USP13 antagonizes gp78 to maintain functionality of a chaperone in ER-associated degradation

Abstract

Physiological adaptation to proteotoxic stress in the endoplasmic reticulum (ER) requires retrotranslocation of misfolded proteins into the cytoplasm for ubiquitination and elimination by ER-associated degradation (ERAD). A surprising paradox emerging from recent studies is that ubiquitin ligases (E3s) and deubiquitinases (DUBs), enzymes with opposing activities, can both promote ERAD. Here we demonstrate that the ERAD E3 gp78 can ubiquitinate not only ERAD substrates, but also the machinery protein Ubl4A, a key component of the Bag6 chaperone complex. Remarkably, instead of targeting Ubl4A for degradation, polyubiquitination is associated with irreversible proteolytic processing and inactivation of Bag6. Importantly, we identify USP13 as a gp78-associated DUB that eliminates ubiquitin conjugates from Ubl4A to maintain the functionality of Bag6. Our study reveals an unexpected paradigm in which a DUB prevents undesired ubiquitination to sharpen substrate specificity for an associated ubiquitin ligase partner and to promote ER quality control.Cells make proteins inside a structure called the endoplasmic reticulum. However, some of these proteins cannot fold into the correct shape, so cells rely on a process called the ERAD pathway to degrade and eliminate these faulty proteins. First, however, the misfolded proteins must be moved from the endoplasmic reticulum to the main body of the cell (the cytosol).The process by which the misfolded proteins are moved through the membrane that encloses the endoplasmic reticulum is complex, with ‘ERAD machinery proteins’ playing an important role. Among them, a series of enzymes called E3 ligases ‘tag’ the faulty proteins with a small protein called ubiquitin, and a complex called the proteasome then recognizes and degrades those proteins that have been tagged with ubiquitin. However, it is not clear why the E3 ligases that tag the misfolded proteins with ubiquitin don’t also tag the machinery proteins that from complexes with the faulty proteins.Now Liu et al. have used a combination of biochemical and genetic tools to shed light on this puzzle by studying the interaction of gp78—which is an E3 ligase—and USP13, an enzyme that opposes the actions of the E3 ligases by removing ubiquitin. Liu et al. showed that gp78 can indeed tag certain machinery proteins with ubiquitin, which would stop the removal of misfolded proteins from the endoplasmic reticulum. However, USP13 opposed the action of gp78, thus allowing the removal to continue.It has been known for some time that enzymes with opposing roles—the addition and removal of ubiquitin—can work together, but the biological significance of this phenomenon was not fully understood. The work of Liu et al. suggests that USP13 makes the elimination of misfolded proteins more efficient by ensuring that gp78 only tags those proteins that are misfolded: it does this by removing ubiquitin from proteins that should not have been tagged. A similar phenomenon is known to occur in genetics during DNA replication, with the enzyme complex that replicates the DNA including an enzyme that performs a proofreading role.