NEDD8 is an evolutionarily conserved 8 kD protein that is closely related to ubiquitin and that can be conjugated like ubiquitin to specific lysine residues of target proteins in eukaryotes. In contrast to ubiquitin, for which a broad range of substrate proteins is known, only a very limited number of NEDD8 target proteins have been identified to date. Best understood, and also evolutionarily conserved, is the NEDD8-modification (neddylation) of cullins, core subunits of the cullin-RING-type E3 ubiquitin ligases that promote the poly-ubiquitylation of degradation targets in eukaryotes. Here, we show that ML3 is a NEDD8- as well as ubiquitin-modified protein in Arabidopsis thaliana and examine the functional role of ML3 in the plant cell. Our analysis indicates that ML3 resides in the vacuole as well as in ER bodies. ER bodies are Brassicales-specific ER-derived organelles and, similarly to other ER body proteins, ML3 orthologues can only be identified in this order of flowering plants. ML3 gene expression is promoted by wounding as well as by the phytohormone jasmonic acid and repressed by ethylene, signals that are known to induce and repress ER body formation, respectively. Furthermore, ML3 protein abundance is dependent on NAI1, a master regulator of ER body formation in Arabidopsis thaliana. The regulation of ML3 expression and the localization of ML3 in ER bodies and the vacuole is in agreement with a demonstrated importance of ML3 in the defense to herbivore attack. Here, we extent the spectrum of ML3 biological functions by demonstrating a role in response to microbial pathogens.