheffield S10 2RX, UK
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The DNA damage response and checkpoint adaptation in Saccharomyces cerevisiae: distinct roles for the replication protein A2 (Rfa2) N-terminus. Genetics 2015; 199:711-27. [PMID: 25595672 PMCID: PMC4349066 DOI: 10.1534/genetics.114.173211] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In response to DNA damage, two general but fundamental processes occur in the cell: (1) a DNA lesion is recognized and repaired, and (2) concomitantly, the cell halts the cell cycle to provide a window of opportunity for repair to occur. An essential factor for a proper DNA-damage response is the heterotrimeric protein complex Replication Protein A (RPA). Of particular interest is hyperphosphorylation of the 32-kDa subunit, called RPA2, on its serine/threonine-rich amino (N) terminus following DNA damage in human cells. The unstructured N-terminus is often referred to as the phosphorylation domain and is conserved among eukaryotic RPA2 subunits, including Rfa2 in Saccharomyces cerevisiae. An aspartic acid/alanine-scanning and genetic interaction approach was utilized to delineate the importance of this domain in budding yeast. It was determined that the Rfa2 N-terminus is important for a proper DNA-damage response in yeast, although its phosphorylation is not required. Subregions of the Rfa2 N-terminus important for the DNA-damage response were also identified. Finally, an Rfa2 N-terminal hyperphosphorylation-mimetic mutant behaves similarly to another Rfa1 mutant (rfa1-t11) with respect to genetic interactions, DNA-damage sensitivity, and checkpoint adaptation. Our data indicate that post-translational modification of the Rfa2 N-terminus is not required for cells to deal with "repairable" DNA damage; however, post-translational modification of this domain might influence whether cells proceed into M-phase in the continued presence of unrepaired DNA lesions as a "last-resort" mechanism for cell survival.
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Ghospurkar PL, Wilson TM, Liu S, Herauf A, Steffes J, Mueller EN, Oakley GG, Haring SJ. Phosphorylation and cellular function of the human Rpa2 N-terminus in the budding yeast Saccharomyces cerevisiae. Exp Cell Res 2014; 331:183-199. [PMID: 25499885 DOI: 10.1016/j.yexcr.2014.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 11/29/2014] [Accepted: 12/02/2014] [Indexed: 11/18/2022]
Abstract
Maintenance of genome integrity is critical for proper cell growth. This occurs through accurate DNA replication and repair of DNA lesions. A key factor involved in both DNA replication and the DNA damage response is the heterotrimeric single-stranded DNA (ssDNA) binding complex Replication Protein A (RPA). Although the RPA complex appears to be structurally conserved throughout eukaryotes, the primary amino acid sequence of each subunit can vary considerably. Examination of sequence differences along with the functional interchangeability of orthologous RPA subunits or regions could provide insight into important regions and their functions. This might also allow for study in simpler systems. We determined that substitution of yeast Replication Factor A (RFA) with human RPA does not support yeast cell viability. Exchange of a single yeast RFA subunit with the corresponding human RPA subunit does not function due to lack of inter-species subunit interactions. Substitution of yeast Rfa2 with domains/regions of human Rpa2 important for Rpa2 function (i.e., the N-terminus and the loop 3-4 region) supports viability in yeast cells, and hybrid proteins containing human Rpa2 N-terminal phospho-mutations result in similar DNA damage phenotypes to analogous yeast Rfa2 N-terminal phospho-mutants. Finally, the human Rpa2 N-terminus (NT) fused to yeast Rfa2 is phosphorylated in a manner similar to human Rpa2 in human cells, indicating that conserved kinases recognize the human domain in yeast. The implication is that budding yeast represents a potential model system for studying not only human Rpa2 N-terminal phosphorylation, but also phosphorylation of Rpa2 N-termini from other eukaryotic organisms.
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Affiliation(s)
- Padmaja L Ghospurkar
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA
| | - Timothy M Wilson
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA
| | - Shengqin Liu
- Department of Oral Biology, University of Nebraska Medical Center, Lincoln, NE 68583, USA
| | - Anna Herauf
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA
| | - Jenna Steffes
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA
| | - Erica N Mueller
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA
| | - Gregory G Oakley
- Department of Oral Biology, University of Nebraska Medical Center, Lincoln, NE 68583, USA
| | - Stuart J Haring
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA; Interdisciplinary Cellular and Molecular Biology Program, North Dakota State University, Fargo, ND 58108, USA.
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75
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Maréchal A, Zou L. RPA-coated single-stranded DNA as a platform for post-translational modifications in the DNA damage response. Cell Res 2014; 25:9-23. [PMID: 25403473 DOI: 10.1038/cr.2014.147] [Citation(s) in RCA: 322] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The Replication Protein A (RPA) complex is an essential regulator of eukaryotic DNA metabolism. RPA avidly binds to single-stranded DNA (ssDNA) through multiple oligonucleotide/oligosaccharide-binding folds and coordinates the recruitment and exchange of genome maintenance factors to regulate DNA replication, recombination and repair. The RPA-ssDNA platform also constitutes a key physiological signal which activates the master ATR kinase to protect and repair stalled or collapsed replication forks during replication stress. In recent years, the RPA complex has emerged as a key target and an important regulator of post-translational modifications in response to DNA damage, which is critical for its genome guardian functions. Phosphorylation and SUMOylation of the RPA complex, and more recently RPA-regulated ubiquitination, have all been shown to control specific aspects of DNA damage signaling and repair by modulating the interactions between RPA and its partners. Here, we review our current understanding of the critical functions of the RPA-ssDNA platform in the maintenance of genome stability and its regulation through an elaborate network of covalent modifications.
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Affiliation(s)
- Alexandre Maréchal
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Lee Zou
- 1] Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA [2] Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
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76
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Arora R, Lee Y, Wischnewski H, Brun CM, Schwarz T, Azzalin CM. RNaseH1 regulates TERRA-telomeric DNA hybrids and telomere maintenance in ALT tumour cells. Nat Commun 2014; 5:5220. [PMID: 25330849 PMCID: PMC4218956 DOI: 10.1038/ncomms6220] [Citation(s) in RCA: 322] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 09/10/2014] [Indexed: 12/21/2022] Open
Abstract
A fraction of cancer cells maintain telomeres through the telomerase-independent, ‘Alternative Lengthening of Telomeres’ (ALT) pathway. ALT relies on homologous recombination (HR) between telomeric sequences; yet, what makes ALT telomeres recombinogenic remains unclear. Here we show that the RNA endonuclease RNaseH1 regulates the levels of RNA–DNA hybrids between telomeric DNA and the long noncoding RNA TERRA, and is a key mediator of telomere maintenance in ALT cells. RNaseH1 associated to telomeres specifically in ALT cells and its depletion led to telomeric hybrid accumulation, exposure of single-stranded telomeric DNA, activation of replication protein A at telomeres and abrupt telomere excision. Conversely, overexpression of RNaseH1 weakened the recombinogenic nature of ALT telomeres and led to telomere shortening. Altering cellular RNaseH1 levels did not perturb telomere homoeostasis in telomerase-positive cells. RNaseH1 maintains regulated levels of telomeric RNA–DNA hybrids at ALT telomeres to trigger HR without compromising telomere integrity too severely. A subset of cancers maintains telomere length independently of telomerase by activating alternative lengthening of telomeres (ALT) pathways. Here the authors show that RNaseH1 modulates telomeric homologous recombination frequencies in ALT cells by regulating the levels of RNA–DNA hybrids between TERRA and telomeric DNA.
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Affiliation(s)
- Rajika Arora
- Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
| | - Yongwoo Lee
- Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
| | - Harry Wischnewski
- Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
| | - Catherine M Brun
- Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
| | - Tobias Schwarz
- Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
| | - Claus M Azzalin
- Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
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77
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Martínez TF, Phillips JW, Karanja KK, Polaczek P, Wang CM, Li BC, Campbell JL, Dervan PB. Replication stress by Py-Im polyamides induces a non-canonical ATR-dependent checkpoint response. Nucleic Acids Res 2014; 42:11546-59. [PMID: 25249630 PMCID: PMC4191428 DOI: 10.1093/nar/gku866] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Pyrrole–imidazole polyamides targeted to the androgen response element were cytotoxic in multiple cell lines, independent of intact androgen receptor signaling. Polyamide treatment induced accumulation of S-phase cells and of PCNA replication/repair foci. Activation of a cell cycle checkpoint response was evidenced by autophosphorylation of ATR, the S-phase checkpoint kinase, and by recruitment of ATR and the ATR activators RPA, 9-1-1, and Rad17 to chromatin. Surprisingly, ATR activation was accompanied by only a slight increase in single-stranded DNA, and the ATR targets RPA2 and Chk1, a cell cycle checkpoint kinase, were not phosphorylated. However, ATR activation resulted in phosphorylation of the replicative helicase subunit MCM2, an ATR effector. Polyamide treatment also induced accumulation of monoubiquitinated FANCD2, which is recruited to stalled replication forks and interacts transiently with phospho-MCM2. This suggests that polyamides induce replication stress that ATR can counteract independently of Chk1 and that the FA/BRCA pathway may also be involved in the response to polyamides. In biochemical assays, polyamides inhibit DNA helicases, providing a plausible mechanism for S-phase inhibition.
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Affiliation(s)
- Thomas F Martínez
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - John W Phillips
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kenneth K Karanja
- Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Piotr Polaczek
- Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Chieh-Mei Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Benjamin C Li
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Judith L Campbell
- Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Peter B Dervan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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78
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Chen R, Wold MS. Replication protein A: single-stranded DNA's first responder: dynamic DNA-interactions allow replication protein A to direct single-strand DNA intermediates into different pathways for synthesis or repair. Bioessays 2014; 36:1156-61. [PMID: 25171654 DOI: 10.1002/bies.201400107] [Citation(s) in RCA: 201] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Replication protein A (RPA), the major single-stranded DNA-binding protein in eukaryotic cells, is required for processing of single-stranded DNA (ssDNA) intermediates found in replication, repair, and recombination. Recent studies have shown that RPA binding to ssDNA is highly dynamic and that more than high-affinity binding is needed for function. Analysis of DNA binding mutants identified forms of RPA with reduced affinity for ssDNA that are fully active, and other mutants with higher affinity that are inactive. Single molecule studies showed that while RPA binds ssDNA with high affinity, the RPA complex can rapidly diffuse along ssDNA and be displaced by other proteins that act on ssDNA. Finally, dynamic DNA binding allows RPA to prevent error-prone repair of double-stranded breaks and promote error-free repair. Together, these findings suggest a new paradigm where RPA acts as a first responder at sites with ssDNA, thereby actively coordinating DNA repair and DNA synthesis.
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Affiliation(s)
- Ran Chen
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
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79
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Gao J, Wang H, Wong AHH, Zeng G, Huang Z, Wang Y, Sang J, Wang Y. Regulation of Rfa2 phosphorylation in response to genotoxic stress in Candida albicans. Mol Microbiol 2014; 94:141-55. [PMID: 25109320 DOI: 10.1111/mmi.12749] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2014] [Indexed: 01/10/2023]
Abstract
Successful pathogens must be able to swiftly respond to and repair DNA damages inflicted by the host defence. The replication protein A (RPA) complex plays multiple roles in DNA damage response and is regulated by phosphorylation. However, the regulators of RPA phosphorylation remain unclear. Here, we investigated Rfa2 phosphorylation in the pathogenic fungus Candida albicans. Rfa2, a RFA subunit, is phosphorylated when DNA replication is inhibited by hydroxyurea and dephosphorylated during the recovery. By screening a phosphatase mutant library, we found that Pph3 associates with different regulatory subunits to differentially control Rfa2 dephosphorylation in stressed and unstressed cells. Site-directed mutagenesis revealed T11, S18, S29, and S30 being critical for Rfa2 phosphorylation in response to genotoxic insult. We obtained evidence that the genome integrity checkpoint kinase Mec1 and the cyclin-dependent kinase Clb2-Cdc28 mediate Rfa2 phosphorylation. Although cells expressing either a phosphomimetic or a non-phosphorylatable version of Rfa2 had defects, the latter exhibited greater sensitivity to genotoxic challenge, failure to repair DNA damages and to deactivate Rad53-mediated checkpoint pathways in a dosage-dependent manner. These mutants were also less virulent in mice. Our results provide important new insights into the regulatory mechanism and biological significance of Rfa2 phosphorylation in C. albicans.
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Affiliation(s)
- Jiaxin Gao
- Key Laboratory of Cell Proliferation and Regulation Biology, College of Life Sciences, Beijing Normal University, Beijing, China; Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
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80
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Glanzer JG, Liu S, Wang L, Mosel A, Peng A, Oakley GG. RPA inhibition increases replication stress and suppresses tumor growth. Cancer Res 2014; 74:5165-72. [PMID: 25070753 DOI: 10.1158/0008-5472.can-14-0306] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The ATR/Chk1 pathway is a critical surveillance network that maintains genomic integrity during DNA replication by stabilizing the replication forks during normal replication to avoid replication stress. One of the many differences between normal cells and cancer cells is the amount of replication stress that occurs during replication. Cancer cells with activated oncogenes generate increased levels of replication stress. This creates an increased dependency on the ATR/Chk1 pathway in cancer cells and opens up an opportunity to preferentially kill cancer cells by inhibiting this pathway. In support of this idea, we have identified a small molecule termed HAMNO ((1Z)-1-[(2-hydroxyanilino)methylidene]naphthalen-2-one), a novel protein interaction inhibitor of replication protein A (RPA), a protein involved in the ATR/Chk1 pathway. HAMNO selectively binds the N-terminal domain of RPA70, effectively inhibiting critical RPA protein interactions that rely on this domain. HAMNO inhibits both ATR autophosphorylation and phosphorylation of RPA32 Ser33 by ATR. By itself, HAMNO treatment creates DNA replication stress in cancer cells that are already experiencing replication stress, but not in normal cells, and it acts synergistically with etoposide to kill cancer cells in vitro and slow tumor growth in vivo. Thus, HAMNO illustrates how RPA inhibitors represent candidate therapeutics for cancer treatment, providing disease selectivity in cancer cells by targeting their differential response to replication stress. Cancer Res; 74(18); 5165-72. ©2014 AACR.
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Affiliation(s)
- Jason G Glanzer
- Department of Oral Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Shengqin Liu
- Department of Oral Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Ling Wang
- Department of Oral Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Adam Mosel
- Department of Oral Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Aimin Peng
- Department of Oral Biology, University of Nebraska Medical Center, Omaha, Nebraska. Eppley Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | - Greg G Oakley
- Department of Oral Biology, University of Nebraska Medical Center, Omaha, Nebraska. Eppley Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska.
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81
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Interplay of DNA damage and cell cycle signaling at the level of human replication protein A. DNA Repair (Amst) 2014; 21:12-23. [PMID: 25091156 DOI: 10.1016/j.dnarep.2014.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 03/17/2014] [Accepted: 05/18/2014] [Indexed: 02/05/2023]
Abstract
Replication protein A (RPA) is the main human single-stranded DNA (ssDNA)-binding protein. It is essential for cellular DNA metabolism and has important functions in human cell cycle and DNA damage signaling. RPA is indispensable for accurate homologous recombination (HR)-based DNA double-strand break (DSB) repair and its activity is regulated by phosphorylation and other post-translational modifications. HR occurs only during S and G2 phases of the cell cycle. All three subunits of RPA contain phosphorylation sites but the exact set of HR-relevant phosphorylation sites on RPA is unknown. In this study, a high resolution capillary isoelectric focusing immunoassay, used under native conditions, revealed the isoforms of the RPA heterotrimer in control and damaged cell lysates in G2. Moreover, the phosphorylation sites of chromatin-bound and cytosolic RPA in S and G2 phases were identified by western and IEF analysis with all available phosphospecific antibodies for RPA2. Strikingly, most of the RPA heterotrimers in control G2 cells are phosphorylated with 5 isoforms containing up to 7 phosphates. These isoforms include RPA2 pSer23 and pSer33. DNA damaged cells in G2 had 9 isoforms with up to 14 phosphates. DNA damage isoforms contained pSer4/8, pSer12, pThr21, pSer23, and pSer33 on RPA2 and up to 8 unidentified phosphorylation sites.
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82
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Lee Y, Brown EJ, Chang S, McKinnon PJ. Pot1a prevents telomere dysfunction and ATM-dependent neuronal loss. J Neurosci 2014; 34:7836-44. [PMID: 24899707 PMCID: PMC4044246 DOI: 10.1523/jneurosci.4245-13.2014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 04/10/2014] [Accepted: 04/16/2014] [Indexed: 11/21/2022] Open
Abstract
Genome stability is essential for neural development and the prevention of neurological disease. Here we determined how DNA damage signaling from dysfunctional telomeres affects neurogenesis. We found that telomere uncapping by Pot1a inactivation resulted in an Atm-dependent loss of cerebellar interneurons and granule neuron precursors in the mouse nervous system. The activation of Atm by Pot1a loss occurred in an Atr-dependent manner, revealing an Atr to Atm signaling axis in the nervous system after telomere dysfunction. In contrast to telomere lesions, Brca2 inactivation in neural progenitors also led to ablation of cerebellar interneurons, but this did not require Atm. These data reveal that neural cell loss after DNA damage selectively engages Atm signaling, highlighting how specific DNA lesions can dictate neuropathology arising in human neurodegenerative syndromes.
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Affiliation(s)
- Youngsoo Lee
- Department of Genetics, St Jude Children's Research Hospital, Memphis, Tennessee 38105, Genomic Instability Research Center (GIRC), Ajou University School of Medicine, Suwon, Korea,
| | - Eric J Brown
- Abramson Family Cancer Research Institute and the Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and
| | - Sandy Chang
- Department of Laboratory Medicine, Yale University, New Haven, Connecticut 06520
| | - Peter J McKinnon
- Department of Genetics, St Jude Children's Research Hospital, Memphis, Tennessee 38105,
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83
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A structure-specific nucleic acid-binding domain conserved among DNA repair proteins. Proc Natl Acad Sci U S A 2014; 111:7618-23. [PMID: 24821763 DOI: 10.1073/pnas.1324143111] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SMARCAL1, a DNA remodeling protein fundamental to genome integrity during replication, is the only gene associated with the developmental disorder Schimke immuno-osseous dysplasia (SIOD). SMARCAL1-deficient cells show collapsed replication forks, S-phase cell cycle arrest, increased chromosomal breaks, hypersensitivity to genotoxic agents, and chromosomal instability. The SMARCAL1 catalytic domain (SMARCAL1(CD)) is composed of an SNF2-type double-stranded DNA motor ATPase fused to a HARP domain of unknown function. The mechanisms by which SMARCAL1 and other DNA translocases repair replication forks are poorly understood, in part because of a lack of structural information on the domains outside of the common ATPase motor. In the present work, we determined the crystal structure of the SMARCAL1 HARP domain and examined its conformation and assembly in solution by small angle X-ray scattering. We report that this domain is conserved with the DNA mismatch and damage recognition domains of MutS/MSH and NER helicase XPB, respectively, as well as with the putative DNA specificity motif of the T4 phage fork regression protein UvsW. Loss of UvsW fork regression activity by deletion of this domain was rescued by its replacement with HARP, establishing the importance of this domain in UvsW and demonstrating a functional complementarity between these structurally homologous domains. Mutation of predicted DNA-binding residues in HARP dramatically reduced fork binding and regression activities of SMARCAL1(CD). Thus, this work has uncovered a conserved substrate recognition domain in DNA repair enzymes that couples ATP-hydrolysis to remodeling of a variety of DNA structures, and provides insight into this domain's role in replication fork stability and genome integrity.
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84
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Ashley AK, Shrivastav M, Nie J, Amerin C, Troksa K, Glanzer JG, Liu S, Opiyo SO, Dimitrova DD, Le P, Sishc B, Bailey SM, Oakley GG, Nickoloff JA. DNA-PK phosphorylation of RPA32 Ser4/Ser8 regulates replication stress checkpoint activation, fork restart, homologous recombination and mitotic catastrophe. DNA Repair (Amst) 2014; 21:131-9. [PMID: 24819595 DOI: 10.1016/j.dnarep.2014.04.008] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Revised: 03/17/2014] [Accepted: 04/14/2014] [Indexed: 11/17/2022]
Abstract
Genotoxins and other factors cause replication stress that activate the DNA damage response (DDR), comprising checkpoint and repair systems. The DDR suppresses cancer by promoting genome stability, and it regulates tumor resistance to chemo- and radiotherapy. Three members of the phosphatidylinositol 3-kinase-related kinase (PIKK) family, ATM, ATR, and DNA-PK, are important DDR proteins. A key PIKK target is replication protein A (RPA), which binds single-stranded DNA and functions in DNA replication, DNA repair, and checkpoint signaling. An early response to replication stress is ATR activation, which occurs when RPA accumulates on ssDNA. Activated ATR phosphorylates many targets, including the RPA32 subunit of RPA, leading to Chk1 activation and replication arrest. DNA-PK also phosphorylates RPA32 in response to replication stress, and we demonstrate that cells with DNA-PK defects, or lacking RPA32 Ser4/Ser8 targeted by DNA-PK, confer similar phenotypes, including defective replication checkpoint arrest, hyper-recombination, premature replication fork restart, failure to block late origin firing, and increased mitotic catastrophe. We present evidence that hyper-recombination in these mutants is ATM-dependent, but the other defects are ATM-independent. These results indicate that DNA-PK and ATR signaling through RPA32 plays a critical role in promoting genome stability and cell survival in response to replication stress.
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Affiliation(s)
- Amanda K Ashley
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States
| | - Meena Shrivastav
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, United States
| | - Jingyi Nie
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States
| | - Courtney Amerin
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States
| | - Kyle Troksa
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States
| | - Jason G Glanzer
- Department of Oral Biology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Shengqin Liu
- Department of Oral Biology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Stephen O Opiyo
- Department of Oral Biology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Diana D Dimitrova
- Department of Oral Biology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Phuong Le
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States
| | - Brock Sishc
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States
| | - Susan M Bailey
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States
| | - Greg G Oakley
- Department of Oral Biology, University of Nebraska Medical Center, Omaha, NE, United States; Eppley Cancer Center, University of Nebraska Medical Center, Omaha, NE, United States
| | - Jac A Nickoloff
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States; Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, United States.
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85
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Lindsey-Boltz LA, Kemp MG, Reardon JT, DeRocco V, Iyer RR, Modrich P, Sancar A. Coupling of human DNA excision repair and the DNA damage checkpoint in a defined in vitro system. J Biol Chem 2014; 289:5074-82. [PMID: 24403078 DOI: 10.1074/jbc.m113.542787] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA repair and DNA damage checkpoints work in concert to help maintain genomic integrity. In vivo data suggest that these two global responses to DNA damage are coupled. It has been proposed that the canonical 30 nucleotide single-stranded DNA gap generated by nucleotide excision repair is the signal that activates the ATR-mediated DNA damage checkpoint response and that the signal is enhanced by gap enlargement by EXO1 (exonuclease 1) 5' to 3' exonuclease activity. Here we have used purified core nucleotide excision repair factors (RPA, XPA, XPC, TFIIH, XPG, and XPF-ERCC1), core DNA damage checkpoint proteins (ATR-ATRIP, TopBP1, RPA), and DNA damaged by a UV-mimetic agent to analyze the basic steps of DNA damage checkpoint response in a biochemically defined system. We find that checkpoint signaling as measured by phosphorylation of target proteins by the ATR kinase requires enlargement of the excision gap generated by the excision repair system by the 5' to 3' exonuclease activity of EXO1. We conclude that, in addition to damaged DNA, RPA, XPA, XPC, TFIIH, XPG, XPF-ERCC1, ATR-ATRIP, TopBP1, and EXO1 constitute the minimum essential set of factors for ATR-mediated DNA damage checkpoint response.
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Affiliation(s)
- Laura A Lindsey-Boltz
- From the Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-7260 and
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86
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Guillemette S, Branagan A, Peng M, Dhruva A, Schärer OD, Cantor SB. FANCJ localization by mismatch repair is vital to maintain genomic integrity after UV irradiation. Cancer Res 2013; 74:932-44. [PMID: 24351291 DOI: 10.1158/0008-5472.can-13-2474] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Nucleotide excision repair (NER) is critical for the repair of DNA lesions induced by UV radiation, but its contribution in replicating cells is less clear. Here, we show that dual incision by NER endonucleases, including XPF and XPG, promotes the S-phase accumulation of the BRCA1 and Fanconi anemia-associated DNA helicase FANCJ to sites of UV-induced damage. FANCJ promotes replication protein A phosphorylation and the arrest of DNA synthesis following UV irradiation. Interaction defective mutants of FANCJ reveal that BRCA1 binding is not required for FANCJ localization, whereas interaction with the mismatch repair (MMR) protein MLH1 is essential. Correspondingly, we find that FANCJ, its direct interaction with MLH1, and the MMR protein MSH2 function in a common pathway in response to UV irradiation. FANCJ-deficient cells are not sensitive to killing by UV irradiation, yet we find that DNA mutations are significantly enhanced. Thus, we considered that FANCJ deficiency could be associated with skin cancer. Along these lines, in melanoma we found several somatic mutations in FANCJ, some of which were previously identified in hereditary breast cancer and Fanconi anemia. Given that, mutations in XPF can also lead to Fanconi anemia, we propose collaborations between Fanconi anemia, NER, and MMR are necessary to initiate checkpoint activation in replicating human cells to limit genomic instability.
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Affiliation(s)
- Shawna Guillemette
- Authors' Affiliations: Department of Cancer Biology, University of Massachusetts Medical School, Women's Cancers Program, UMASS Memorial Cancer Center, Worcester, Massachusetts; and Department of Pharmacological Sciences & Department of Chemistry, Stony Brook University, Stony Brook, New York
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87
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Sokol AM, Cruet-Hennequart S, Pasero P, Carty MP. DNA polymerase η modulates replication fork progression and DNA damage responses in platinum-treated human cells. Sci Rep 2013; 3:3277. [PMID: 24253929 PMCID: PMC6505966 DOI: 10.1038/srep03277] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 11/05/2013] [Indexed: 01/03/2023] Open
Abstract
Human cells lacking DNA polymerase η (polη) are sensitive to platinum-based cancer chemotherapeutic agents. Using DNA combing to directly investigate the role of polη in bypass of platinum-induced DNA lesions in vivo, we demonstrate that nascent DNA strands are up to 39% shorter in human cells lacking polη than in cells expressing polη. This provides the first direct evidence that polη modulates replication fork progression in vivo following cisplatin and carboplatin treatment. Severe replication inhibition in individual platinum-treated polη-deficient cells correlates with enhanced phosphorylation of the RPA2 subunit of replication protein A on serines 4 and 8, as determined using EdU labelling and immunofluorescence, consistent with formation of DNA strand breaks at arrested forks in the absence of polη. Polη-mediated bypass of platinum-induced DNA lesions may therefore represent one mechanism by which cancer cells can tolerate platinum-based chemotherapy.
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Affiliation(s)
- Anna M. Sokol
- DNA Damage Response Laboratory, Centre for Chromosome Biology, Biochemistry, School of Natural Sciences, National University of Ireland, Galway, Ireland
- Current address: Laboratory of Mitochondrial Biogenesis, International Institute of Molecular and Cell Biology, 4 Ks. Trojdena Street, 02-109 Warsaw, Poland
| | - Séverine Cruet-Hennequart
- DNA Damage Response Laboratory, Centre for Chromosome Biology, Biochemistry, School of Natural Sciences, National University of Ireland, Galway, Ireland
- Current address: Microenvironment and Pathology Laboratory (MILPAT, EA 4652), Niveau 3, Faculté de Médecine, Avenue de la Côte de Nacre, 14032 Caen cedex. France
| | - Philippe Pasero
- Department of Molecular Basis of Human Diseases, Institute of Human Genetics, CNRS UPR 1142, Montpellier, France
| | - Michael P. Carty
- DNA Damage Response Laboratory, Centre for Chromosome Biology, Biochemistry, School of Natural Sciences, National University of Ireland, Galway, Ireland
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88
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Cdk1 regulates the temporal recruitment of telomerase and Cdc13-Stn1-Ten1 complex for telomere replication. Mol Cell Biol 2013; 34:57-70. [PMID: 24164896 DOI: 10.1128/mcb.01235-13] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
In budding yeast (Saccharomyces cerevisiae), the cell cycle-dependent telomere elongation by telomerase is controlled by the cyclin-dependent kinase 1 (Cdk1). The telomere length homeostasis is balanced between telomerase-unextendable and telomerase-extendable states that both require Cdc13. The recruitment of telomerase complex by Cdc13 promotes telomere elongation, while the formation of Cdc13-Stn1-Ten1 (CST) complex at the telomere blocks telomere elongation by telomerase. However, the cellular signaling that regulates the timing of the telomerase-extendable and telomerase-unextendable states is largely unknown. Phosphorylation of Cdc13 by Cdk1 promotes the interaction between Cdc13 and Est1 and hence telomere elongation. Here, we show that Cdk1 also phosphorylates Stn1 at threonine 223 and serine 250 both in vitro and in vivo, and these phosphorylation events are essential for the stability of the CST complexes at the telomeres. By controlling the timing of Cdc13 and Stn1 phosphorylations during cell cycle progression, Cdk1 regulates the temporal recruitment of telomerase complexes and CST complexes to the telomeres to facilitate telomere maintenance.
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89
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The complexity of DNA double strand breaks is a critical factor enhancing end-resection. DNA Repair (Amst) 2013; 12:936-46. [PMID: 24041488 DOI: 10.1016/j.dnarep.2013.08.009] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 08/09/2013] [Accepted: 08/17/2013] [Indexed: 11/22/2022]
Abstract
DNA double strand breaks (DSBs) induced by ionizing radiation (IR) are deleterious damages. Two major pathways repair DSBs in human cells, DNA non-homologous end-joining (NHEJ) and homologous recombination (HR). It has been suggested that the balance between the two repair pathways varies depending on the chromatin structure surrounding the damage site and/or the complexity of damage at the DNA break ends. Heavy ion radiation is known to induce complex-type DSBs, and the efficiency of NHEJ in repairing these DSBs was shown to be diminished. Taking advantage of the ability of high linear energy transfer (LET) radiation to produce complex DSBs effectively, we investigated how the complexity of DSB end structure influences DNA damage responses. An early step in HR is the generation of 3'-single strand DNA (SSD) via a process of DNA end resection that requires CtIP. To assess this process, we analyzed the level of phosphorylated CtIP, as well as RPA phosphorylation and focus formation, which occur on the exposed SSD. We show that complex DSBs efficiently activate DNA end resection. After heavy ion beam irradiation, resection signals appear both in the vicinity of heterochromatic areas, which is also observed after X-irradiation, and additionally in euchromatic areas. Consequently, ~85% of complex DSBs are subjected to resection in heavy ion particle tracks. Furthermore, around 20-40% of G1 cells exhibit resection signals. Taken together, our observations reveal that the complexity of DSB ends is a critical factor regulating the choice of DSB repair pathway and drastically alters the balance toward resection-mediated rejoining. As demonstrated here, studies on DNA damage responses induced by heavy ion radiation provide an important tool to shed light on mechanisms regulating DNA end resection.
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90
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Feldkamp MD, Frank AO, Kennedy JP, Patrone JD, Vangamudi B, Waterson AG, Fesik SW, Chazin WJ. Surface reengineering of RPA70N enables cocrystallization with an inhibitor of the replication protein A interaction motif of ATR interacting protein. Biochemistry 2013; 52:6515-24. [PMID: 23962067 DOI: 10.1021/bi400542z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Replication protein A (RPA) is the primary single-stranded DNA (ssDNA) binding protein in eukaryotes. The N-terminal domain of the RPA70 subunit (RPA70N) interacts via a basic cleft with a wide range of DNA processing proteins, including several that regulate DNA damage response and repair. Small molecule inhibitors that disrupt these protein-protein interactions are therefore of interest as chemical probes of these critical DNA processing pathways and as inhibitors to counter the upregulation of DNA damage response and repair associated with treatment of cancer patients with radiation or DNA-damaging agents. Determination of three-dimensional structures of protein-ligand complexes is an important step for elaboration of small molecule inhibitors. However, although crystal structures of free RPA70N and an RPA70N-peptide fusion construct have been reported, RPA70N-inhibitor complexes have been recalcitrant to crystallization. Analysis of the P61 lattice of RPA70N crystals led us to hypothesize that the ligand-binding surface was occluded. Surface reengineering to alter key crystal lattice contacts led to the design of RPA70N E7R, E100R, and E7R/E100R mutants. These mutants crystallized in a P212121 lattice that clearly had significant solvent channels open to the critical basic cleft. Analysis of X-ray crystal structures, target peptide binding affinities, and (15)N-(1)H heteronuclear single-quantum coherence nuclear magnetic resonance spectra showed that the mutations do not result in perturbations of the RPA70N ligand-binding surface. The success of the design was demonstrated by determining the structure of RPA70N E7R soaked with a ligand discovered in a previously reported molecular fragment screen. A fluorescence anisotropy competition binding assay revealed this compound can inhibit the interaction of RPA70N with the peptide binding motif from the DNA damage response protein ATRIP. The implications of the results are discussed in the context of ongoing efforts to design RPA70N inhibitors.
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Affiliation(s)
- Michael D Feldkamp
- Department of Biochemistry, ‡Department of Chemistry, §Department of Pharmacology, and ∥Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37232, United States
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91
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Vidal-Eychenié S, Décaillet C, Basbous J, Constantinou A. DNA structure-specific priming of ATR activation by DNA-PKcs. ACTA ACUST UNITED AC 2013; 202:421-9. [PMID: 23897887 PMCID: PMC3734074 DOI: 10.1083/jcb.201304139] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The juxtaposition of a double-stranded DNA end and a short single-stranded DNA gap triggers robust activation of endogenous ATR and Chk1 mediated by DNA-PKcs. Three phosphatidylinositol-3-kinase–related protein kinases implement cellular responses to DNA damage. DNA-dependent protein kinase catalytic subunit (DNA-PKcs) and ataxia-telangiectasia mutated respond primarily to DNA double-strand breaks (DSBs). Ataxia-telangiectasia and RAD3-related (ATR) signals the accumulation of replication protein A (RPA)–covered single-stranded DNA (ssDNA), which is caused by replication obstacles. Stalled replication intermediates can further degenerate and yield replication-associated DSBs. In this paper, we show that the juxtaposition of a double-stranded DNA end and a short ssDNA gap triggered robust activation of endogenous ATR and Chk1 in human cell-free extracts. This DNA damage signal depended on DNA-PKcs and ATR, which congregated onto gapped linear duplex DNA. DNA-PKcs primed ATR/Chk1 activation through DNA structure-specific phosphorylation of RPA32 and TopBP1. The synergistic activation of DNA-PKcs and ATR suggests that the two kinases combine to mount a prompt and specific response to replication-born DSBs.
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Affiliation(s)
- Sophie Vidal-Eychenié
- Institute of Human Genetics, Unité Propre de Recherche 1142, Centre National de la Recherche Scientifique, 34396 Montpellier, France
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92
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APE2 is required for ATR-Chk1 checkpoint activation in response to oxidative stress. Proc Natl Acad Sci U S A 2013; 110:10592-7. [PMID: 23754435 DOI: 10.1073/pnas.1301445110] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The base excision repair pathway is largely responsible for the repair of oxidative stress-induced DNA damage. However, it remains unclear how the DNA damage checkpoint is activated by oxidative stress at the molecular level. Here, we provide evidence showing that hydrogen peroxide (H2O2) triggers checkpoint kinase 1 (Chk1) phosphorylation in an ATR [ataxia-telangiectasia mutated (ATM) and Rad3-related]-dependent but ATM-independent manner in Xenopus egg extracts. A base excision repair protein, Apurinic/apyrimidinic (AP) endonuclease 2 (APE2, APN2, or APEX2), is required for the generation of replication protein A (RPA)-bound single-stranded DNA, the recruitment of a checkpoint protein complex [ATR, ATR-interacting protein (ATRIP), and Rad9] to damage sites, and H2O2-induced Chk1 phosphorylation. A conserved proliferating cell nuclear antigen interaction protein box of APE2 is important for the recruitment of APE2 to H2O2-damaged chromatin. APE2 3'-phosphodiesterase and 3'-5' exonuclease activity is essential for single-stranded DNA generation in the 3'-5' direction from single-stranded breaks, referred to as single-stranded break end resection. In addition, APE2 associates with Chk1, and a serine residue (S86) in the Chk1-binding motif of APE2 is essential for Chk1 phosphorylation, indicating a Claspin-like but distinct role for APE2 in ATR-Chk1 signaling. Our data indicate that APE2 plays a vital and previously unexpected role in ATR-Chk1 checkpoint signaling in response to oxidative stress. Thus, our findings shed light on a distinct mechanism of how an ATR-Chk1-dependent DNA damage checkpoint is mediated by APE2 in the oxidative stress response.
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93
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Chaudhury I, Sareen A, Raghunandan M, Sobeck A. FANCD2 regulates BLM complex functions independently of FANCI to promote replication fork recovery. Nucleic Acids Res 2013; 41:6444-59. [PMID: 23658231 PMCID: PMC3711430 DOI: 10.1093/nar/gkt348] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Fanconi Anemia (FA) and Bloom Syndrome share overlapping phenotypes including spontaneous chromosomal abnormalities and increased cancer predisposition. The FA protein pathway comprises an upstream core complex that mediates recruitment of two central players, FANCD2 and FANCI, to sites of stalled replication forks. Successful fork recovery depends on the Bloom’s helicase BLM that participates in a larger protein complex (‘BLMcx’) containing topoisomerase III alpha, RMI1, RMI2 and replication protein A. We show that FANCD2 is an essential regulator of BLMcx functions: it maintains BLM protein stability and is crucial for complete BLMcx assembly; moreover, it recruits BLMcx to replicating chromatin during normal S-phase and mediates phosphorylation of BLMcx members in response to DNA damage. During replication stress, FANCD2 and BLM cooperate to promote restart of stalled replication forks while suppressing firing of new replication origins. In contrast, FANCI is dispensable for FANCD2-dependent BLMcx regulation, demonstrating functional separation of FANCD2 from FANCI.
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Affiliation(s)
- Indrajit Chaudhury
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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94
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Ashton NW, Bolderson E, Cubeddu L, O'Byrne KJ, Richard DJ. Human single-stranded DNA binding proteins are essential for maintaining genomic stability. BMC Mol Biol 2013; 14:9. [PMID: 23548139 PMCID: PMC3626794 DOI: 10.1186/1471-2199-14-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 03/20/2013] [Indexed: 12/25/2022] Open
Abstract
The double-stranded conformation of cellular DNA is a central aspect of DNA stabilisation and protection. The helix preserves the genetic code against chemical and enzymatic degradation, metabolic activation, and formation of secondary structures. However, there are various instances where single-stranded DNA is exposed, such as during replication or transcription, in the synthesis of chromosome ends, and following DNA damage. In these instances, single-stranded DNA binding proteins are essential for the sequestration and processing of single-stranded DNA. In order to bind single-stranded DNA, these proteins utilise a characteristic and evolutionary conserved single-stranded DNA-binding domain, the oligonucleotide/oligosaccharide-binding (OB)-fold. In the current review we discuss a subset of these proteins involved in the direct maintenance of genomic stability, an important cellular process in the conservation of cellular viability and prevention of malignant transformation. We discuss the central roles of single-stranded DNA binding proteins from the OB-fold domain family in DNA replication, the restart of stalled replication forks, DNA damage repair, cell cycle-checkpoint activation, and telomere maintenance.
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Affiliation(s)
- Nicholas W Ashton
- Genome Stability Laboratory, Cancer and Ageing Research Program, Institute of Health and Biomedical Innovation, Translational Research Institute, Queensland University of Technology, Woolloongabba, Queensland, 4102, Australia
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95
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Abstract
Rfa2 is a ssDNA (single-stranded DNA)-binding protein that plays an important role in DNA replication, recombination and repair. Rfa2 is regulated by phosphorylation, which alters its protein–protein interaction and protein–DNA interaction. In the present study, we found that the Pph3–Psy2 phosphatase complex is responsible for Rfa2 dephosphorylation both during normal G1-phase and under DNA replication stress in Candida albicans. Phosphorylated Rfa2 extracted from pph3Δ or psy2Δ G1 cells exhibited diminished binding affinity to dsDNA (double-stranded DNA) but not to ssDNA. We also discovered that Cdc28 (cell division cycle 28) and Mec1 are responsible for Rfa2 phosphorylation in G1-phase and under DNA replication stress respectively. Moreover, MS revealed that the domain of Rfa2 that was phosphorylated in G1-phase differed from that phosphorylated under the stress conditions. The results of the present study imply that differential phosphorylation plays a crucial role in RPA (replication protein A) regulation.
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96
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Abstract
Parvoviruses are a group of small DNA viruses with ssDNA genomes flanked by two inverted terminal structures. Due to a limited genetic resource they require host cellular factors and sometimes a helper virus for efficient viral replication. Recent studies have shown that parvoviruses interact with the DNA damage machinery, which has a significant impact on the life cycle of the virus as well as the fate of infected cells. In addition, due to special DNA structures of the viral genomes, parvoviruses are useful tools for the study of the molecular mechanisms underlying viral infection-induced DNA damage response (DDR). This review aims to summarize recent advances in parvovirus-induced DDR, with a focus on the diverse DDR pathways triggered by different parvoviruses and the consequences of DDR on the viral life cycle as well as the fate of infected cells.
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Affiliation(s)
- Yong Luo
- Department of Microbiology, Molecular Genetics & Immunology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Jianming Qiu
- Department of Microbiology, Molecular Genetics & Immunology, University of Kansas Medical Center, Kansas City, KS, USA
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97
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Tuul M, Kitao H, Iimori M, Matsuoka K, Kiyonari S, Saeki H, Oki E, Morita M, Maehara Y. Rad9, Rad17, TopBP1 and claspin play essential roles in heat-induced activation of ATR kinase and heat tolerance. PLoS One 2013; 8:e55361. [PMID: 23383325 PMCID: PMC3562228 DOI: 10.1371/journal.pone.0055361] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 12/21/2012] [Indexed: 12/22/2022] Open
Abstract
Hyperthermia is widely used to treat patients with cancer, especially in combination with other treatments such as radiation therapy. Heat treatment per se activates DNA damage responses mediated by the ATR-Chk1 and ATM-Chk2 pathways but it is not fully understood how these DNA damage responses are activated and affect heat tolerance. By performing a genetic analysis of human HeLa cells and chicken B lymphoma DT40 cells, we found that heat-induced Chk1 Ser345 phosphorylation by ATR was largely dependent on Rad9, Rad17, TopBP1 and Claspin. Activation of the ATR-Chk1 pathway by heat, however, was not associated with FancD2 monoubiquitination or RPA32 phosphorylation, which are known as downstream events of ATR kinase activation when replication forks are stalled. Downregulation of ATR, Rad9, Rad17, TopBP1 or Claspin drastically reduced clonogenic cell viability upon hyperthermia, while gene knockout or inhibition of ATM kinase reduced clonogenic viability only modestly. Suppression of the ATR-Chk1 pathway activation enhanced heat-induced phosphorylation of Chk2 Thr68 and simultaneous inhibition of ATR and ATM kinases rendered severe heat cytotoxicity. These data indicate that essential factors for activation of the ATR-Chk1 pathway at stalled replication forks are also required for heat-induced activation of ATR kinase, which predominantly contributes to heat tolerance in a non-overlapping manner with ATM kinase.
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Affiliation(s)
- Munkhbold Tuul
- Department of Molecular Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroyuki Kitao
- Department of Molecular Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Innovative anticancer strategy for therapeutics and diagnosis group, Innovation Center for Medical Redox Navigation, Kyushu University, Fukuoka, Japan
- * E-mail:
| | - Makoto Iimori
- Department of Molecular Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kazuaki Matsuoka
- Innovative anticancer strategy for therapeutics and diagnosis group, Innovation Center for Medical Redox Navigation, Kyushu University, Fukuoka, Japan
- Tokushima Research Center, Taiho Pharmaceutical Co., Ltd., Tokushima, Japan
| | - Shinichi Kiyonari
- Innovative anticancer strategy for therapeutics and diagnosis group, Innovation Center for Medical Redox Navigation, Kyushu University, Fukuoka, Japan
| | - Hiroshi Saeki
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Eiji Oki
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masaru Morita
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshihiko Maehara
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Innovative anticancer strategy for therapeutics and diagnosis group, Innovation Center for Medical Redox Navigation, Kyushu University, Fukuoka, Japan
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98
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Renaud E, Rosselli F. FANC pathway promotes UV-induced stalled replication forks recovery by acting both upstream and downstream Polη and Rev1. PLoS One 2013; 8:e53693. [PMID: 23365640 PMCID: PMC3554758 DOI: 10.1371/journal.pone.0053693] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 12/04/2012] [Indexed: 11/18/2022] Open
Abstract
To cope with ultraviolet C (UVC)-stalled replication forks and restart DNA synthesis, cells either undergo DNA translesion synthesis (TLS) by specialised DNA polymerases or tolerate the lesions using homologous recombination (HR)-based mechanisms. To gain insight into how cells manage UVC-induced stalled replication forks, we analysed the molecular crosstalk between the TLS DNA polymerases Polη and Rev1, the double-strand break repair (DSB)-associated protein MDC1 and the FANC pathway. We describe three novel functional interactions that occur in response to UVC-induced DNA lesions. First, Polη and Rev1, whose optimal expression and/or relocalisation depend on the FANC core complex, act upstream of FANCD2 and are required for the proper relocalisation of monoubiquitinylated FANCD2 (Ub-FANCD2) to subnuclear foci. Second, during S-phase, Ub-FANCD2 and MDC1 relocalise to UVC-damaged nuclear areas or foci simultaneously but independently of each other. Third, Ub-FANCD2 and MDC1 are independently required for optimal BRCA1 relocalisation. While RPA32 phosphorylation (p-RPA32) and RPA foci formation were reduced in parallel with increasing levels of H2AX phosphorylation and MDC1 foci in UVC-irradiated FANC pathway-depleted cells, MDC1 depletion was associated with increased UVC-induced Ub-FANCD2 and FANCD2 foci as well as p-RPA32 levels and p-RPA32 foci. On the basis of the previous observations, we propose that the FANC pathway participates in the rescue of UVC-stalled replication forks in association with TLS by maintaining the integrity of ssDNA regions and by preserving genome stability and preventing the formation of DSBs, the resolution of which would require the intervention of MDC1.
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Affiliation(s)
- Emilie Renaud
- Université Paris Sud, UMR8200, « Equipe Labellisée Ligue Contre le Cancer », Institut de Cancérologie Gustave-Roussy, Villejuif, France
- CNRS, UMR8200, « Equipe Labellisée Ligue Contre le Cancer », Institut de Cancérologie Gustave-Roussy, Villejuif, France
| | - Filippo Rosselli
- Université Paris Sud, UMR8200, « Equipe Labellisée Ligue Contre le Cancer », Institut de Cancérologie Gustave-Roussy, Villejuif, France
- CNRS, UMR8200, « Equipe Labellisée Ligue Contre le Cancer », Institut de Cancérologie Gustave-Roussy, Villejuif, France
- * E-mail:
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99
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Zhang L, Chen H, Gong M, Gong F. The chromatin remodeling protein BRG1 modulates BRCA1 response to UV irradiation by regulating ATR/ATM activation. Front Oncol 2013; 3:7. [PMID: 23346553 PMCID: PMC3552176 DOI: 10.3389/fonc.2013.00007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 01/09/2013] [Indexed: 01/08/2023] Open
Abstract
The SWI/SNF chromatin remodeling complex plays a role in the repair of UV-induced DNA damage. It was proposed that chromatin remodeling activities are utilized to increase the accessibility of nucleotide excision repair (NER) machinery and checkpoint factors to the damaged DNA. It was shown recently that BRCA1 contributes to UV damage response by promoting photoproduct excision, triggering post-UV checkpoint activation and post-replicative repair. In this study, we show that BRCA1 rapidly binds to UV damage sites when cells are undergoing DNA synthesis. In contrast, two phosphorylated forms of BRCA1 do not accumulate at sites of UV damage. Depletion of BRG1, a core subunit of the human SWI/SNF-BAF complex, impairs the recruitment of BRCA1 to the damage sites and attenuates DNA damage induced BRCA1 phosphorylation. At UV lesions-stalled replication forks, BRG1 promotes RPA phosphorylation in response to UV irradiation, since UV-induced phosphorylation of chromatin bound RPA drops significantly when BRG1 is depleted in human cells. Importantly, activation of the ATM/ATR kinases is attenuated when BRG1 is depleted. We propose that BRG1 modulates BRCA1 response to UV irradiation by regulating ATM/ATR activation.
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Affiliation(s)
- Ling Zhang
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine Miami, FL, USA
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100
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Ordinario E, Han HJ, Furuta S, Heiser LM, Jakkula LR, Rodier F, Spellman PT, Campisi J, Gray JW, Bissell MJ, Kohwi Y, Kohwi-Shigematsu T. ATM suppresses SATB1-induced malignant progression in breast epithelial cells. PLoS One 2012; 7:e51786. [PMID: 23251624 PMCID: PMC3519734 DOI: 10.1371/journal.pone.0051786] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 11/12/2012] [Indexed: 11/24/2022] Open
Abstract
SATB1 drives metastasis when expressed in breast tumor cells by radically reprogramming gene expression. Here, we show that SATB1 also has an oncogenic activity to transform certain non-malignant breast epithelial cell lines. We studied the non-malignant MCF10A cell line, which is used widely in the literature. We obtained aliquots from two different sources (here we refer to them as MCF10A-1 and MCF10A-2), but found them to be surprisingly dissimilar in their responses to oncogenic activity of SATB1. Ectopic expression of SATB1 in MCF10A-1 induced tumor-like morphology in three-dimensional cultures, led to tumor formation in immunocompromised mice, and when injected into tail veins, led to lung metastasis. The number of metastases correlated positively with the level of SATB1 expression. In contrast, SATB1 expression in MCF10A-2 did not lead to any of these outcomes. Yet DNA copy-number analysis revealed that MCF10A-1 is indistinguishable genetically from MCF10A-2. However, gene expression profiling analysis revealed that these cell lines have significantly divergent signatures for the expression of genes involved in oncogenesis, including cell cycle regulation and signal transduction. Above all, the early DNA damage-response kinase, ATM, was greatly reduced in MCF10A-1 cells compared to MCF10A-2 cells. We found the reason for reduction to be phenotypic drift due to long-term cultivation of MCF10A. ATM knockdown in MCF10A-2 and two other non-malignant breast epithelial cell lines, 184A1 and 184B4, enabled SATB1 to induce malignant phenotypes similar to that observed for MCF10A-1. These data indicate a novel role for ATM as a suppressor of SATB1-induced malignancy in breast epithelial cells, but also raise a cautionary note that phenotypic drift could lead to dramatically different functional outcomes.
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Affiliation(s)
- Ellen Ordinario
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California, United States of America
| | - Hye-Jung Han
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California, United States of America
| | - Saori Furuta
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California, United States of America
| | - Laura M. Heiser
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California, United States of America
| | - Lakshmi R. Jakkula
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California, United States of America
| | - Francis Rodier
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California, United States of America
| | - Paul T. Spellman
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California, United States of America
| | - Judith Campisi
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California, United States of America
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Joe W. Gray
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California, United States of America
| | - Mina J. Bissell
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California, United States of America
| | - Yoshinori Kohwi
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California, United States of America
| | - Terumi Kohwi-Shigematsu
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California, United States of America
- * E-mail:
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