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O’Sullivan J, Kothari C, Caron MC, Gagné JP, Jin Z, Nonfoux L, Beneyton A, Coulombe Y, Thomas M, Atalay N, Meng X, Milano L, Jean D, Boisvert FM, Kaufmann S, Hendzel M, Masson JY, Poirier G. ZNF432 stimulates PARylation and inhibits DNA resection to balance PARPi sensitivity and resistance. Nucleic Acids Res 2023; 51:11056-11079. [PMID: 37823600 PMCID: PMC10639050 DOI: 10.1093/nar/gkad791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 09/05/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023] Open
Abstract
Zinc finger (ZNF) motifs are some of the most frequently occurring domains in the human genome. It was only recently that ZNF proteins emerged as key regulators of genome integrity in mammalian cells. In this study, we report a new role for the Krüppel-type ZNF-containing protein ZNF432 as a novel poly(ADP-ribose) (PAR) reader that regulates the DNA damage response. We show that ZNF432 is recruited to DNA lesions via DNA- and PAR-dependent mechanisms. Remarkably, ZNF432 stimulates PARP-1 activity in vitro and in cellulo. Knockdown of ZNF432 inhibits phospho-DNA-PKcs and increases RAD51 foci formation following irradiation. Moreover, purified ZNF432 preferentially binds single-stranded DNA and impairs EXO1-mediated DNA resection. Consequently, the loss of ZNF432 in a cellular system leads to resistance to PARP inhibitors while its overexpression results in sensitivity. Taken together, our results support the emerging concept that ZNF-containing proteins can modulate PARylation, which can be embodied by the pivotal role of ZNF432 to finely balance the outcome of PARPi response by regulating homologous recombination.
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Affiliation(s)
- Julia O’Sullivan
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - Charu Kothari
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QCG1V 4G2, Canada
| | - Marie-Christine Caron
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - Jean-Philippe Gagné
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QCG1V 4G2, Canada
| | - Zhigang Jin
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, 11560 University Avenue, Edmonton, Alberta T6G 1Z2, Canada
| | - Louis Nonfoux
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QCG1V 4G2, Canada
| | - Adèle Beneyton
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - Yan Coulombe
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - Mélissa Thomas
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - Nurgul Atalay
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - X Wei Meng
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Larissa Milano
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - Dominique Jean
- Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - François-Michel Boisvert
- Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Scott H Kaufmann
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Michael J Hendzel
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, 11560 University Avenue, Edmonton, Alberta T6G 1Z2, Canada
| | - Jean-Yves Masson
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - Guy G Poirier
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QCG1V 4G2, Canada
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Rodriguez J, Battistini F, Learte-Aymamí S, Orozco M, Mascareñas JL. Molecular dynamics modelling of the interaction of a synthetic zinc-finger miniprotein with DNA. RSC Chem Biol 2023; 4:486-493. [PMID: 37415868 PMCID: PMC10320839 DOI: 10.1039/d3cb00053b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/09/2023] [Indexed: 07/08/2023] Open
Abstract
We report the modelling of the DNA complex of an artificial miniprotein composed of two zinc finger modules and an AT-hook linking peptide. The computational study provides for the first time a structural view of these types of complexes, dissecting interactions that are key to modulate their stability. The relevance of these interactions was validated experimentally. These results confirm the potential of this type of computational approach for studying peptide-DNA complexes and suggest that they could be very useful for the rational design of non-natural, DNA binding miniproteins.
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Affiliation(s)
- Jessica Rodriguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), and Departamento de Química Orgánica, Universidade de Santiago de Compostela Rúa Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10-12 08028 Barcelona Spain
| | - Federica Battistini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10-12 08028 Barcelona Spain
- Department of Biochemistry and Molecular Biology, University of Barcelona 08028 Barcelona Spain
| | - Soraya Learte-Aymamí
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), and Departamento de Química Orgánica, Universidade de Santiago de Compostela Rúa Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10-12 08028 Barcelona Spain
- Department of Biochemistry and Molecular Biology, University of Barcelona 08028 Barcelona Spain
| | - José L Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), and Departamento de Química Orgánica, Universidade de Santiago de Compostela Rúa Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
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3
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Talluri S. Engineering and Design of Programmable Genome Editors. J Phys Chem B 2022; 126:5140-5150. [PMID: 35819243 DOI: 10.1021/acs.jpcb.2c03761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Programmable genome editors are enzymes that can be targeted to a specific location in the genome for making site-specific alterations or deletions. The engineering, design, and development of sequence-specific editors has resulted in a dramatic increase in the precision of editing for nucleotide sequences. These editors can target specific locations in a genome, in vivo. The genome editors are being deployed for the development of genetically modified organisms for agriculture and industry, and for gene therapy of inherited human genetic disorders, cancer, and immunotherapy. Experimental and computational studies of structure, binding, activity, dynamics, and folding, reviewed here, have provided valuable insights that have the potential for increasing the functional efficiency of these gene/genome editors. Biochemical and biophysical studies of the specificities of natural and engineered genome editors reveal that increased binding affinity can be detrimental because of the increase of off-target effects and that the engineering and design of genome editors with higher specificity may require modulation and control of the conformational dynamics.
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Affiliation(s)
- Sekhar Talluri
- Department of Biotechnology, GITAM, Visakhapatnam, India 530045
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4
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Brue CR, Dukes MW, Masotti M, Holmgren R, Meade TJ. Functional Disruption of Gli1-DNA Recognition via a Cobalt(III) Complex. ChemMedChem 2022; 17:e202200025. [PMID: 35302712 PMCID: PMC10826845 DOI: 10.1002/cmdc.202200025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Indexed: 12/29/2022]
Abstract
The aberrant activation of the Gli family of zinc finger transcription factors (ZFTFs) is associated with several types of human cancer, including medulloblastoma and basal cell carcinoma. We have reported the use of cobalt(III) Schiff-base complexes (Co(III)-sb) as potent inhibitors of ZFTFs in vivo. These complexes inhibit transcription by displacing the zinc finger domain's structural Zn(II) ion, destabilizing the alpha helix necessary for DNA recognition. Here, we describe the use of Co(III)-sb complexes for the selective inhibition of Gli1. Spectroscopic and computational studies of the Gli1 DNA binding domain found that Co(III)-sb displaced Zn(II) through direct coordination with the His residues of the Cys2 His2 Zn(II) binding site. As a result, there is a dose-dependent degradation of the alpha-helix content in the DNA binding domain of Gli1 and corresponding inhibition of consensus sequence recognition. We conclude that this strategy is well suited for the development of new and potent inhibitors of Gli1.
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Affiliation(s)
- Christopher R Brue
- Departments of Chemistry, Molecular Biosciences, Neurobiology, and Radiology, Northwestern University, Evanston, IL, 60208-3113, USA
| | - Meghan W Dukes
- Departments of Chemistry, Molecular Biosciences, Neurobiology, and Radiology, Northwestern University, Evanston, IL, 60208-3113, USA
| | - Meghan Masotti
- Departments of Chemistry, Molecular Biosciences, Neurobiology, and Radiology, Northwestern University, Evanston, IL, 60208-3113, USA
| | - Robert Holmgren
- Departments of Chemistry, Molecular Biosciences, Neurobiology, and Radiology, Northwestern University, Evanston, IL, 60208-3113, USA
| | - Thomas J Meade
- Departments of Chemistry, Molecular Biosciences, Neurobiology, and Radiology, Northwestern University, Evanston, IL, 60208-3113, USA
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5
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Silva BM, Santos LH, de Almeida JPP, de Magalhães MTQ. Rad5 HIRAN domain: Structural insights into its interaction with ssDNA through molecular modeling approaches. J Biomol Struct Dyn 2022; 41:3062-3075. [PMID: 35249470 DOI: 10.1080/07391102.2022.2045222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The Rad5 protein is an SWI/SNF family ubiquitin ligase that contains an N-terminal HIRAN domain and a RING C3HC4 motif. The HIRAN domain is critical for recognition of the stalled replication fork during the replication process and acts as a sensor to initiate the damaged DNA checkpoint. It is a conserved domain widely distributed in eukaryotic organisms and is present in several DNA-binding proteins from all kingdoms. Here we showed that distant species have important differences in key residues that affect affinity for ssDNA. Based on these findings, we hypothesized that different HIRAN domains might affect fork reversal and translesion synthesis through different metabolic processes. To address this question, we predicted the tertiary structure of both yeast and human HIRAN domains using molecular modeling. Structural dynamics experiments showed that the yeast HIRAN domain exhibited higher structural denaturation than its human homolog, although both domains became stable in the presence of ssDNA. Analysis of atomic contacts revealed that a greater number of interactions between the ssDNA nucleotides and the Rad5 domain are electrostatic. Taken together, these results provide new insights into the molecular mechanism of the HIRAN domain of Rad5 and may guide us to further elucidate differences in the ancient eukaryotes HIRAN sequences and their DNA affinity. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bruno M Silva
- Inter-unit postgraduate studies program in Bioinformatics, Federal University of Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Brazil.,Macromolecular Biophysics Laboratory (LBM), Biological Sciences Institute (ICB), Federal University of Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Brazil
| | - Lucianna H Santos
- Inter-unit postgraduate studies program in Bioinformatics, Federal University of Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Brazil.,Molecular Modeling and Drug Planning Laboratory, Department of Biochemistry and Immunology, Biological Sciences Institute (ICB), Federal University of Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Brazil
| | - João Paulo P de Almeida
- Inter-unit postgraduate studies program in Bioinformatics, Federal University of Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Brazil
| | - Mariana T Q de Magalhães
- Inter-unit postgraduate studies program in Bioinformatics, Federal University of Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Brazil.,Macromolecular Biophysics Laboratory (LBM), Biological Sciences Institute (ICB), Federal University of Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Brazil
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6
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The role of zinc finger linkers in zinc finger protein binding to DNA. J Comput Aided Mol Des 2021; 35:973-986. [PMID: 34350488 DOI: 10.1007/s10822-021-00413-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 07/26/2021] [Indexed: 10/20/2022]
Abstract
Zinc finger proteins (ZFP) play important roles in cellular processes. The DNA binding region of ZFP consists of 3 zinc finger DNA binding domains connected by amino acid linkers, the sequence TGQKP connects ZF1 and ZF2, and TGEKP connects ZF2 with ZF3. Linkers act to tune the zinc finger protein in the right position to bind its DNA target, the type of amino acid residues and length of linkers reflect on ZF1-ZF2-ZF3 interactions and contribute to the search and recognition process of ZF protein to its DNA target. Linker mutations and the affinity of the resulting mutants to specific and nonspecific DNA targets were studied by MD simulations and MM_GB(PB)SA. The affinity of mutants to DNA varied with type and position of amino acid residue. Mutation of K in TGQKP resulted in loss in affinity due to the loss of positive K interaction with phosphates, mutation of G showed loss in affinity to DNA, WT protein and all linker mutants showed loss in affinity to a nonspecific DNA target, this finding confirms previous reports which interpreted this loss in affinity as due to ZF1 having an anchoring role, and ZF3 playing an explorer role in the binding mechanism. The change in ZFP-DNA affinity with linker mutations is discussed in view of protein structure and role of linker residues in binding.
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