Substrate spectrum of PPM1D in the cellular response to DNA double-strand breaks
Summary: PPM1D is a p53-regulated protein phosphatase that modulates the DNA damage response (DDR) and is frequently altered in cancer. Here, we employed chemical inhibition of PPM1D and quantitative mass spectrometry-based phosphoproteomics to identify the substrates of PPM1D upon induction of DNA...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-09-01
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| Series: | iScience |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004222011646 |
| _version_ | 1811281232101638144 |
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| author | Justus F. Gräf Ivan Mikicic Xiaofei Ping Claudia Scalera Katharina Mayr Lukas S. Stelzl Petra Beli Sebastian A. Wagner |
| author_facet | Justus F. Gräf Ivan Mikicic Xiaofei Ping Claudia Scalera Katharina Mayr Lukas S. Stelzl Petra Beli Sebastian A. Wagner |
| author_sort | Justus F. Gräf |
| collection | DOAJ |
| description | Summary: PPM1D is a p53-regulated protein phosphatase that modulates the DNA damage response (DDR) and is frequently altered in cancer. Here, we employed chemical inhibition of PPM1D and quantitative mass spectrometry-based phosphoproteomics to identify the substrates of PPM1D upon induction of DNA double-strand breaks (DSBs) by etoposide. We identified 73 putative PPM1D substrates that are involved in DNA repair, regulation of transcription, and RNA processing. One-third of DSB-induced S/TQ phosphorylation sites are dephosphorylated by PPM1D, demonstrating that PPM1D only partially counteracts ATM/ATR/DNA-PK signaling. PPM1D-targeted phosphorylation sites are found in a specific amino acid sequence motif that is characterized by glutamic acid residues, high intrinsic disorder, and poor evolutionary conservation. We identified a functionally uncharacterized protein Kanadaptin as ATM and PPM1D substrate upon DSB induction. We propose that PPM1D plays a role during the response to DSBs by regulating the phosphorylation of DNA- and RNA-binding proteins in intrinsically disordered regions. |
| first_indexed | 2024-04-13T01:30:04Z |
| format | Article |
| id | doaj.art-912edcee7e754412a04cbb51e89a815a |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-04-13T01:30:04Z |
| publishDate | 2022-09-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-912edcee7e754412a04cbb51e89a815a2022-12-22T03:08:32ZengElsevieriScience2589-00422022-09-01259104892Substrate spectrum of PPM1D in the cellular response to DNA double-strand breaksJustus F. Gräf0Ivan Mikicic1Xiaofei Ping2Claudia Scalera3Katharina Mayr4Lukas S. Stelzl5Petra Beli6Sebastian A. Wagner7Institute of Molecular Biology (IMB), 55128 Mainz, GermanyInstitute of Molecular Biology (IMB), 55128 Mainz, GermanyInstitute of Molecular Biology (IMB), 55128 Mainz, Germany; Faculty of Biology, Johannes Gutenberg University, 55128 Mainz, Germany; KOMET 1, Institute of Physics, Johannes Gutenberg University, 55099 Mainz, GermanyInstitute of Molecular Biology (IMB), 55128 Mainz, GermanyInstitute of Molecular Biology (IMB), 55128 Mainz, GermanyInstitute of Molecular Biology (IMB), 55128 Mainz, Germany; Faculty of Biology, Johannes Gutenberg University, 55128 Mainz, Germany; KOMET 1, Institute of Physics, Johannes Gutenberg University, 55099 Mainz, GermanyInstitute of Molecular Biology (IMB), 55128 Mainz, Germany; Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg University, 55128 Mainz, GermanyDepartment of Medicine, Hematology/Oncology, Goethe University, 60590 Frankfurt, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Frankfurt Cancer Institute (FCI), 60596 Frankfurt, Germany; Corresponding authorSummary: PPM1D is a p53-regulated protein phosphatase that modulates the DNA damage response (DDR) and is frequently altered in cancer. Here, we employed chemical inhibition of PPM1D and quantitative mass spectrometry-based phosphoproteomics to identify the substrates of PPM1D upon induction of DNA double-strand breaks (DSBs) by etoposide. We identified 73 putative PPM1D substrates that are involved in DNA repair, regulation of transcription, and RNA processing. One-third of DSB-induced S/TQ phosphorylation sites are dephosphorylated by PPM1D, demonstrating that PPM1D only partially counteracts ATM/ATR/DNA-PK signaling. PPM1D-targeted phosphorylation sites are found in a specific amino acid sequence motif that is characterized by glutamic acid residues, high intrinsic disorder, and poor evolutionary conservation. We identified a functionally uncharacterized protein Kanadaptin as ATM and PPM1D substrate upon DSB induction. We propose that PPM1D plays a role during the response to DSBs by regulating the phosphorylation of DNA- and RNA-binding proteins in intrinsically disordered regions.http://www.sciencedirect.com/science/article/pii/S2589004222011646Biochemistrymolecular biologycancerproteomics |
| spellingShingle | Justus F. Gräf Ivan Mikicic Xiaofei Ping Claudia Scalera Katharina Mayr Lukas S. Stelzl Petra Beli Sebastian A. Wagner Substrate spectrum of PPM1D in the cellular response to DNA double-strand breaks iScience Biochemistry molecular biology cancer proteomics |
| title | Substrate spectrum of PPM1D in the cellular response to DNA double-strand breaks |
| title_full | Substrate spectrum of PPM1D in the cellular response to DNA double-strand breaks |
| title_fullStr | Substrate spectrum of PPM1D in the cellular response to DNA double-strand breaks |
| title_full_unstemmed | Substrate spectrum of PPM1D in the cellular response to DNA double-strand breaks |
| title_short | Substrate spectrum of PPM1D in the cellular response to DNA double-strand breaks |
| title_sort | substrate spectrum of ppm1d in the cellular response to dna double strand breaks |
| topic | Biochemistry molecular biology cancer proteomics |
| url | http://www.sciencedirect.com/science/article/pii/S2589004222011646 |
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