Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation

• Published in: Nature structural & molecular biology Vol. 24; no. 3; pp. 325 - 336
• Main Authors: Hendriks, Ivo A, Lyon, David, Young, Clifford, Jensen, Lars J, Vertegaal, Alfred C O, Nielsen, Michael L
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.03.2017; Nature Publishing Group
• Subjects: 631/1647/296; 631/337/458/538; 631/553; Acetylation; Adenosine diphosphate; Biochemistry; Biological Microscopy; Cell regulation; Consensus Sequence; Cyclin-Dependent Kinases - metabolism; Genetic aspects; HeLa Cells; Humans; Intrinsically Disordered Proteins - metabolism; Life Sciences; Mass spectrometry; Membrane Biology; Methylation; Observations; Peptides; Phosphorylation; Proline - metabolism; Protein Processing, Post-Translational; Protein research; Protein Structure; Proteome - metabolism; Proteomics; Proteomics - methods; resource; Small Ubiquitin-Related Modifier Proteins - metabolism; Stress, Physiological; Sumoylation; Translation (Genetics); Ubiquitin - metabolism
• ISSN: 1545-9993; 1545-9985
• DOI: 10.1038/nsmb.3366

A comprehensive analysis of the human SUMO proteome, in HeLa and U2OS cell lines and under different conditions, identifies new SUMOylated sites and reveals cross-talk between SUMO and other post-translational modifications, such as phosphorylation. Small ubiquitin-like modifiers (SUMOs) are post-translational modifications (PTMs) that regulate nuclear cellular processes. Here we used an augmented K0–SUMO proteomics strategy to identify 40,765 SUMO acceptor sites and quantify their fractional contribution for 6,747 human proteins. Structural–predictive analyses revealed that lysines residing in disordered regions are preferentially targeted by SUMO, in notable contrast to other widespread lysine modifications. In our data set, we identified 807 SUMOylated peptides that were co-modified by phosphorylation, along with dozens of SUMOylated peptides that were co-modified by ubiquitylation, acetylation and methylation. Notably, 9% of the identified SUMOylome occurred proximal to phosphorylation, and numerous SUMOylation sites were found to be fully dependent on prior phosphorylation events. SUMO-proximal phosphorylation occurred primarily in a proline-directed manner, and inhibition of cyclin-dependent kinases dynamically affected co-modification. Collectively, we present a comprehensive analysis of the SUMOylated proteome, uncovering the structural preferences for SUMO and providing system-wide evidence for a remarkable degree of cross-talk between SUMOylation and other major PTMs.