Bacterial clippases shift ubiquitin

Ubiquitination, a crucial post-translational modification in eukaryotic cells, has a pivotal role in the regulation of protein function, by either inducing protein degradation or altering protein activity. This system is subject to stringent regulation and is essential for maintaining cellular homeostasis and immune responses, particularly in identifying and eliminating pathogenic threats. However, intracellular bacteria have evolved sophisticated strategies to subvert the host defense mechanism, including the secretion of deubiquitinase (DUB) effectors that remove ubiquitin marks, thereby interfering with immune signaling and promoting bacterial fitness.

Hermanns et al. identify a family of bacterial DUBs structurally related to eukaryotic Josephin-type DUBs, which exhibit a unique irreversible deubiquitination mechanism. Conventional deubiquitinases and these ubiquitin C-terminal clippases (UCCs) differ in that the former cleave ubiquitin after the C-terminal diGly motif, whereas the latter cleave before this motif, leaving a residual fragment that marks the substrate as irreversibly deubiquitinated. The researchers performed a detailed structural analysis of the substrate-bound clippases and conventional DUBs to determine the observed cleavage shift, which was found to be attributable to distinct ubiquitin orientations. Structural analysis further revealed that UCCs possess a distinctive catalytic architecture that favors irreversible cleavage over the reversible hydrolysis exhibited by Josephin DUBs. This difference is primarily driven by evolutionary shifts in the catalytic pocket, in which the repositioning of key residues enforces a cleavage mechanism that leaves a residual fragment of ubiquitin attached to the substrate, effectively blocking re-ubiquitination.