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Marshall S, Navarro MVAS, Ascenҫão CFR, Dibitetto D, Smolka MB. In-Depth Mapping of DNA-PKcs Signaling Uncovers Non-Canonical Features of Its Kinase Specificity. J Biol Chem 2024:107513. [PMID: 38945450 DOI: 10.1016/j.jbc.2024.107513] [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: 01/30/2024] [Revised: 06/11/2024] [Accepted: 06/25/2024] [Indexed: 07/02/2024] Open
Abstract
DNA-PKcs is a DNA damage sensor kinase with established roles in DNA double-strand break repair via non-homologous end joining. Recent studies have revealed additional roles of DNA-PKcs in the regulation of transcription, translation, and DNA replication. However, the substrates through which DNA-PKcs regulates these processes remain largely undefined. Here we utilized quantitative phosphoproteomics to generate a high coverage map of DNA-PKcs signaling in response to ionizing radiation and mapped its interplay with the ATM kinase. Beyond the detection of the canonical S/T-Q phosphorylation motif, we uncovered a non-canonical mode of DNA-PKcs signaling targeting S/T-ψ-D/E motifs. Sequence and structural analyses of the DNA-PKcs substrate recognition pocket revealed unique features compared to closely related PIKK kinases that may explain its broader substrate preference. These findings expand the repertoire of DNA-PKcs and ATM substrates while establishing a novel preferential phosphorylation motif for DNA-PKcs.
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Affiliation(s)
- Shannon Marshall
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Marcos V A S Navarro
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; IFSC Institute of Physics of São Carlos, University of São Paulo, São Carlos - SP, 13566-590, Brazil.
| | - Carolline F R Ascenҫão
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Diego Dibitetto
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Department of Experimental Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, 20156 Milan, Italy
| | - Marcus B Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.
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Marshall S, Navarro MV, Ascenҫão CF, Smolka MB. IN-DEPTH MAPPING OF DNA-PKcs SIGNALING UNCOVERS CONSERVED FEATURES OF ITS KINASE SPECIFICITY. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.17.576037. [PMID: 38293078 PMCID: PMC10827184 DOI: 10.1101/2024.01.17.576037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
DNA-PKcs is a DNA damage sensor kinase with established roles in DNA double-strand break repair via non-homologous end joining. Recent studies have revealed additional roles of DNA-PKcs in the regulation of transcription, translation and DNA replication. However, the substrates through which DNA-PKcs regulates these processes remain largely undefined. Here we utilized quantitative phosphoproteomics to generate a high coverage map of DNA-PKcs signaling in response to ionizing radiation and mapped its interplay with the ATM kinase. Beyond the detection of the canonical S/T-Q phosphorylation motif, we uncovered a non-canonical mode of DNA-PKcs signaling targeting S/T-ψ-D/E motifs. Cross-species analysis in mouse pre-B and human HCT116 cell lines revealed splicing factors and transcriptional regulators phosphorylated at this novel motif, several of which contain SAP domains. These findings expand the list of DNA-PKcs and ATM substrates and establish a novel preferential phosphorylation motif for DNA-PKcs that connects it to proteins involved in nucleotide processes and interactions.
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Affiliation(s)
- Shannon Marshall
- 1. Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Marcos V.A.S. Navarro
- 1. Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- 2. IFSC Institute of Physics of São Carlos, University of São Paulo, São Carlos - SP, 13566-590, Brazil
| | - Carolline F.R. Ascenҫão
- 1. Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Marcus B. Smolka
- 1. Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
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Li H, Zhang Y, Zhang B, Chen D. A novel PRKDC mutation caused B lymphocytes V(D)J rearrangement disorder in the SLE-DAH like symptoms patient. Pediatr Rheumatol Online J 2023; 21:84. [PMID: 37580814 PMCID: PMC10424403 DOI: 10.1186/s12969-023-00840-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 06/05/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND Analyzed the clinical features and treatment process of the patient suffering from immunodeficiency with systemic lupus erythematosus(SLE)-like syndrome in a novel mutation of PRKDC. CASE PRESENTATION The patient had multiple positive auto-antibodies, chest CT and bronchoscopy showed Diffuse alveolar hemorrhage(DAH), and psychiatric symptoms showed brain atrophy by magnetic resonance imaging (MRI). Whole exon sequencing showed that novel complex heterozygous mutations of PRKDC gene (C. 1777 - 710_1777-709INSA (IVS16/IC16), C.1337T > A(p.Phe446Tyr). The mature B cell (CD19 + CD27 + CD38 dimIgD IgM-) were absent. The treatment of high-dose methylprednisolone (MP) and cyclophosphamide(CTX) can quickly relieve the symptoms of the patient. CONCLUSION We described the case of an infant immunodeficiency with SLE like-syndrome, which may cause by PRKDC mutation, treated successfully with high-dose MP and CTX.
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Affiliation(s)
- Hongwei Li
- Department of Pediatrics, The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang Rd, Guangzhou, 510120, China
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yawen Zhang
- Department of Pediatrics, The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang Rd, Guangzhou, 510120, China
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Biyun Zhang
- Department of Pediatrics, The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang Rd, Guangzhou, 510120, China
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Dehui Chen
- Department of Pediatrics, The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang Rd, Guangzhou, 510120, China.
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
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Berthault N, Bergam P, Pereira F, Girard PM, Dutreix M. Inhibition of DNA Repair by Inappropriate Activation of ATM, PARP, and DNA-PK with the Drug Agonist AsiDNA. Cells 2022; 11:cells11142149. [PMID: 35883597 PMCID: PMC9320633 DOI: 10.3390/cells11142149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 12/10/2022] Open
Abstract
AsiDNA is a DNA repair inhibitor mimicking DNA double-strand breaks (DSB) that was designed to disorganize DSB repair pathways to sensitize tumors to DNA damaging therapies such as radiotherapy and chemotherapy. We used the property of AsiDNA of triggering artificial DNA damage signaling to examine the activation of DSB repair pathways and to study the main steps of inhibition of DNA repair foci after irradiation. We show that, upon AsiDNA cellular uptake, cytoplasmic ATM and PARP are rapidly activated (within one hour) even in the absence of irradiation. ATM activation by AsiDNA leads to its transient autophosphorylation and sequestration in the cytoplasm, preventing the formation of ATM nuclear foci on irradiation-induced damage. In contrast, the activation of PARP did not seem to alter its ability to form DNA repair foci, but prevented 53BP1 and XRCC4 recruitment at the damage sites. In the nucleus, AsiDNA is essentially associated with DNA-PK, which triggers its activation leading to phosphorylation of H2AX all over chromatin. This pan-nuclear phosphorylation of H2AX correlates with the massive inhibition, at damage sites induced by irradiation, of the recruitment of repair enzymes involved in DSB repair by homologous recombination and nonhomologous end joining. These results highlight the interest in a new generation of DNA repair inhibitors targeting DNA damage signaling.
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Affiliation(s)
- Nathalie Berthault
- Institut Curie, PSL Research University, CNRS, INSERM, UMR 3347, 91405 Orsay, France; (N.B.); (F.P.); (P.-M.G.)
- Université Paris-Saclay, CNRS, UMR 3347, 91405 Orsay, France
| | - Ptissam Bergam
- Institut Curie, PSL Research University, CNRS, INSERM, UMS 2016, Multimodal Imaging Centre, 91405 Orsay, France;
- Université Paris-Saclay, CNRS, UMS 2016, 91405 Orsay, France
| | - Floriane Pereira
- Institut Curie, PSL Research University, CNRS, INSERM, UMR 3347, 91405 Orsay, France; (N.B.); (F.P.); (P.-M.G.)
- Université Paris-Saclay, CNRS, UMR 3347, 91405 Orsay, France
| | - Pierre-Marie Girard
- Institut Curie, PSL Research University, CNRS, INSERM, UMR 3347, 91405 Orsay, France; (N.B.); (F.P.); (P.-M.G.)
- Université Paris-Saclay, CNRS, UMR 3347, 91405 Orsay, France
| | - Marie Dutreix
- Institut Curie, PSL Research University, CNRS, INSERM, UMR 3347, 91405 Orsay, France; (N.B.); (F.P.); (P.-M.G.)
- Université Paris-Saclay, CNRS, UMR 3347, 91405 Orsay, France
- Correspondence:
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