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The STUbL RNF4 regulates protein group SUMOylation by targeting the SUMO conjugation machinery

Author

Listed:
  • Ramesh Kumar

    (Leiden University Medical Center
    Duke–NUS Graduate Medical School)

  • Román González-Prieto

    (Leiden University Medical Center)

  • Zhenyu Xiao

    (Leiden University Medical Center)

  • Matty Verlaan-de Vries

    (Leiden University Medical Center)

  • Alfred C. O. Vertegaal

    (Leiden University Medical Center)

Abstract

SUMO-targeted ubiquitin ligases (STUbLs) mediate the ubiquitylation of SUMOylated proteins to modulate their functions. In search of direct targets for the STUbL RNF4, we have developed TULIP (targets for ubiquitin ligases identified by proteomics) to covalently trap targets for ubiquitin E3 ligases. TULIP methodology could be widely employed to delineate E3 substrate wiring. Here we report that the single SUMO E2 Ubc9 and the SUMO E3 ligases PIAS1, PIAS2, PIAS3, ZNF451, and NSMCE2 are direct RNF4 targets. We confirm PIAS1 as a key RNF4 substrate. Furthermore, we establish the ubiquitin E3 ligase BARD1, a tumor suppressor and partner of BRCA1, as an indirect RNF4 target, regulated by PIAS1. Interestingly, accumulation of BARD1 at local sites of DNA damage increases upon knockdown of RNF4. Combined, we provide an insight into the role of the STUbL RNF4 to balance the role of SUMO signaling by directly targeting Ubc9 and SUMO E3 ligases.

Suggested Citation

  • Ramesh Kumar & Román González-Prieto & Zhenyu Xiao & Matty Verlaan-de Vries & Alfred C. O. Vertegaal, 2017. "The STUbL RNF4 regulates protein group SUMOylation by targeting the SUMO conjugation machinery," Nature Communications, Nature, vol. 8(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_s41467-017-01900-x
    DOI: 10.1038/s41467-017-01900-x
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    Citations

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    Cited by:

    1. Fredrik Trulsson & Vyacheslav Akimov & Mihaela Robu & Nila Overbeek & David Aureliano Pérez Berrocal & Rashmi G. Shah & Jürgen Cox & Girish M. Shah & Blagoy Blagoev & Alfred C. O. Vertegaal, 2022. "Deubiquitinating enzymes and the proteasome regulate preferential sets of ubiquitin substrates," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    2. Sarah Tessier & Omar Ferhi & Marie-Claude Geoffroy & Román González-Prieto & Antoine Canat & Samuel Quentin & Marika Pla & Michiko Niwa-Kawakita & Pierre Bercier & Domitille Rérolle & Marilyn Tirard &, 2022. "Exploration of nuclear body-enhanced sumoylation reveals that PML represses 2-cell features of embryonic stem cells," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    3. Daniel Salas-Lloret & Néstor García-Rodríguez & Emily Soto-Hidalgo & Lourdes González-Vinceiro & Carmen Espejo-Serrano & Lisanne Giebel & María Luisa Mateos-Martín & Arnoud H. Ru & Peter A. Veelen & P, 2024. "BRCA1/BARD1 ubiquitinates PCNA in unperturbed conditions to promote continuous DNA synthesis," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    4. Orhi Barroso-Gomila & Laura Merino-Cacho & Veronica Muratore & Coralia Perez & Vincenzo Taibi & Elena Maspero & Mikel Azkargorta & Ibon Iloro & Fredrik Trulsson & Alfred C. O. Vertegaal & Ugo Mayor & , 2023. "BioE3 identifies specific substrates of ubiquitin E3 ligases," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    5. Jenny Kaur Singh & Rebecca Smith & Magdalena B. Rother & Anton J. L. Groot & Wouter W. Wiegant & Kees Vreeken & Ostiane D’Augustin & Robbert Q. Kim & Haibin Qian & Przemek M. Krawczyk & Román González, 2021. "Zinc finger protein ZNF384 is an adaptor of Ku to DNA during classical non-homologous end-joining," Nature Communications, Nature, vol. 12(1), pages 1-21, December.
    6. Orhi Barroso-Gomila & Fredrik Trulsson & Veronica Muratore & Iñigo Canosa & Laura Merino-Cacho & Ana Rosa Cortazar & Coralia Pérez & Mikel Azkargorta & Ibon Iloro & Arkaitz Carracedo & Ana M. Aransay , 2021. "Identification of proximal SUMO-dependent interactors using SUMO-ID," Nature Communications, Nature, vol. 12(1), pages 1-19, December.
    7. Zeliha Yalçin & Shiu Yeung Lam & Marieke H. Peuscher & Jaco Torre & Sha Zhu & Prasanna V. Iyengar & Daniel Salas-Lloret & Inge Krijger & Nathalie Moatti & Ruben Lugt & Mattia Falcone & Aurora Cerutti , 2024. "UBE2D3 facilitates NHEJ by orchestrating ATM signalling through multi-level control of RNF168," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    8. Laura A. Claessens & Matty Verlaan-de Vries & Ilona J. Graaf & Alfred C. O. Vertegaal, 2023. "SENP6 regulates localization and nuclear condensation of DNA damage response proteins by group deSUMOylation," Nature Communications, Nature, vol. 14(1), pages 1-19, December.

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