Biochemical Characterization of the Activity and Specificity of ULP1 Family Members

The reversible posttranslational modification, SUMO, modulates the activity of a diverse set of target proteins. Conjugation machinery charges the processed-SUMO so that it can be linked via an isopeptide bond to a target protein. The removal of SUMO moieties from conjugated proteins by isopeptidases regenerates pools of processed-SUMOs and unmodified target proteins. Yeast Ulp1 is the founding member of a growing family of these isopeptidases, or deSUMOylating enzymes. Another Ulp1, XopD from Xanthomonas campestris pv. vesicatoria, is expressed as a secreted virulence factor by this plant bacterial pathogen. In vitro peptidase assays were performed to characterize the activity of XopD and showed that XopD can process plant SUMOs, but is unable to process mammalian SUMOs. Enzymatic studies further demonstrated that XopD functions as a cysteine protease. Isopeptide bond cleavage was demonstrated by the ability of XopD to cleave the plant SUMO moiety from in vitro SUMOylated RanGAP. These studies showed that XopD has a rigid SUMO substrate specificity in contrast to yeast Ulp1, which is a more promiscuous protease in its choice of SUMO substrate. To further investigate the SUMO substrate specificity of XopD the crystal structures of the catalytic core of XopD and XopD C470A were determined. Although the catalytic core residues align between the XopD and Ulp1 structures, there are apparent structural differences that may account for the differences in choice of SUMO substrate. Mutational studies on tomato SUMO and yeast Smt3 identified some key residues in the enzyme-substrate recognition, but ultimately showed that there are many regions in the SUMO proteins that are accounting for the enzyme's ability to recognize certain substrates. Experiments with the Arabidopsis thaliana family of SUMOs and ULP1s identified varying specificity of the AtULP1s. The evolutionarily conserved SUMO conjugating proteins, E1 and E2, recognize a diverse set of AtSUMO proteins using them to modify protein substrates. By contrast, the deSUMOylating enzymes differentially recognize the Arabidopsis SUMO proteins, resulting in specificity of the de-conjugating machinery. Therefore, the SUMO proteins in this signaling system have evolved to contain information that allows for both redundancy with the conjugation system and the diversity with deconjugating enzymes.