Mapping of SUMO sites and analysis of SUMOylation changes induced by external stimuli

SUMOylation is an essential ubiquitin-like modification involved in important biological processes in eukaryotic cells. Identification of small ubiquitin-related modifier (SUMO)-conjugated residues in proteins is critical for understanding the role of SUMOylation but remains experimentally challenging. We have set up a powerful and high-throughput method combining quantitative proteomics and peptide immunocapture to map SUMOylation sites and have analyzed changes in SUMOylation in response to stimuli. With this technique we identified 295 SUMO1 and 167 SUMO2 sites on endogenous substrates of human cells. We further used this strategy to characterize changes in SUMOylation induced by listeriolysin O, a bacterial toxin that impairs the host cell SUMOylation machinery, and identified several classes of host proteins specifically deSUMOylated in response to this toxin. Our approach constitutes an unprecedented tool, broadly applicable to various SUMO-regulated cellular processes in health and disease.Posttranslational modifications (PTMs) are key mechanisms used by both prokaryotes and eukaryotes to regulate protein activity specifically, locally, and temporally. Ubiquitin and ubiquitin-like proteins (UBLs) constitute a specific class of small protein modifiers that can be covalently attached to a target protein via the formation of an isopeptide bond in a reversible manner. Small ubiquitin-related modifier (SUMO), one of these UBLs, is an essential PTM in eukaryotic cells that is involved in various cellular functions including gene expression regulation, DNA repair, intracellular transport, and response to viral and bacterial infections (1–5). The human genome encodes three different functional SUMO isoforms (SUMO1, SUMO2, and SUMO3) that are conjugated to distinct but overlapping sets of target proteins (1, 2, 6). Conjugation of SUMO to its targets in humans requires an E1-activating enzyme (the SAE1/SAE2 heterodimer), an E2-conjugating enzyme (Ubc9), and several E3 SUMO enzymes. Once conjugated to its target, SUMO can be deconjugated by several different SUMO isopeptidases that tightly regulate the SUMOylation levels of proteins (7).Since the discovery of SUMO two decades ago, much effort has been dedicated to the identification of SUMO-conjugated proteins in different organisms including yeast, plants, and mammals (8). However, isolation of SUMOylated proteins has proven to be challenging. Indeed, for most SUMO substrates, only a small proportion of the total amount of protein is SUMO-modified. In addition, the high activity of SUMO isopeptidases in cell lysates results in the rapid loss of SUMO conjugation in the absence of appropriate inhibitors. Thus, the most common approach used to isolate SUMOylated proteins is based on the expression of His-tagged versions of SUMO allowing the purification of SUMO-conjugated proteins by nickel chromatography under denaturing conditions (8, 9). Denaturing conditions inactivate SUMO isopeptidases and also prevent contamination by proteins interacting noncovalently with SUMO via specific domains such as SUMO-interacting motifs (SIMs) (2). Once SUMOylated proteins have been isolated, their analysis by mass spectrometry (MS) has been widely used to identify SUMO-modified proteins and, albeit less successfully, SUMO-conjugation sites.Mapping the exact lysine residue to which SUMO is attached in modified proteins is a critical step to get further insight into the function of SUMOylation. Indeed, the identification of SUMO sites allows the generation of non-SUMOylatable mutants and the study of associated phenotypes. Identification of SUMO sites by MS is not straightforward (8). Unlike ubiquitin, which leaves a small diglycine (GG) signature tag on the modified lysine residue after trypsin digestion, SUMO leaves a larger signature that severely hampers the identification of modified peptides.In addition to the identification of the SUMO site per se, a comparison of the SUMOylation status of sites in different cell-growth conditions is critical for better characterizing the biological implications of SUMOylation. For example, analysis of SUMOylation changes induced after heat shock, arsenic treatment, inhibition of the proteasome, or during the cell cycle has led to numerous insights into the role of SUMOylation in cell physiology (refs. 10–14 and reviewed in ref. 2). Here, we devised a performant approach which combines the use of SUMO variants, peptide immunocapture, and quantitative proteomics for high-throughput identification of SUMO sites. We then show that our approach is able to characterize global changes in the cell SUMOylome in response to a given stimulus, such as exposure to a bacterial toxin, listeriolysin O (LLO).