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Sahay O, Barik GK, Sharma T, Pillai AD, Rapole S, Santra MK. Damsel in distress calling on her knights: Illuminating the pioneering role of E3 ubiquitin ligases in guarding the genome integrity. DNA Repair (Amst) 2021; 109:103261. [PMID: 34920250 DOI: 10.1016/j.dnarep.2021.103261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/30/2021] [Accepted: 12/07/2021] [Indexed: 11/03/2022]
Abstract
The maintenance of genomic integrity is of utmost importance for the organisms to survive and to accurately inherit traits to their progenies. Any kind of DNA damage either due to defect in DNA duplication and/ or uncontrolled cell division or intracellular insults or environment radiation can result in gene mutation, chromosomal aberration and ultimately genomic instability, which may cause several diseases including cancers. Therefore, cells have evolved machineries for the surveillance of genomic integrity. Enormous exciting studies in the past indicate that ubiquitination (a posttranslational modification of proteins) plays a crucial role in maintaining the genomic integrity by diverse ways. In fact, various E3 ubiquitin ligases catalyse ubiquitination of key proteins to control their central role during cell cycle, DNA damage response (DDR) and DNA repair. Some E3 ligases promote genomic instability while others prevent it, deregulation of both of which leads to several malignancies. In this review, we consolidate the recent findings wherein the role of ubiquitination in conferring genome integrity is highlighted. We also discuss the latest discoveries on the mechanisms utilized by various E3 ligases to preserve genomic stability, with a focus on their actions during cell cycle progression and different types of DNA damage response as well as repair pathways.
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Affiliation(s)
- Osheen Sahay
- National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India; Department of Biotechnology, S.P. Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Ganesh Kumar Barik
- National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India; Department of Biotechnology, S.P. Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Tanisha Sharma
- National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India; Department of Biotechnology, S.P. Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Ajay D Pillai
- National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Srikanth Rapole
- National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Manas Kumar Santra
- National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India.
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2
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Bustamante-Jaramillo LF, Ramos C, Martín-Castellanos C. The Meiosis-Specific Crs1 Cyclin Is Required for Efficient S-Phase Progression and Stable Nuclear Architecture. Int J Mol Sci 2021; 22:ijms22115483. [PMID: 34067465 PMCID: PMC8196990 DOI: 10.3390/ijms22115483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/13/2021] [Accepted: 05/19/2021] [Indexed: 11/26/2022] Open
Abstract
Cyclins and CDKs (Cyclin Dependent Kinases) are key players in the biology of eukaryotic cells, representing hubs for the orchestration of physiological conditions with cell cycle progression. Furthermore, as in the case of meiosis, cyclins and CDKs have acquired novel functions unrelated to this primal role in driving the division cycle. Meiosis is a specialized developmental program that ensures proper propagation of the genetic information to the next generation by the production of gametes with accurate chromosome content, and meiosis-specific cyclins are widespread in evolution. We have explored the diversification of CDK functions studying the meiosis-specific Crs1 cyclin in fission yeast. In addition to the reported role in DSB (Double Strand Break) formation, this cyclin is required for meiotic S-phase progression, a canonical role, and to maintain the architecture of the meiotic chromosomes. Crs1 localizes at the SPB (Spindle Pole Body) and is required to stabilize the cluster of telomeres at this location (bouquet configuration), as well as for normal SPB motion. In addition, Crs1 exhibits CDK(Cdc2)-dependent kinase activity in a biphasic manner during meiosis, in contrast to a single wave of protein expression, suggesting a post-translational control of its activity. Thus, Crs1 displays multiple functions, acting both in cell cycle progression and in several key meiosis-specific events.
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3
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Hekman RM, Hume AJ, Goel RK, Abo KM, Huang J, Blum BC, Werder RB, Suder EL, Paul I, Phanse S, Youssef A, Alysandratos KD, Padhorny D, Ojha S, Mora-Martin A, Kretov D, Ash PEA, Verma M, Zhao J, Patten JJ, Villacorta-Martin C, Bolzan D, Perea-Resa C, Bullitt E, Hinds A, Tilston-Lunel A, Varelas X, Farhangmehr S, Braunschweig U, Kwan JH, McComb M, Basu A, Saeed M, Perissi V, Burks EJ, Layne MD, Connor JH, Davey R, Cheng JX, Wolozin BL, Blencowe BJ, Wuchty S, Lyons SM, Kozakov D, Cifuentes D, Blower M, Kotton DN, Wilson AA, Mühlberger E, Emili A. Actionable Cytopathogenic Host Responses of Human Alveolar Type 2 Cells to SARS-CoV-2. Mol Cell 2020; 80:1104-1122.e9. [PMID: 33259812 PMCID: PMC7674017 DOI: 10.1016/j.molcel.2020.11.028] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/16/2020] [Accepted: 11/11/2020] [Indexed: 12/11/2022]
Abstract
Human transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causative pathogen of the COVID-19 pandemic, exerts a massive health and socioeconomic crisis. The virus infects alveolar epithelial type 2 cells (AT2s), leading to lung injury and impaired gas exchange, but the mechanisms driving infection and pathology are unclear. We performed a quantitative phosphoproteomic survey of induced pluripotent stem cell-derived AT2s (iAT2s) infected with SARS-CoV-2 at air-liquid interface (ALI). Time course analysis revealed rapid remodeling of diverse host systems, including signaling, RNA processing, translation, metabolism, nuclear integrity, protein trafficking, and cytoskeletal-microtubule organization, leading to cell cycle arrest, genotoxic stress, and innate immunity. Comparison to analogous data from transformed cell lines revealed respiratory-specific processes hijacked by SARS-CoV-2, highlighting potential novel therapeutic avenues that were validated by a high hit rate in a targeted small molecule screen in our iAT2 ALI system.
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Affiliation(s)
- Ryan M Hekman
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Adam J Hume
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Raghuveera Kumar Goel
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Kristine M Abo
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Jessie Huang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Benjamin C Blum
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Rhiannon B Werder
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Ellen L Suder
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Indranil Paul
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Sadhna Phanse
- Center for Network Systems Biology, Boston University, Boston, MA, USA
| | - Ahmed Youssef
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; Bioinformatics Program, Boston University, Boston, MA, USA
| | - Konstantinos D Alysandratos
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Dzmitry Padhorny
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Sandeep Ojha
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | | | - Dmitry Kretov
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Peter E A Ash
- Department of Pharmacology, Boston University School of Medicine, Boston, MA, USA
| | - Mamta Verma
- Department of Pharmacology, Boston University School of Medicine, Boston, MA, USA
| | - Jian Zhao
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - J J Patten
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Carlos Villacorta-Martin
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA
| | - Dante Bolzan
- Department of Computer Science, University of Miami, Miami, FL, USA
| | - Carlos Perea-Resa
- Department of Molecular Biology, Harvard Medical School, Boston, MA, USA
| | - Esther Bullitt
- Department of Physiology and Biophysics, Boston University, Boston, MA, USA
| | - Anne Hinds
- The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Andrew Tilston-Lunel
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Xaralabos Varelas
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Shaghayegh Farhangmehr
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | - Julian H Kwan
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Mark McComb
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA, USA
| | - Avik Basu
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Mohsan Saeed
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Valentina Perissi
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Eric J Burks
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Matthew D Layne
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - John H Connor
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Robert Davey
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Ji-Xin Cheng
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Benjamin L Wolozin
- Department of Pharmacology, Boston University School of Medicine, Boston, MA, USA
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Stefan Wuchty
- Department of Computer Science, University of Miami, Miami, FL, USA; Department of Biology, University of Miami, Miami, FL, USA; Miami Institute of Data Science and Computing, Miami, FL, USA
| | - Shawn M Lyons
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Daniel Cifuentes
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Michael Blower
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; Department of Molecular Biology, Harvard Medical School, Boston, MA, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA.
| | - Andrew A Wilson
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA.
| | - Elke Mühlberger
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA.
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; Department of Biology, Boston University, Boston, MA, USA.
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4
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Carballar R, Martínez-Láinez JM, Samper B, Bru S, Bállega E, Mirallas O, Ricco N, Clotet J, Jiménez J. CDK-mediated Yku80 Phosphorylation Regulates the Balance Between Non-homologous End Joining (NHEJ) and Homologous Directed Recombination (HDR). J Mol Biol 2020; 432:166715. [PMID: 33217428 DOI: 10.1016/j.jmb.2020.11.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 11/04/2020] [Accepted: 11/11/2020] [Indexed: 11/28/2022]
Abstract
There are two major pathways for repairing DNA double-strand breaks (DSBs): homologous directed recombination (HDR) and non-homologous end-joining (NHEJ). While NHEJ functions throughout the cell cycle, HDR is only possible during S/G2 phases, suggesting that there are cell cycle-specific mechanisms regulating the balance between the two repair systems. The regulation exerted by CDKs on HDR has been extensively demonstrated, and here we present evidence that the CDK Pho85, in association with the G1 cyclin Pcl1, phosphorylates Yku80 on Ser 623 to regulate NHEJ activity. Cells bearing a non-phosphorylatable version of Yku80 show increased NHEJ and reduced HDR activity. Accordingly, yku80S623A cells present diminished viability upon treatment with the DSB-producer bleomycin, specifically in the G2 phase of the cell cycle. Interestingly, the mutation of the equivalent residue in human Ku80 increases sensitivity to bleomycin in several cancer cell lines, suggesting that this mechanism is conserved in humans. Altogether, our results reveal a new mechanism whereby G1-CDKs mediate the choice between HDR and NHEJ repair pathways, putting the error prone NHEJ on a leash and enabling error free HDR in G2 when homologous sequences are available.
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Affiliation(s)
- Reyes Carballar
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Joan M Martínez-Láinez
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Bàrbara Samper
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Samuel Bru
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Elisabet Bállega
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Oriol Mirallas
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Natalia Ricco
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Josep Clotet
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain.
| | - Javier Jiménez
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain.
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5
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Palmer N, Kaldis P. Less-well known functions of cyclin/CDK complexes. Semin Cell Dev Biol 2020; 107:54-62. [PMID: 32386818 DOI: 10.1016/j.semcdb.2020.04.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 12/31/2022]
Abstract
Cyclin-dependent kinases (CDKs) are activated by cyclins, which play important roles in dictating the actions of CDK/cyclin complexes. Cyclin binding influences the substrate specificity of these complexes in addition to their susceptibility to inhibition or degradation. CDK/cyclin complexes are best known to promote cell cycle progression in the mitotic cell cycle but are also crucial for important cellular processes not strictly associated with cellular division. This chapter primarily explores the understudied topic of CDK/cyclin complex functionality during the DNA damage response. We detail how CDK/cyclin complexes perform dual roles both as targets of DNA damage checkpoint signaling as well as effectors of DNA repair. Additionally, we discuss the potential CDK-independent roles of cyclins in these processes and the impact of such roles in human diseases such as cancer. Our goal is to place the spotlight on these important functions of cyclins either acting as independent entities or within CDK/cyclin complexes which have attracted less attention in the past. We consider that this will be important for a more complete understanding of the intricate functions of cell cycle proteins in the DNA damage response.
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Affiliation(s)
- Nathan Palmer
- Institute of Molecular and Cell Biology (IMCB), A⁎STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore; National University of Singapore (NUS), Department of Biochemistry, Singapore, 117597, Republic of Singapore
| | - Philipp Kaldis
- Institute of Molecular and Cell Biology (IMCB), A⁎STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore; National University of Singapore (NUS), Department of Biochemistry, Singapore, 117597, Republic of Singapore; Department of Clinical Sciences, Lund University, Clinical Research Centre (CRC), Box 50332, SE-202 13, Malmö, Sweden.
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6
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Drissi R, Chauvin A, McKenna A, Lévesque D, Blais-Brochu S, Jean D, Boisvert FM. Destabilization of the MiniChromosome Maintenance (MCM) complex modulates the cellular response to DNA double strand breaks. Cell Cycle 2018; 17:2593-2609. [PMID: 30516086 PMCID: PMC6300108 DOI: 10.1080/15384101.2018.1553336] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
DNA replication during S phase involves thousands of replication forks that must be coordinated to ensure that every DNA section is replicated only once. The minichromosome maintenance proteins, MCM2 to MCM7, form a heteromeric DNA helicase required for both the initiation and elongation of DNA replication. Although only two DNA helicase activities are necessary to establish a bidirectional replication fork from each replication origin, a large excess of MCM complexes is amassed and distributed along the chromatin. The function of the additional MCM complexes is not well understood, as most are displaced from the DNA during the S-phase, apparently without playing an active role in DNA replication. DNA damage response (DDR) kinases activated by stalled forks prevent the replication machinery from being activated, indicating a tight relationship between DDR and DNA replication. To investigate the role of MCM proteins in the cellular response to DNA damage, we used shRNA targeting MCM2 or MCM3 to determine the impact of a reduction in MCM complex. The alteration of MCM proteins induced a change in the activation of key factors of the DDR in response to Etoposide treatment. Etoposide-induced DNA damage affected the phosphorylation of γ-H2AX, CHK1 and CHK2 without affecting cell viability. Using assays measuring homologous recombination (HR) and non-homologous end-joining (NHEJ), we identified a decrease in both HR and NHEJ associated with a decrease in MCM complex.
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Affiliation(s)
- Romain Drissi
- a Department of Anatomy and Cell Biology , Université de Sherbrooke , 3201 Jean-Mignaul, Sherbrooke , Québec , Canada
| | - Anaïs Chauvin
- a Department of Anatomy and Cell Biology , Université de Sherbrooke , 3201 Jean-Mignaul, Sherbrooke , Québec , Canada
| | - Alyson McKenna
- a Department of Anatomy and Cell Biology , Université de Sherbrooke , 3201 Jean-Mignaul, Sherbrooke , Québec , Canada
| | - Dominique Lévesque
- a Department of Anatomy and Cell Biology , Université de Sherbrooke , 3201 Jean-Mignaul, Sherbrooke , Québec , Canada
| | - Simon Blais-Brochu
- a Department of Anatomy and Cell Biology , Université de Sherbrooke , 3201 Jean-Mignaul, Sherbrooke , Québec , Canada
| | - Dominique Jean
- a Department of Anatomy and Cell Biology , Université de Sherbrooke , 3201 Jean-Mignaul, Sherbrooke , Québec , Canada
| | - François-Michel Boisvert
- a Department of Anatomy and Cell Biology , Université de Sherbrooke , 3201 Jean-Mignaul, Sherbrooke , Québec , Canada
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7
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Liao H, Ji F, Geng X, Xing M, Li W, Chen Z, Shen H, Ying S. CDK1 promotes nascent DNA synthesis and induces resistance of cancer cells to DNA-damaging therapeutic agents. Oncotarget 2017; 8:90662-90673. [PMID: 29207595 PMCID: PMC5710876 DOI: 10.18632/oncotarget.21730] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 09/20/2017] [Indexed: 12/01/2022] Open
Abstract
Cyclin dependent kinase 1 (CDK1) is essential for cell viability and plays a vital role in many biological events including cell cycle control, DNA damage repair, and checkpoint activation. Here, we identify an unanticipated role for CDK1 in promoting nascent DNA synthesis during S-phase. We report that a short duration of CDK1 inhibition, which does not perturb cell cycle progression, triggers a replication-associated DNA damage response (DDR). This DDR is associated with a disruption of replication fork progression and leads to genome instability. Moreover, we show that compromised CDK1 activity dramatically increases the efficacy of chemotherapeutic agents that kill cancer cells through perturbing DNA replication, including Olaparib, an FDA approved PARP inhibitor. Our study has revealed an important role for CDK1 in the DNA replication program, and suggests that the therapeutic targeting CDK1 may be a novel approach for combination chemotherapy.
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Affiliation(s)
- Hongwei Liao
- Department of Respiratory and Critical Care Medicine of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, China
| | - Fang Ji
- Department of Respiratory and Critical Care Medicine of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, China
| | - Xinwei Geng
- Department of Respiratory and Critical Care Medicine of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, China
| | - Meichun Xing
- Department of Respiratory and Critical Care Medicine of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, China
| | - Wen Li
- Department of Respiratory and Critical Care Medicine of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhihua Chen
- Department of Respiratory and Critical Care Medicine of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Huahao Shen
- Department of Respiratory and Critical Care Medicine of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Songmin Ying
- Department of Respiratory and Critical Care Medicine of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, China
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8
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Roles of CDK and DDK in Genome Duplication and Maintenance: Meiotic Singularities. Genes (Basel) 2017; 8:genes8030105. [PMID: 28335524 PMCID: PMC5368709 DOI: 10.3390/genes8030105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 03/13/2017] [Accepted: 03/14/2017] [Indexed: 12/16/2022] Open
Abstract
Cells reproduce using two types of divisions: mitosis, which generates two daughter cells each with the same genomic content as the mother cell, and meiosis, which reduces the number of chromosomes of the parent cell by half and gives rise to four gametes. The mechanisms that promote the proper progression of the mitotic and meiotic cycles are highly conserved and controlled. They require the activities of two types of serine-threonine kinases, the cyclin-dependent kinases (CDKs) and the Dbf4-dependent kinase (DDK). CDK and DDK are essential for genome duplication and maintenance in both mitotic and meiotic divisions. In this review, we aim to highlight how these kinases cooperate to orchestrate diverse processes during cellular reproduction, focusing on meiosis-specific adaptions of their regulation and functions in DNA metabolism.
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9
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Rulten SL, Grundy GJ. Non-homologous end joining: Common interaction sites and exchange of multiple factors in the DNA repair process. Bioessays 2017; 39. [PMID: 28133776 DOI: 10.1002/bies.201600209] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Non-homologous end-joining (NHEJ) is the dominant means of repairing chromosomal DNA double strand breaks (DSBs), and is essential in human cells. Fifteen or more proteins can be involved in the detection, signalling, synapsis, end-processing and ligation events required to repair a DSB, and must be assembled in the confined space around the DNA ends. We review here a number of interaction points between the core NHEJ components (Ku70, Ku80, DNA-PKcs, XRCC4 and Ligase IV) and accessory factors such as kinases, phosphatases, polymerases and structural proteins. Conserved protein-protein interaction sites such as Ku-binding motifs (KBMs), XLF-like motifs (XLMs), FHA and BRCT domains illustrate that different proteins compete for the same binding sites on the core machinery, and must be spatially and temporally regulated. We discuss how post-translational modifications such as phosphorylation, ADP-ribosylation and ubiquitinylation may regulate sequential steps in the NHEJ pathway or control repair at different types of DNA breaks.
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Affiliation(s)
- Stuart L Rulten
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Gabrielle J Grundy
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
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10
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Regulation of non-homologous end joining via post-translational modifications of components of the ligation step. Curr Genet 2016; 63:591-605. [PMID: 27915381 DOI: 10.1007/s00294-016-0670-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 11/25/2016] [Accepted: 11/26/2016] [Indexed: 12/29/2022]
Abstract
DNA double-strand breaks are the most serious type of DNA damage and non-homologous end joining (NHEJ) is an important pathway for their repair. In Saccharomyces cerevisiae, three complexes mediate the canonical NHEJ pathway, Ku (Ku70/Ku80), MRX (Mre11/Rad50/Xrs2) and DNA ligase IV (Dnl4/Lif1). Mammalian NHEJ is more complex, primarily as a consequence of the fact that more factors are involved in the process, and also because higher chromatin organization and more complex regulatory networks exist in mammals. In addition, a stronger interconnection between the NHEJ and DNA damage response (DDR) pathways seems to occur in mammals compared to yeast. DDR employs multiple post-translational modifications (PTMs) of the target proteins and mutual crosstalk among them to ensure highly efficient down-stream effects. Checkpoint-mediated phosphorylation is the best understood PTM that regulates DDR, although recently SUMOylation has also been shown to be involved. Both phosphorylation and SUMOylation affect components of NHEJ. In this review, we discuss a role of these two PTMs in regulation of NHEJ via targeting the components of the ligation step.
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Woods ML, Barnes CP. Mechanistic Modelling and Bayesian Inference Elucidates the Variable Dynamics of Double-Strand Break Repair. PLoS Comput Biol 2016; 12:e1005131. [PMID: 27741226 PMCID: PMC5065155 DOI: 10.1371/journal.pcbi.1005131] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 09/05/2016] [Indexed: 12/12/2022] Open
Abstract
DNA double-strand breaks are lesions that form during metabolism, DNA replication and exposure to mutagens. When a double-strand break occurs one of a number of repair mechanisms is recruited, all of which have differing propensities for mutational events. Despite DNA repair being of crucial importance, the relative contribution of these mechanisms and their regulatory interactions remain to be fully elucidated. Understanding these mutational processes will have a profound impact on our knowledge of genomic instability, with implications across health, disease and evolution. Here we present a new method to model the combined activation of non-homologous end joining, single strand annealing and alternative end joining, following exposure to ionising radiation. We use Bayesian statistics to integrate eight biological data sets of double-strand break repair curves under varying genetic knockouts and confirm that our model is predictive by re-simulating and comparing to additional data. Analysis of the model suggests that there are at least three disjoint modes of repair, which we assign as fast, slow and intermediate. Our results show that when multiple data sets are combined, the rate for intermediate repair is variable amongst genetic knockouts. Further analysis suggests that the ratio between slow and intermediate repair depends on the presence or absence of DNA-PKcs and Ku70, which implies that non-homologous end joining and alternative end joining are not independent. Finally, we consider the proportion of double-strand breaks within each mechanism as a time series and predict activity as a function of repair rate. We outline how our insights can be directly tested using imaging and sequencing techniques and conclude that there is evidence of variable dynamics in alternative repair pathways. Our approach is an important step towards providing a unifying theoretical framework for the dynamics of DNA repair processes.
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Affiliation(s)
- Mae L. Woods
- Department of Cell and Developmental Biology, University College London, London, England
| | - Chris P. Barnes
- Department of Cell and Developmental Biology, University College London, London, England
- Department of Genetics, Evolution and Environment, University College London, London, England
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12
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Weimer AK, Biedermann S, Harashima H, Roodbarkelari F, Takahashi N, Foreman J, Guan Y, Pochon G, Heese M, Van Damme D, Sugimoto K, Koncz C, Doerner P, Umeda M, Schnittger A. The plant-specific CDKB1-CYCB1 complex mediates homologous recombination repair in Arabidopsis. EMBO J 2016; 35:2068-2086. [PMID: 27497297 PMCID: PMC5048351 DOI: 10.15252/embj.201593083] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 07/14/2016] [Indexed: 01/30/2023] Open
Abstract
Upon DNA damage, cyclin‐dependent kinases (CDKs) are typically inhibited to block cell division. In many organisms, however, it has been found that CDK activity is required for DNA repair, especially for homology‐dependent repair (HR), resulting in the conundrum how mitotic arrest and repair can be reconciled. Here, we show that Arabidopsis thaliana solves this dilemma by a division of labor strategy. We identify the plant‐specific B1‐type CDKs (CDKB1s) and the class of B1‐type cyclins (CYCB1s) as major regulators of HR in plants. We find that RADIATION SENSITIVE 51 (RAD51), a core mediator of HR, is a substrate of CDKB1‐CYCB1 complexes. Conversely, mutants in CDKB1 and CYCB1 fail to recruit RAD51 to damaged DNA. CYCB1;1 is specifically activated after DNA damage and we show that this activation is directly controlled by SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1), a transcription factor that acts similarly to p53 in animals. Thus, while the major mitotic cell‐cycle activity is blocked after DNA damage, CDKB1‐CYCB1 complexes are specifically activated to mediate HR.
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Affiliation(s)
- Annika K Weimer
- Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes du CNRS, IBMP-CNRS UPR2357, Université de Strasbourg, Strasbourg Cedex, France
| | - Sascha Biedermann
- Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes du CNRS, IBMP-CNRS UPR2357, Université de Strasbourg, Strasbourg Cedex, France
| | | | | | - Naoki Takahashi
- Plant Growth Regulation Laboratory, Nara Institute of Science and Technology, Graduate School of Biological Sciences, Ikoma, Nara, Japan
| | - Julia Foreman
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Yonsheng Guan
- Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes du CNRS, IBMP-CNRS UPR2357, Université de Strasbourg, Strasbourg Cedex, France
| | - Gaëtan Pochon
- Department of Developmental Biology, Biozentrum Klein Flottbek, University of Hamburg, Hamburg, Germany
| | - Maren Heese
- Department of Developmental Biology, Biozentrum Klein Flottbek, University of Hamburg, Hamburg, Germany
| | - Daniël Van Damme
- Department of Plant Systems Biology, VIB, Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Japan
| | - Csaba Koncz
- Max-Planck-Institut für Pflanzenzüchtungsforschung, Köln, Germany
| | - Peter Doerner
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Masaaki Umeda
- Plant Growth Regulation Laboratory, Nara Institute of Science and Technology, Graduate School of Biological Sciences, Ikoma, Nara, Japan JST, CREST, Ikoma, Nara, Japan
| | - Arp Schnittger
- Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes du CNRS, IBMP-CNRS UPR2357, Université de Strasbourg, Strasbourg Cedex, France Department of Developmental Biology, Biozentrum Klein Flottbek, University of Hamburg, Hamburg, Germany Trinationales Institut für Pflanzenforschung, Institut de Biologie Moléculaire des Plantes du CNRS, IBMP-CNRS, Strasbourg Cedex, France
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13
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Zheng XF, Kalev P, Chowdhury D. Emerging role of protein phosphatases changes the landscape of phospho-signaling in DNA damage response. DNA Repair (Amst) 2015; 32:58-65. [DOI: 10.1016/j.dnarep.2015.04.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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14
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Gan W, Liu P, Wei W. Akt promotes tumorigenesis in part through modulating genomic instability via phosphorylating XLF. Nucleus 2015. [PMID: 26225792 DOI: 10.1080/19491034.2015.1074365] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
To maintain genome stability, mammalian cells have developed a delicate, yet efficient, system to sense and repair damaged DNA, including two evolutionarily conserved DNA damage repair (DDR) pathways: homologous recombination (HR) and non-homologous-end-joining (NHEJ). Deregulation in these repair pathways may lead to genomic instability and subsequent human diseases, including cancer. On the other hand, hyper-activation of the oncogenic Akt signaling pathway has been observed in almost all solid tumors. Emerging evidence has begun to reveal a possible role of active Akt in regulating DDR, possibly through suppression of HR. However, whether and how Akt regulates NHEJ remains largely undefined. To this end, we recently reported that Akt impairs NHEJ by phosphorylating XLF at T181, to trigger its dissociation from the functional DNA ligase IV (LIG4)/XRCC4 complex. Here, we provide an additional perspective discussing how Akt is activated upon DNA damage to regulate DNA repair pathways as well as the cellular apoptotic responses.
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Affiliation(s)
- Wenjian Gan
- a Department of Pathology ; Beth Israel Deaconess Medical Center ; Harvard Medical School ; Boston , MA USA
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15
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Schaue D, McBride WH. Opportunities and challenges of radiotherapy for treating cancer. Nat Rev Clin Oncol 2015; 12:527-40. [PMID: 26122185 DOI: 10.1038/nrclinonc.2015.120] [Citation(s) in RCA: 399] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The past 20 years have seen dramatic changes in the delivery of radiation therapy, but the impact of radiobiology on the clinic has been far less substantial. A major consideration in the use of radiotherapy has been on how best to exploit differences between the tumour and host tissue characteristics, which in the past has been achieved empirically by radiation-dose fractionation. New advances are uncovering some of the mechanistic processes that underlie this success story. In this Review, we focus on how these processes might be targeted to improve the outcome of radiotherapy at the individual patient level. This approach would seem a more productive avenue of treatment than simply trying to increase the radiation dose delivered to the tumour.
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Affiliation(s)
- Dörthe Schaue
- Department of Radiation Oncology, Room B3-109, Center for Health Sciences, Westwood, University of California, Los Angeles (UCLA), Los Angeles, CA 90095-1714, USA
| | - William H McBride
- Department of Radiation Oncology, Room B3-109, Center for Health Sciences, Westwood, University of California, Los Angeles (UCLA), Los Angeles, CA 90095-1714, USA
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