Aims
Ubiquitylation is reversibly regulated by ubiquitin ligases (E3s) and deubiquitylases (DUBs). DUBs prevent excessive ubiquitylation and protect substrates from degradation. Ubiquitin molecules are linked to one another to form eight different types of polyubiquitin chains, each exhibiting diverse functional properties. In addition to homotypic ubiquitin chains, branched chains containing different linkage types have emerged as potent signals for proteasomal degradation. In particular, K29/K48-branched ubiquitin chains have been suggested to promote substrates degradation. In this study, we focused on TRIP12, a K29 linkage-specific E3 ligase, and searched for novel targets.
Results
We identified the deubiquitylase OTUD5. OTUD5 was modified by both TRIP12 and UBR5, a K48 linkage-specific E3 ligase. We demonstrated that OTUD5, as a DUB, cleaves K48 linkages but does not affect K29 linkages; consequently, K29/K48-branched ubiquitin chains can overcome OTUD5’s deubiquitylating activity. Together with cell-based analyses, these findings revealed that K29 linkages antagonize DUB activity and promote substrate degradation. We also found that this degradation mechanism applies to other proteasomal substrates protected by DUBs.
Furthermore, to investigate the biological significance of TRIP12–OTUD5 regulation, we performed RNA-seq and found a connection with inflammation-related genes. We revealed that TRIP12 and OTUD5 reciprocally regulate NF-κB signaling.
Conclusion
In conclusion, our results propose a novel concept: the combination of “K29 linkages resistant to deubiquitination” and “K48 linkages as degradation signals” promotes efficient degradation of substrates protected by deubiquitylation.