Multipotent ubiquitin/ubiquitin-like deconjugation activity of the rhizobial effector NopD

Post-translational modification of proteins by ubiquitin-like modifiers (UbL), such as SUMO, ubiquitin or Nedd8, contribute to regulate most pathways in the cell. Protein modification can be reversed by dedicated UbL deconjugating proteases families. During bacterial infection, a repertoire of effector proteins, including deconjugating proteases, are released to perturb the host cell defense to favor bacterial survival. NopD, an effector protein from rhizobia involved in nodule symbiosis in legumes, possesses deSUMOylation, and unexpectedly, deubiquitination and deNeddylation activities. Here we show two crystal structures of Bradyrhizobium NopD in complex with either Arabidopsis SUMO2 and ubiquitin at 1.50 or 1.94 [A], respectively. Despite their low sequence identity, SUMO and ubiquitin interact with a similar NopD interface by means of a unique loop insertion in the NopD sequence. Biochemical and infiltrations in tobacco leaves reveal specific residues that discriminate between deubiquitination and deSUMOylation. These unusual multiple deconjugating activities against SUMO, ubiquitin and Nedd8, represent a paradigmatic example of an optimized protease to perturb distinct UbL post-translational modifications during host cell infection. Significance StatementDuring bacterial infection, including rhizobia symbiosis in legume plants to fix atmospheric nitrogen, a set of effector proteins, such as ubiquitin/ubiquitin-like deconjugating proteases, are released to perturb the host cell defense to favor bacterial survival. We have discovered that the rhizobial effector protein, NopD, encompasses triple deconjugation activities against SUMO, ubiquitin and Nedd8. Structural analysis of NopD in complex with SUMO and ubiquitin reveals the presence of a loop insertion in the protease-substrate interface to allow this multiple substrate binding capability. Such unusual deconjugating activities in NopD for ubiquitin, SUMO and Nedd8 modifiers, represent a paradigmatic example of an optimized protease domain to perturb distinct UbL post-translational modifications during host cell infection.