Site-specific characterization of endogenous SUMOylation across species and organs

• Published in: Nature communications Vol. 9; no. 1; pp. 2456 - 17
• Main Authors: Hendriks, Ivo A., Lyon, David, Su, Dan, Skotte, Niels H., Daniel, Jeremy A., Jensen, Lars J., Nielsen, Michael L.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 25.06.2018; Nature Publishing Group; Nature Portfolio
• Subjects: 631/1647/296; 631/337/475; 631/80/458/538; 82/58; 96/1; 96/106; Animals; Antibodies; Cancer; Cell Line, Tumor; Conjugation; Enzymes; Genetic engineering; Heat stress; Heat tolerance; HEK293 Cells; HeLa Cells; Humanities and Social Sciences; Humans; Immunoprecipitation; Male; Metabolism; Mice; Mice, Inbred C57BL; multidisciplinary; Neoplasms - pathology; Organs; Peptides; Post-translation; Proteasomes; Proteins; Proteome - metabolism; Proteomics; Science; Science (multidisciplinary); Small Ubiquitin-Related Modifier Proteins - metabolism; SUMO protein; Sumoylation - physiology; Tissues; Ubiquitin; Ubiquitins - metabolism
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-018-04957-4

Small ubiquitin-like modifiers (SUMOs) are post-translational modifications that play crucial roles in most cellular processes. While methods exist to study exogenous SUMOylation, large-scale characterization of endogenous SUMO2/3 has remained technically daunting. Here, we describe a proteomics approach facilitating system-wide and in vivo identification of lysines modified by endogenous and native SUMO2. Using a peptide-level immunoprecipitation enrichment strategy, we identify 14,869 endogenous SUMO2/3 sites in human cells during heat stress and proteasomal inhibition, and quantitatively map 1963 SUMO sites across eight mouse tissues. Characterization of the SUMO equilibrium highlights striking differences in SUMO metabolism between cultured cancer cells and normal tissues. Targeting preferences of SUMO2/3 vary across different organ types, coinciding with markedly differential SUMOylation states of all enzymes involved in the SUMO conjugation cascade. Collectively, our systemic investigation details the SUMOylation architecture across species and organs and provides a resource of endogenous SUMOylation sites on factors important in organ-specific functions. Proteomics is a powerful method to study protein SUMOylation, but system-wide insights into endogenous SUMO2/3 modification events are still sparse. Here, the authors develop a more sensitive SUMO proteomics approach, providing detailed maps of endogenous SUMO2/3 sites in human cells and mouse tissues.