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Nicolas Y, Bret H, Cannavo E, Acharya A, Cejka P, Borde V, Guerois R. Molecular insights into the activation of Mre11-Rad50 endonuclease activity by Sae2/CtIP. Mol Cell 2024; 84:2223-2237.e4. [PMID: 38870937 DOI: 10.1016/j.molcel.2024.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 02/25/2024] [Accepted: 05/20/2024] [Indexed: 06/15/2024]
Abstract
In Saccharomyces cerevisiae (S. cerevisiae), Mre11-Rad50-Xrs2 (MRX)-Sae2 nuclease activity is required for the resection of DNA breaks with secondary structures or protein blocks, while in humans, the MRE11-RAD50-NBS1 (MRN) homolog with CtIP is needed to initiate DNA end resection of all breaks. Phosphorylated Sae2/CtIP stimulates the endonuclease activity of MRX/N. Structural insights into the activation of the Mre11 nuclease are available only for organisms lacking Sae2/CtIP, so little is known about how Sae2/CtIP activates the nuclease ensemble. Here, we uncover the mechanism of Mre11 activation by Sae2 using a combination of AlphaFold2 structural modeling of biochemical and genetic assays. We show that Sae2 stabilizes the Mre11 nuclease in a conformation poised to cleave substrate DNA. Several designs of compensatory mutations establish how Sae2 activates MRX in vitro and in vivo, supporting the structural model. Finally, our study uncovers how human CtIP, despite considerable sequence divergence, employs a similar mechanism to activate MRN.
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Affiliation(s)
- Yoann Nicolas
- Institut Curie, PSL University, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, 75005 Paris, France
| | - Hélène Bret
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Elda Cannavo
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona 6500, Switzerland
| | - Ananya Acharya
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona 6500, Switzerland
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona 6500, Switzerland.
| | - Valérie Borde
- Institut Curie, PSL University, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, 75005 Paris, France.
| | - Raphaël Guerois
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
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2
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Kuster A, Mozaffari NL, Wilkinson OJ, Wojtaszek JL, Zurfluh C, Przetocka S, Zyla D, von Aesch C, Dillingham MS, Williams RS, Sartori AA. A stapled peptide mimetic of the CtIP tetramerization motif interferes with double-strand break repair and replication fork protection. SCIENCE ADVANCES 2021; 7:7/8/eabc6381. [PMID: 33608267 PMCID: PMC7895427 DOI: 10.1126/sciadv.abc6381] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
Cancer cells display high levels of DNA damage and replication stress, vulnerabilities that could be exploited by drugs targeting DNA repair proteins. Human CtIP promotes homology-mediated repair of DNA double-strand breaks (DSBs) and protects stalled replication forks from nucleolytic degradation, thus representing an attractive candidate for targeted cancer therapy. Here, we establish a peptide mimetic of the CtIP tetramerization motif that inhibits CtIP activity. The hydrocarbon-stapled peptide encompassing amino acid residues 18 to 28 of CtIP (SP18-28) stably binds to CtIP tetramers in vitro and facilitates their aggregation into higher-order structures. Efficient intracellular uptake of SP18-28 abrogates CtIP localization to damaged chromatin, impairs DSB repair, and triggers extensive fork degradation. Moreover, prolonged SP18-28 treatment causes hypersensitivity to DNA-damaging agents and selectively reduces the viability of BRCA1-mutated cancer cell lines. Together, our data provide a basis for the future development of CtIP-targeting compounds with the potential to treat patients with cancer.
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Affiliation(s)
- Anika Kuster
- Institute of Molecular Cancer Research, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Nour L Mozaffari
- Institute of Molecular Cancer Research, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Oliver J Wilkinson
- School of Biochemistry, University of Bristol, University Walk, Clifton BS8 1TD, Bristol, UK
| | - Jessica L Wojtaszek
- Structural Cell Biology Group, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, U.S. National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Christina Zurfluh
- Institute of Molecular Cancer Research, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Sara Przetocka
- Institute of Molecular Cancer Research, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Dawid Zyla
- Institute of Molecular Biology and Biophysics, ETH-Zürich, Otto-Stern-Weg 5, CH-8093 Zürich, Switzerland
| | - Christine von Aesch
- Institute of Molecular Cancer Research, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Mark S Dillingham
- School of Biochemistry, University of Bristol, University Walk, Clifton BS8 1TD, Bristol, UK
| | - R Scott Williams
- Structural Cell Biology Group, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, U.S. National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Alessandro A Sartori
- Institute of Molecular Cancer Research, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.
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Thomas JMH, Keegan RM, Rigden DJ, Davies OR. Extending the scope of coiled-coil crystal structure solution by AMPLE through improved ab initio modelling. Acta Crystallogr D Struct Biol 2020; 76:272-284. [PMID: 32133991 PMCID: PMC7057219 DOI: 10.1107/s2059798320000443] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/14/2020] [Indexed: 11/10/2022] Open
Abstract
The phase problem remains a major barrier to overcome in protein structure solution by X-ray crystallography. In recent years, new molecular-replacement approaches using ab initio models and ideal secondary-structure components have greatly contributed to the solution of novel structures in the absence of clear homologues in the PDB or experimental phasing information. This has been particularly successful for highly α-helical structures, and especially coiled-coils, in which the relatively rigid α-helices provide very useful molecular-replacement fragments. This has been seen within the program AMPLE, which uses clustered and truncated ensembles of numerous ab initio models in structure solution, and is already accomplished for α-helical and coiled-coil structures. Here, an expansion in the scope of coiled-coil structure solution by AMPLE is reported, which has been achieved through general improvements in the pipeline, the removal of tNCS correction in molecular replacement and two improved methods for ab initio modelling. Of the latter improvements, enforcing the modelling of elongated helices overcame the bias towards globular folds and provided a rapid method (equivalent to the time requirements of the existing modelling procedures in AMPLE) for enhanced solution. Further, the modelling of two-, three- and four-helical oligomeric coiled-coils, and the use of full/partial oligomers in molecular replacement, provided additional success in difficult and lower resolution cases. Together, these approaches have enabled the solution of a number of parallel/antiparallel dimeric, trimeric and tetrameric coiled-coils at resolutions as low as 3.3 Å, and have thus overcome previous limitations in AMPLE and provided a new functionality in coiled-coil structure solution at lower resolutions. These new approaches have been incorporated into a new release of AMPLE in which automated elongated monomer and oligomer modelling may be activated by selecting `coiled-coil' mode.
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Affiliation(s)
- Jens M. H. Thomas
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Ronan M. Keegan
- Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Didcot OX11 0FA, England
| | - Daniel J. Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Owen R. Davies
- Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, England
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4
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Liu X, Wang XS, Lee BJ, Wu-Baer FK, Lin X, Shao Z, Estes VM, Gautier J, Baer R, Zha S. CtIP is essential for early B cell proliferation and development in mice. J Exp Med 2019; 216:1648-1663. [PMID: 31097467 PMCID: PMC6605744 DOI: 10.1084/jem.20181139] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 09/10/2018] [Accepted: 04/24/2019] [Indexed: 11/08/2022] Open
Abstract
B cell development requires efficient proliferation and successful assembly and modifications of the immunoglobulin gene products. CtIP is an essential gene implicated in end resection and DNA repair. Here, we show that CtIP is essential for early B cell development but dispensable in naive B cells. CtIP loss is well tolerated in G1-arrested B cells and during V(D)J recombination, but in proliferating B cells, CtIP loss leads to a progressive cell death characterized by ATM hyperactivation, G2/M arrest, genomic instability, and 53BP1 nuclear body formation, indicating that the essential role of CtIP during proliferation underscores its stage-specific requirement in B cells. B cell proliferation requires phosphorylation of CtIP at T847 presumably by CDK, but not its interaction with CtBP or Rb or its nuclease activity. CtIP phosphorylation by ATM/ATR at T859 (T855 in mice) promotes end resection in G1-arrested cells but is dispensable for B cell development and class switch recombination, suggesting distinct roles for T859 and T847 phosphorylation in B cell development.
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Affiliation(s)
- Xiangyu Liu
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University Carson Cancer Center, Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, China
| | - Xiaobin S Wang
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- Pathobiology and Human Disease Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Brian J Lee
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Foon K Wu-Baer
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Xiaohui Lin
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Zhengping Shao
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Verna M Estes
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Jean Gautier
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Richard Baer
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Shan Zha
- Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- Division of Pediatric Oncology, Hematology and Stem Cell Transplantation, Department of Pediatrics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
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5
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Wilkinson OJ, Martín-González A, Kang H, Northall SJ, Wigley DB, Moreno-Herrero F, Dillingham MS. CtIP forms a tetrameric dumbbell-shaped particle which bridges complex DNA end structures for double-strand break repair. eLife 2019; 8:42129. [PMID: 30601117 PMCID: PMC6344080 DOI: 10.7554/elife.42129] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 01/01/2019] [Indexed: 12/16/2022] Open
Abstract
CtIP is involved in the resection of broken DNA during the S and G2 phases of the cell cycle for repair by recombination. Acting with the MRN complex, it plays a particularly important role in handling complex DNA end structures by localised nucleolytic processing of DNA termini in preparation for longer range resection. Here we show that human CtIP is a tetrameric protein adopting a dumbbell architecture in which DNA binding domains are connected by long coiled-coils. The protein complex binds two short DNA duplexes with high affinity and bridges DNA molecules in trans. DNA binding is potentiated by dephosphorylation and is not specific for DNA end structures per se. However, the affinity for linear DNA molecules is increased if the DNA terminates with complex structures including forked ssDNA overhangs and nucleoprotein conjugates. This work provides a biochemical and structural basis for the function of CtIP at complex DNA breaks.
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Affiliation(s)
| | - Alejandro Martín-González
- Department of Macromolecular Structures, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid, Spain
| | - Haejoo Kang
- Department of Medicine, Imperial College London, London, United Kingdom
| | - Sarah J Northall
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Dale B Wigley
- Department of Medicine, Imperial College London, London, United Kingdom
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid, Spain
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Abstract
Vertebrate CtIP, and its fission yeast (Ctp1), budding yeast (Sae2) and plant (Com1) orthologs have emerged as key regulatory molecules in cellular responses to DNA double strand breaks (DSBs). By modulating the nucleolytic 5'-3' resection activity of the Mre11/Rad50/Nbs1 (MRN) DSB repair processing and signaling complex, CtIP/Ctp1/Sae2/Com1 is integral to the channeling of DNA double strand breaks through DSB repair by homologous recombination (HR). Nearly two decades since its discovery, emerging new data are defining the molecular underpinnings for CtIP DSB repair regulatory activities. CtIP homologs are largely intrinsically unstructured proteins comprised of expanded regions of low complexity sequence, rather than defined folded domains typical of DNA damage metabolizing enzymes and nucleases. A compact structurally conserved N-terminus forms a functionally critical tetrameric helical dimer of dimers (THDD) region that bridges CtIP oligomers, and is flexibly appended to a conserved C-terminal Sae2-homology DNA binding and DSB repair pathway choice regulatory hub which influences nucleolytic activities of the MRN core nuclease complex. The emerging evidence from structural, biophysical, and biological studies converges on CtIP having functional roles in DSB repair that include: 1) dynamic DNA strand coordination through direct DNA binding and DNA bridging activities, 2) MRN nuclease complex cofactor functions that direct MRN endonucleolytic cleavage of protein-blocked DSB ends and 3) acting as a protein binding hub targeted by the cell cycle regulatory apparatus, which influences CtIP expression and activity via layers of post-translational modifications, protein-protein interactions and DNA binding.
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Affiliation(s)
- Sara N Andres
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, United States
| | - R Scott Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, United States.
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