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.diverse functions | post-translational modification | small protein modifiers I n eukaryotes, posttranslational modification by the attachment of small ubiquitin-like modifier (SUMO) alters the activity of many substrate proteins. In yeast and mammalian cells, this regulatory mechanism is involved in diverse cellular processes, including nuclear-cytoplasmic shuttling, DNA and chromatin activities, transcriptional regulation, RNA transport, proteinprotein interaction, and various other biological processes (1-5). Many of the SUMO substrate proteins involved in these processes were identified by systematic screening (6-13). Despite genetic demonstration of the importance of SUMOylation in plants, few SUMO substrates have been identified, and the extent to which these are conserved with other eukyarotes is unclear. Here we describe a proteome-wide identification of SUMO substrates in Arabidopsis.The enzymatic activities required for protein SUMOylation are well characterized. Three enzymes mediate covalent attachment of SUMO to substrate proteins: SUMO-activating enzyme (SAE or E1), SUMO-conjugating enzyme (SCE or E2), and SUMO ligase (E3) (14,15). SAE, a heterodimer (SAE1 and SAE2), forms a thioester bond between a reactive cysteine residue in its large subunit (SAE2) and the C-terminal end of SUMO. SCE binds both SUMO and the potential substrate and mediates the transfer and conjugation of SUMO from SAE to the substrate. Specific residues in SCE interact with a sequence motif present in the substrate called the SUMO attachment site (SAS) (16). A SAS consensus sequence (ΨKXE/D) consists of a lysine residue to which SUMO is attached (position 2), flanked by a hydro...