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Identification of proximal SUMO-dependent interactors using SUMO-ID

Author

Listed:
  • Orhi Barroso-Gomila

    (Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park)

  • Fredrik Trulsson

    (Cell and Chemical Biology, Leiden University Medical Center (LUMC))

  • Veronica Muratore

    (Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park)

  • Iñigo Canosa

    (Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park)

  • Laura Merino-Cacho

    (Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park)

  • Ana Rosa Cortazar

    (Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park
    CIBERONC, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0)

  • Coralia Pérez

    (Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park)

  • Mikel Azkargorta

    (Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park
    CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0
    ProteoRed-ISCIII, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0)

  • Ibon Iloro

    (Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park
    CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0
    ProteoRed-ISCIII, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0)

  • Arkaitz Carracedo

    (Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park
    CIBERONC, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0
    Ikerbasque, Basque Foundation for Science
    University of the Basque Country (UPV/EHU))

  • Ana M. Aransay

    (Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park
    CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0)

  • Felix Elortza

    (Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park
    CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0
    ProteoRed-ISCIII, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0)

  • Ugo Mayor

    (Ikerbasque, Basque Foundation for Science
    University of the Basque Country (UPV/EHU))

  • Alfred C. O. Vertegaal

    (Cell and Chemical Biology, Leiden University Medical Center (LUMC))

  • Rosa Barrio

    (Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park)

  • James D. Sutherland

    (Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park)

Abstract

The fast dynamics and reversibility of posttranslational modifications by the ubiquitin family pose significant challenges for research. Here we present SUMO-ID, a technology that merges proximity biotinylation by TurboID and protein-fragment complementation to find SUMO-dependent interactors of proteins of interest. We develop an optimized split-TurboID version and show SUMO interaction-dependent labelling of proteins proximal to PML and RANGAP1. SUMO-dependent interactors of PML are involved in transcription, DNA damage, stress response and SUMO modification and are highly enriched in SUMO Interacting Motifs, but may only represent a subset of the total PML proximal proteome. Likewise, SUMO-ID also allow us to identify interactors of SUMOylated SALL1, a less characterized SUMO substrate. Furthermore, using TP53 as a substrate, we identify SUMO1, SUMO2 and Ubiquitin preferential interactors. Thus, SUMO-ID is a powerful tool that allows to study the consequences of SUMO-dependent interactions, and may further unravel the complexity of the ubiquitin code.

Suggested Citation

  • 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.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-26807-6
    DOI: 10.1038/s41467-021-26807-6
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    References listed on IDEAS

    as
    1. Annie M. Sriramachandran & Katrin Meyer-Teschendorf & Stefan Pabst & Helle D. Ulrich & Niels H. Gehring & Kay Hofmann & Gerrit J. K. Praefcke & R. Jürgen Dohmen, 2019. "Arkadia/RNF111 is a SUMO-targeted ubiquitin ligase with preference for substrates marked with SUMO1-capped SUMO2/3 chain," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
    2. Isabel Myriam Schopp & Cinthia Claudia Amaya Ramirez & Jerneja Debeljak & Elisa Kreibich & Merle Skribbe & Klemens Wild & Julien Béthune, 2017. "Split-BioID a conditional proteomics approach to monitor the composition of spatiotemporally defined protein complexes," Nature Communications, Nature, vol. 8(1), pages 1-14, August.
    3. 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.
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