SUMO-activated target traps (SATTs) enable the identification of a comprehensive E3-specific SUMO proteome

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Abstract

Ubiquitin and ubiquitin-like conjugation cascades consist of dedicated E1, E2, and E3 enzymes with E3s providing substrate specificity. Mass spectrometry–based approaches have enabled the identification of more than 6500 SUMO2/3 target proteins. The limited number of SUMO E3s provides the unique opportunity to systematically study E3 substrate wiring. We developed SUMO-activated target traps (SATTs) and systematically identified substrates for eight different SUMO E3s, PIAS1, PIAS2, PIAS3, PIAS4, NSMCE2, ZNF451, LAZSUL (ZNF451-3), and ZMIZ2. SATTs enabled us to identify 427 SUMO1 and 961 SUMO2/3 targets in an E3-specific manner. We found pronounced E3 substrate preference. Quantitative proteomics enabled us to measure substrate specificity of E3s, quantified using the SATT index. Furthermore, we developed the Polar SATTs web-based tool to browse the dataset in an interactive manner. Overall, we uncover E3-to-target wiring of 1388 SUMO substrates, highlighting unique and overlapping sets of substrates for eight different SUMO E3 ligases.

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Salas-Lloret, D., Jansen, N. S., Nagamalleswari, E., van der Meulen, C., Gracheva, E., de Ru, A. H., … González-Prieto, R. (2023). SUMO-activated target traps (SATTs) enable the identification of a comprehensive E3-specific SUMO proteome. Science Advances, 9(31). https://doi.org/10.1126/sciadv.adh2073

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