Proteome-wide identification of SUMO modification sites by mass spectrometry

TY - JOUR

T1 - Proteome-wide identification of SUMO modification sites by mass spectrometry

AU - Tammsalu, Triin

AU - Matic, Ivan

AU - Jaffray, Ellis G.

AU - Ibrahim, Adel F. M.

AU - Tatham, Michael H.

AU - Hay, Ronald T.

PY - 2015/9

Y1 - 2015/9

N2 - The protein called 'small ubiquitin-like modifier' (SUMO) is post-translationally linked to target proteins at the η -amino group of lysine residues. This 'SUMOylation' alters the behavior of the target protein, a change that is utilized to regulate diverse cellular processes. Understanding the target-specific consequences of SUMO modification requires knowledge of the location of conjugation sites, and we have developed a straightforward protocol for the proteome-wide identification of SUMO modification sites using mass spectrometry (MS). The approach described herein requires the expression of a mutant form of SUMO, in which the residue preceding the C-terminal Gly-Gly (diGly) is replaced with a lysine (SUMO KGG). Digestion of SUMO KGG protein conjugates with endoproteinase Lys-C yields a diGly motif attached to target lysines. Peptides containing this adduct are enriched using a diGly-Lys (K-η -GG)-specific antibody and identified by MS. This diGly signature is characteristic of SUMO KGG conjugation alone, as no other ubiquitin-like protein (Ubl) yields this adduct upon Lys-C digestion. We have demonstrated the utility of the approach in SUMOylation studies, but, in principle, it may be adapted for the site-specific identification of proteins modified by any Ubl. Starting from cell lysis, this protocol can be completed in ∼5 d.

AB - The protein called 'small ubiquitin-like modifier' (SUMO) is post-translationally linked to target proteins at the η -amino group of lysine residues. This 'SUMOylation' alters the behavior of the target protein, a change that is utilized to regulate diverse cellular processes. Understanding the target-specific consequences of SUMO modification requires knowledge of the location of conjugation sites, and we have developed a straightforward protocol for the proteome-wide identification of SUMO modification sites using mass spectrometry (MS). The approach described herein requires the expression of a mutant form of SUMO, in which the residue preceding the C-terminal Gly-Gly (diGly) is replaced with a lysine (SUMO KGG). Digestion of SUMO KGG protein conjugates with endoproteinase Lys-C yields a diGly motif attached to target lysines. Peptides containing this adduct are enriched using a diGly-Lys (K-η -GG)-specific antibody and identified by MS. This diGly signature is characteristic of SUMO KGG conjugation alone, as no other ubiquitin-like protein (Ubl) yields this adduct upon Lys-C digestion. We have demonstrated the utility of the approach in SUMOylation studies, but, in principle, it may be adapted for the site-specific identification of proteins modified by any Ubl. Starting from cell lysis, this protocol can be completed in ∼5 d.

UR - https://www.scopus.com/pages/publications/84940540249

U2 - 10.1038/nprot.2015.095

DO - 10.1038/nprot.2015.095

M3 - Article

C2 - 26292070

AN - SCOPUS:84940540249

SN - 1754-2189

VL - 10

SP - 1374

EP - 1388

JO - Nature Protocols

JF - Nature Protocols

IS - 9

ER -