SUMOylation is an essential modification that regulates hundreds of proteins in eukaryotic cells. Owing to its dynamic nature and low steady-state levels, endogenous SUMOylation is challenging to detect. Here, we present a method that allows efficient enrichment and identification of endogenous targets of SUMO1 and the nearly identical SUMO2 and 3 (SUMO 2/3) from vertebrate cells and complex organ tissue. Using monoclonal antibodies for which we mapped the epitope, we enriched SUMOylated proteins by immunoprecipitation and peptide elution. We used this approach in combination with MS to identify SUMOylated proteins, which resulted in the first direct comparison of the endogenous SUMO1- and SUMO2/3-modified proteome in mammalian cells, to our knowledge. This protocol provides an affordable and feasible tool to investigate endogenous SUMOylation in primary cells, tissues and organs, and it will facilitate understanding of SUMO's role in physiology and disease.
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We gratefully acknowledge M. Matunis (Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA) for making hybridomas for monoclonal anti-SUMO antibodies available to the community and H. de Thé (Université Paris Diderot, Sorbonne Paris Cité, Hôpital St. Louis 1, Paris, France) for generously providing anti-PML antibodies, R. Ramaker and N. Stankovic for help with antibody characterization and all lab members for sharing reagents and advice. This work was supported by the Deutsche Forschungsgemeinschaft (SPP1365, ME 2279/3 to F.M.) and the EU Network of Excellence Rubicon (to F.M.) and by fellowships of the Excellence Cluster CellNetworks (to S.V.B.) and the Deutsche Krebshilfe (to S.H.).
The authors declare no competing financial interests.
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Becker, J., Barysch, S., Karaca, S. et al. Detecting endogenous SUMO targets in mammalian cells and tissues. Nat Struct Mol Biol 20, 525–531 (2013). https://doi.org/10.1038/nsmb.2526
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