Proteome-wide screens for small ubiquitin-like modifier (SUMO) substrates identify Arabidopsis proteins implicated in diverse biological processes

Abstract

Covalent modification of proteins by small ubiquitin-like modifier (SUMO) regulates various cellular activities in yeast and mammalian cells. In Arabidopsis, inactivation of genes encoding SUMO or SUMO-conjugation enzymes is lethal, emphasizing the importance of SUMOylation in plant development. Despite this, little is known about SUMO targets in plants. Here we identified 238 Arabidopsis proteins as potential SUMO substrates because they interacted with SUMO-conjugating enzyme and/or SUMO protease (ESD4) in the yeast two-hybrid system. Compared with the whole Arabidopsis proteome, the identified proteins were strongly enriched for those containing high-probability consensus SUMO attachment sites, further supporting that they are true SUMO substrates. A high-throughput assay was developed in Escherichia coli and used to test the SUMOylation of 56% of these proteins. More than 92% of the proteins tested were SUMOylated in this assay by at least one SUMO isoform. Furthermore, ADA2b, an ESD4 interactor that was SUMOylated in the E. coli system, also was shown to be SUMOylated in Arabidopsis. The identified SUMO substrates are involved in a wide range of plant processes, many of which were not previously known to involve SUMOylation. These proteins provide a basis for exploring the function of SUMOylation in the regulation of diverse processes in Arabidopsis.