ARTICLE DOI: 10.1038/s41467-017-01271-3 OPEN Site-specific identification and quantitation of endogenous SUMO modifications under native conditions Ryan J. Lumpkin1, Hongbo Gu2, Yiying Zhu2, Marilyn Leonard3, Alla S. Ahmad 1, Karl R. Clauser4, Jesse G. Meyer 1, Eric J. Bennett 3 & Elizabeth A. Komives1 fi fi 1234567890 Small ubiquitin-like modi er (SUMO) modi cation regulates numerous cellular processes. Unlike ubiquitin, detection of endogenous SUMOylated proteins is limited by the lack of naturally occurring protease sites in the C-terminal tail of SUMO proteins. Proteome-wide detection of SUMOylation sites on target proteins typically requires ectopic expression of mutant SUMOs with introduced tryptic sites. Here, we report a method for proteome-wide, site-level detection of endogenous SUMOylation that uses α-lytic protease, WaLP. WaLP digestion of SUMOylated proteins generates peptides containing SUMO-remnant diglycyl- lysine (KGG) at the site of SUMO modification. Using previously developed immuno-affinity isolation of KGG-containing peptides followed by mass spectrometry, we identified 1209 unique endogenous SUMO modification sites. We also demonstrate the impact of protea- some inhibition on ubiquitin and SUMO-modified proteomes using parallel quantitation of ubiquitylated and SUMOylated peptides. This methodological advancement enables deter- mination of endogenous SUMOylated proteins under completely native conditions. 1 Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378, USA. 2 Proteomic Service Group Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923, USA. 3 Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093-0380, USA. 4 Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA 02142, USA. Eric J. Bennett and Elizabeth A. Komives contributed equally to this work. Correspondence and requests for materials should be addressed to E.J.B. (email: [email protected]) or to E.A.K. (email: [email protected]) NATURE COMMUNICATIONS | 8: 1171 | DOI: 10.1038/s41467-017-01271-3 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-017-01271-3 fi he family of small ubiquitin-like modi er (SUMO) pro- a sp|P0CG48|UBC_HUMAN QKESTLHLVLRLRGG Tteins in humans includes four distinct genes with three sp|P63165|SUMO1_HUMAN EEEDVIEVYQEQTGG types of members: SUMO1, SUMO2/3 (which differ by sp|P61956|SUMO2_HUMAN EDEDTIDVFQQQTGG only three residues), and SUMO4. SUMO proteins regulate the sp|P55854|SUMO3_HUMAN EDEDTIDVFQQQTGG function of various proteins by reversible covalent isopeptide sp|Q6EEV6|SUMO4_HUMAN EDEDTIDVFQQPTGG bond attachment between the C terminus of SUMO and a free ε- amine group typically on lysine residues within target proteins1, bc similar to ubiquitin (Ub). Ub conjugation mainly targets proteins Ub RGG K Target Sm TGG K Target for degradation by the proteasome, but has also been implicated 2 in DNA repair, receptor signaling, and cell communication . The Trypsin WaLP function of SUMO conjugation on target proteins is similarly cleavage cleavage diverse with SUMOylation catalyzing alteration of protein activity for targets involved in gene expression, DNA repair, 1,3 nuclear import, heat shock, cell motility, and lipid metabolism . GG -K GG -K SUMO targets are generally low-abundance proteins, and the amount of the modification at steady state is also low4. Given its importance in numerous cellular functions, several groups have developed proteomic methods for analysis of SUMOylated Diglycyl-lysine IP Diglycyl-lysine IP proteins. Three general approaches have been previously utilized to GG -K GG -K isolate and identify the SUMOylated proteome5. Ectopic expres- sion of epitope-tagged SUMO followed by standard isolation Nanoscale Nanoscale techniques and mass spectrometry has been widely used in a LC-MS/MS LC-MS/MS – variety of organisms6 10. These approaches have yielded various maps of SUMO-interacting proteins but few sites of SUMOyla- MS1 MS1 tion are identified by this approach and the extent to which fi exogenous expression of modi ed SUMOs alters substrate tar- MS2 MS2 Intensity geting is unknown. Immuno-affinity approaches utilizing anti- Intensity bodies that recognize endogenous SUMO2/3 or SUMO1 have been used to identify SUMO-interacting proteins under endo- m/z m/z 4 genous conditions . However, as with the epitope-tagging fi fi Fig. 1 A strategy for mapping endogenous SUMO-modi cation sites. approach, few actual sites of SUMO modi cation were identi- a C-terminal sequence alignment of processed human SUMO1-4 and fied using this method. Therefore, methods that allow proteome- fi ubiquitin. The proximal amino acid to the diGlycine C-terminal residues is level identi cation of endogenous SUMOylation sites are needed. indicated in red. b Schematic depicting the Ub site mapping strategy. A robust proteomic method has been developed to measure fi 11 Proteins modi ed by ubiquitin are digested with trypsin leaving a diGlycine thousands of endogenous ubiquitylation sites . The method attached to the ε-amine of the lysine where ubiquitin was attached. An takes advantage of the C-terminal sequence of Ub (RGG) antibody specific for KGG-peptides is used to enrich peptides from (Fig. 1a). When cleaved with trypsin, ubiquitylated substrate ubiquitylated sites that are then identified by mass spectrometry. c The proteins will generate peptides containing a Ub-remnant diglycyl- same as b but WaLP digestion is used to generate the KGG-peptides from lysine (KGG) that can be enriched using specific antibodies and – SUMO attachment sites identified by tandem mass spectrometry (Fig. 1b)12 14. Instead of the trypsin-friendly arginine residue preceding the C-terminal diGlycine sequence observed in the processed Ub sequence, fi mature human SUMO paralogs have a threonine preceding the preclude analysis of SUMO-modi cation sites in native settings C-terminal diGlycine sequence and no other tryptic cleavage sites or from human tissues. Currently, no method exists for identi- near the C terminus (Fig. 1a). To overcome this problem, various fying endogenous SUMO sites on a global proteome scale without introduction of mutant SUMO. schemes that introduce mutations within the C terminus of α SUMO to render it more amenable to trypsin-based cleavage and We recently described the application of wild-type -lytic fi protease (WaLP) to proteome digestion for shotgun pro- identi cation by mass spectrometry have been developed for 21 fi global profiling of SUMO attachment sites15,16. Several groups teomics . Although relatively relaxed speci city was observed, fi WaLP prefers to cleave after threonine residues and rarely cleaved have reported global pro ling approaches in which mutant 21 SUMOs with various affinity tags and protease recognition sites after arginine . In addition, WaLP generates peptides of the same average length as trypsin despite its more relaxed substrate were introduced into cells. For example, Hendriks et al. intro- fi 21 duced a lysine-deficient SUMO-3 with a C-terminal trypsin speci city . We show here that WaLP cleaves at the C-terminal – 17,18 TGG sequence (all SUMO paralogs) leaving a SUMO-remnant cleavage site, His10 SUMO-3 K0 Q87R . The SUMOylated proteins were enriched by immobilized metal affinity chromato- KGG at the position of SUMO attachment in target proteins. fi The resulting KGG-containing peptides can then be identified graphy (IMAC) and digested with Lys-C. Peptides modi ed with fi fi SUMO were then purified again with IMAC and finally digested using methods already developed for pro ling the Ub-modi ed with trypsin to generate a five amino acid C-terminal SUMO- proteome as described above (Fig. 1c). The method allows iden- fi tification of SUMO attachment sites under completely native remnant modi cation. This group has compiled all available data fi fl resulting in 7327 SUMOylation sites in 3617 proteins17. Other conditions using the Ub-pro ling work ow by simply substitut- ing WaLP for trypsin. The same sample can be subjected to groups have used similar engineering approaches to express fi mutant SUMOs and identify up to 1000 unique SUMOylation analysis of both the Ub- and SUMO-modi ed proteomes simply 15,16,18–20 by digesting the sample with either trypsin or WaLP, respectively. sites upon induction of cell stress . While these methods fi have proved effective in mapping SUMOylation sites, they all We demonstrate the effectiveness of this parallel identi cation of require exogenous expression of mutant version of SUMO, which ubiquitylation and SUMOylation sites in cells treated with 2 NATURE COMMUNICATIONS | 8: 1171 | DOI: 10.1038/s41467-017-01271-3 | www.nature.com/naturecommunications NATURE COMMUNICATIONS | DOI: 10.1038/s41467-017-01271-3 ARTICLE proteasome inhibitors. We provide the description a unique sample. This method can be simply applied to any sample, method of identifying proteins containing individual lysine resi- including human tissues samples, to identify endogenous dues that are modified by both SUMO and Ub from the same SUMOylation sites. a Hendricks et al. (7710) This study (1209) 370 826 6661 679 Phosphosite Plus (780) b Precursor m/z 632.3327, z=2 50 b2 b3 b4 b5 b7 b8 b9 b9[+2] y9 y7 y6 y5 y4 y3 y2 y7 y6 25 b8 y4 b9-H2O b3 b7 b4 y5 y9 b5-H O y3 2 y2-H2O y2 b9 b2 m/z 200 300 400 500 600 700 800 900 1000 1100 1200 m/z c Precursor m/z 703.8680, z=2 100 b3 b4 b5 b6 b7 b8 b9 b6 y10 y9y8 y7 y6 y5 y3 y5 b7-NH y9 b3 3 50 y6 y7 b5 y9-H O y8 2 y9-NH 3 b9 b8 y10-NH3 y3-H O b3 b4 2 b7 -H2O y3-NH3 m/z 200 300 400 500 600 700 800 900 1000 1100 1200 1300 1400 1500 m/z Fig. 2 Summary of SUMOylation site identifications from this study and comparison with previous studies. a Venn diagram showing overlap between the 1209 SUMO sites identified in this study from both Hela and HCT116 cell lines (blue) and all SUMO modifications from either Hendriks et al.