Cdc48 and ubiquilins confer selective anterograde protein sorting and entry into the multivesicular body in yeast

Cdc48/p97 is known primarily for the retrotranslocation of misfolded proteins in endoplasmic reticulum (ER)-associated protein degradation (ERAD). Here we uncover a novel function for both Cdc48 and the conserved ubiquitin-associated/ubiquitin-like ubiquitin receptor (ubiquilin) proteins in yeast (e.g., Ddi1, Dsk2, and Rad23), which deliver ubiquitinated proteins to the proteasome for degradation. We show that Cdc48, its core adaptors Npl4 and Ufd1, and the ubiquilins confer the constitutive anterograde delivery of carboxypeptidase S (Cps1), a membranal hydrolase, to the multivesicular body (MVB) and vacuolar lumen. Cdc48 and Ddi1 act downstream of Rsp5-dependent Cps1 ubiquitination to facilitate the disassembly of insoluble Cps1 oligomers and upstream of ESCRT-0 to facilitate the entry of soluble protein into the MVB. Consequentially, detergent-insoluble Cps1 accumulates in cells bearing mutations in CDC48, DDI1, and all three ubiquilins (ddi1 Delta, dsk2 Delta, rad23 Delta). Thus, Cdc48 and the ubiquilins have ERAD- and proteasome-independent functions in the anterograde delivery of specific proteins to the yeast vacuole for proteolytic activation. As Cdc48/p97 and the ubiquilins are major linkage groups associated with the onset of human neurodegenerative disease (e.g., amytrophic lateral sclerosis, Alzheimer's, and Paget's disease of the bone), there may be a connection between their involvement in anterograde protein sorting and disease pathogenesis.