A new family of eukaryotic and bacterial deubiquitinases spreading and diversifying through transposons and horizontal gene transfer

Abstract Several distinct families of eukaryotic deubiquitinases (DUBs) regulate various aspects of ubiquitin signaling. Apart from one metalloenzyme family, six classes of eukaryotic papain-fold cysteine proteases are known to have DUB activity. A seventh cysteine-based DUB class is found in intracellular bacteria, which use DUB effectors to evade the ubiquitin-based defense response. Here, we report on the presence of an additional DUB class broadly distributed in eukaryotes and several bacteria. So far, the only known members of this family are the large tegument proteins of α/β/γ herpesviruses, which act as relatively unspecific deubiquitinases and deneddylases attached to the outer face of the viral capsid. By using a bioinformatical screen, we identified distant homologs of this family in transposons of vertebrates and invertebrates, in agaricomycete fungi, insects, nematodes, cnidaria, protists and selected intracellular bacteria. Members of this VTD (Viral tegument-like DUB) family use an atypical Cys-Asp-His catalytic triad to cleave ubiquitin chains. Some activities resemble the viral tegument DUBs in preferring K48-linked ubiquitin chains and also cleaving NEDD8, while other members are highly specific for K6- or K63-linked ubiquitin chains. Judging by the crystal structures of K48- and K6-specific members, the subfamilies differ considerably in their ubiquitin recognition mode. Our analyses suggest that this deubiquitinase family evolved from YopT/HopN-like non-DUB proteases and was co-opted early by DNA transposons, helping the spread of this family. In several independent events, the deubiquitinase domain of these transposons was ‘domesticated’ by various taxa, giving rise e.g. to the Drosophila male sterile (3)76Ca gene and several nematode genes with male-specific expression.