Allosteric activation of the SPRTN protease by ubiquitin maintains genome stability
Abstract The DNA-dependent protease SPRTN maintains genome stability by degrading toxic DNA-protein crosslinks (DPCs). To understand how SPRTN’s promiscuous protease activity is confined to cleavage of crosslinked proteins, we reconstitute the repair of DPCs including their modification with SUMO an...
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Nature Portfolio
2025-07-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-61224-z |
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| author | Sophie Dürauer Hyun-Seo Kang Christian Wiebeler Yuka Machida Dina S. Schnapka Denitsa Yaneva Christian Renz Maximilian J. Götz Pedro Weickert Abigail C. Major Aldwin S. Rahmanto Sophie M. Gutenthaler-Tietze Lena J. Daumann Petra Beli Helle D. Ulrich Michael Sattler Yuichi J. Machida Nadine Schwierz Julian Stingele |
| author_facet | Sophie Dürauer Hyun-Seo Kang Christian Wiebeler Yuka Machida Dina S. Schnapka Denitsa Yaneva Christian Renz Maximilian J. Götz Pedro Weickert Abigail C. Major Aldwin S. Rahmanto Sophie M. Gutenthaler-Tietze Lena J. Daumann Petra Beli Helle D. Ulrich Michael Sattler Yuichi J. Machida Nadine Schwierz Julian Stingele |
| author_sort | Sophie Dürauer |
| collection | DOAJ |
| description | Abstract The DNA-dependent protease SPRTN maintains genome stability by degrading toxic DNA-protein crosslinks (DPCs). To understand how SPRTN’s promiscuous protease activity is confined to cleavage of crosslinked proteins, we reconstitute the repair of DPCs including their modification with SUMO and ubiquitin chains in vitro. We discover that DPC ubiquitylation strongly activates SPRTN independently of SPRTN’s known ubiquitin-binding domains. Using protein structure prediction, MD simulations and NMR spectroscopy we reveal that ubiquitin binds to SPRTN’s protease domain, promoting an open, active conformation. Replacing key interfacial residues prevents allosteric activation of SPRTN by ubiquitin, leading to genomic instability and cell cycle defects in cells expressing truncated SPRTN variants that cause premature aging and liver cancer in Ruijs-Aalfs syndrome patients. Collectively, our results reveal a ubiquitin-dependent regulatory mechanism that ensures SPRTN activity is deployed precisely when and where it is needed. |
| format | Article |
| id | doaj-art-8aca53a53b2f451fa6e5208799f2813f |
| institution | DOAJ |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-8aca53a53b2f451fa6e5208799f2813f2025-08-20T03:05:14ZengNature PortfolioNature Communications2041-17232025-07-0116111710.1038/s41467-025-61224-zAllosteric activation of the SPRTN protease by ubiquitin maintains genome stabilitySophie Dürauer0Hyun-Seo Kang1Christian Wiebeler2Yuka Machida3Dina S. Schnapka4Denitsa Yaneva5Christian Renz6Maximilian J. Götz7Pedro Weickert8Abigail C. Major9Aldwin S. Rahmanto10Sophie M. Gutenthaler-Tietze11Lena J. Daumann12Petra Beli13Helle D. Ulrich14Michael Sattler15Yuichi J. Machida16Nadine Schwierz17Julian Stingele18Gene Center, Ludwig-Maximilians-Universität MünchenInstitute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz MunichInstitute of Physics, University of AugsburgDevelopmental Therapeutics Branch, Center for Cancer Research, National Cancer InstituteGene Center, Ludwig-Maximilians-Universität MünchenGene Center, Ludwig-Maximilians-Universität MünchenInstitute of Molecular Biology gGmbHGene Center, Ludwig-Maximilians-Universität MünchenGene Center, Ludwig-Maximilians-Universität MünchenInstitute of Physics, University of AugsburgInstitute of Molecular Biology gGmbHChair of Bioinorganic Chemistry, Heinrich-Heine Universität DüsseldorfChair of Bioinorganic Chemistry, Heinrich-Heine Universität DüsseldorfInstitute of Molecular Biology gGmbHInstitute of Molecular Biology gGmbHInstitute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz MunichDevelopmental Therapeutics Branch, Center for Cancer Research, National Cancer InstituteInstitute of Physics, University of AugsburgGene Center, Ludwig-Maximilians-Universität MünchenAbstract The DNA-dependent protease SPRTN maintains genome stability by degrading toxic DNA-protein crosslinks (DPCs). To understand how SPRTN’s promiscuous protease activity is confined to cleavage of crosslinked proteins, we reconstitute the repair of DPCs including their modification with SUMO and ubiquitin chains in vitro. We discover that DPC ubiquitylation strongly activates SPRTN independently of SPRTN’s known ubiquitin-binding domains. Using protein structure prediction, MD simulations and NMR spectroscopy we reveal that ubiquitin binds to SPRTN’s protease domain, promoting an open, active conformation. Replacing key interfacial residues prevents allosteric activation of SPRTN by ubiquitin, leading to genomic instability and cell cycle defects in cells expressing truncated SPRTN variants that cause premature aging and liver cancer in Ruijs-Aalfs syndrome patients. Collectively, our results reveal a ubiquitin-dependent regulatory mechanism that ensures SPRTN activity is deployed precisely when and where it is needed.https://doi.org/10.1038/s41467-025-61224-z |
| spellingShingle | Sophie Dürauer Hyun-Seo Kang Christian Wiebeler Yuka Machida Dina S. Schnapka Denitsa Yaneva Christian Renz Maximilian J. Götz Pedro Weickert Abigail C. Major Aldwin S. Rahmanto Sophie M. Gutenthaler-Tietze Lena J. Daumann Petra Beli Helle D. Ulrich Michael Sattler Yuichi J. Machida Nadine Schwierz Julian Stingele Allosteric activation of the SPRTN protease by ubiquitin maintains genome stability Nature Communications |
| title | Allosteric activation of the SPRTN protease by ubiquitin maintains genome stability |
| title_full | Allosteric activation of the SPRTN protease by ubiquitin maintains genome stability |
| title_fullStr | Allosteric activation of the SPRTN protease by ubiquitin maintains genome stability |
| title_full_unstemmed | Allosteric activation of the SPRTN protease by ubiquitin maintains genome stability |
| title_short | Allosteric activation of the SPRTN protease by ubiquitin maintains genome stability |
| title_sort | allosteric activation of the sprtn protease by ubiquitin maintains genome stability |
| url | https://doi.org/10.1038/s41467-025-61224-z |
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