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December 28, 2020 preprint Open access Aachen paper

Identification of proximal SUMO-dependent interactors using SUMO-ID

bioRxiv (Cold Spring Harbor Laboratory)

DOI: 10.1101/2020.12.28.424528 Full text (OA) OpenAlex

Abstract

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 developed 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 allowed us to identify novel interactors of SUMOylated SALL1, a less characterized SUMO substrate. 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.

Authors 16

  1. Orhi Barroso‐Gomila

    CIC bioGUNE

    Affiliation as printed

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

    Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 80A, 4860 Derio, Spain

  2. Fredrik Trulsson Aachen Cell and Chemical Biology

    Leiden University Medical Center

    Affiliation as printed

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

    Cell and Chemical Biology, Leiden University Medical Center (LUMC), 333 ZA Leiden, The Netherlands

  3. Veronica Muratore

    CIC bioGUNE

    Affiliation as printed

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

    Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 80A, 4860 Derio, Spain

  4. Iñigo Canosa

    CIC bioGUNE

    Affiliation as printed

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

    Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 80A, 4860 Derio, Spain

  5. Laura Merino‐Cacho

    CIC bioGUNE

    Affiliation as printed

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

    Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 80A, 4860 Derio, Spain

  6. Ana R. Cortázar

    Instituto de Salud Carlos III · CIC bioGUNE · Centro de Investigación Biomédica en Red de Cáncer

    Affiliation as printed

    CIBERONC, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5

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

    Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 80A, 4860 Derio, Spain

  7. Coralia Pérez

    CIC bioGUNE

    Affiliation as printed

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

    Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 80A, 4860 Derio, Spain

  8. Mikel Azkargorta

    Instituto de Salud Carlos III · CIC bioGUNE · Centro de Investigación Biomédica en Red · Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas

    Affiliation as printed

    CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5

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

    ProteoRed-ISCIII, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5

    CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos -5, Pabellón 11, Planta 0, 28029 Madrid, Spain

    Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 80A, 4860 Derio, Spain

  9. Ibón Iloro

    Instituto de Salud Carlos III · CIC bioGUNE · Centro de Investigación Biomédica en Red · Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas

    Affiliation as printed

    CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5

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

    ProteoRed-ISCIII, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5

    CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos -5, Pabellón 11, Planta 0, 28029 Madrid, Spain

    Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 80A, 4860 Derio, Spain

  10. Arkaitz Carracedo

    Ikerbasque · University of the Basque Country · Instituto de Salud Carlos III · CIC bioGUNE · Centro de Investigación Biomédica en Red de Cáncer

    Affiliation as printed

    Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU)

    CIBERONC, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5

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

    Ikerbasque, Basque Foundation for Science

    Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), E-48940, Leioa, Spain

    CIBERONC, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-, Pabellón 11, Planta 0, 28029 Madrid, Spain

    Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 80A, 4860 Derio, Spain

  11. Ana María Aransay

    Instituto de Salud Carlos III · CIC bioGUNE · Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas

    Affiliation as printed

    CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5

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

    Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 80A, 4860 Derio, Spain

  12. Félix Elortza

    Instituto de Salud Carlos III · CIC bioGUNE · Centro de Investigación Biomédica en Red · Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas

    Affiliation as printed

    CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5

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

    ProteoRed-ISCIII, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5

    CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos -5, Pabellón 11, Planta 0, 28029 Madrid, Spain

    Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 80A, 4860 Derio, Spain

  13. Ugo Mayor

    Ikerbasque · University of the Basque Country

    Affiliation as printed

    Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU)

    Ikerbasque, Basque Foundation for Science

    Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), E-48940, Leioa, Spain

    Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain

  14. Alfred C.O. Vertegaal Aachen Cell and Chemical Biology

    Leiden University Medical Center

    Affiliation as printed

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

    Cell and Chemical Biology, Leiden University Medical Center (LUMC), 333 ZA Leiden, The Netherlands

  15. Rosa Barrio corresponding

    CIC bioGUNE

    Affiliation as printed

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

    Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 80A, 4860 Derio, Spain

  16. James David Sutherland corresponding

    CIC bioGUNE

    Affiliation as printed

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

    Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 80A, 4860 Derio, Spain

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References 76