In Vivo Ubiquitin Linkage-type Analysis Reveals that the Cdc48-Rad23/Dsk2 Axis Contributes to K48-Linked Chain Specificity of the Proteasome

Abstract

Ubiquitin-binding domain (UBD) proteins regulate numerous cellular processes, but their specificities toward ubiquitin chain types in cells remain obscure. Here, we perform a quantitative proteomic analysis of ubiquitin linkage-type selectivity of 14 UBD proteins and the proteasome in yeast. We find that K48-linked chains are directed to proteasomal degradation through selectivity of the Cdc48 cofactor Npl4. Mutating Cdc48 results in decreased selectivity, and lacking Rad23/Dsk2 abolishes interactions between ubiquitylated substrates and the proteasome. Among them, only Npl4 has K48 chain specificity in vitro. Thus, the Cdc48 complex functions as a K48 linkage-specifying factor upstream of Rad23/Dsk2 for proteasomal degradation. On the other hand, K63 chains are utilized in endocytic pathways, whereas both K48 and K63 chains are found in the MVB and autophagic pathways. Collectively, our results provide an overall picture of the ubiquitin network via UBD proteins and identify the Cdc48-Rad23/Dsk2 axis as a major route to the proteasome.

Global proteomics ofUbqln2-based murine models of ALS

“…While Dsk2 has been implicated in the large-scale proteasomal degradation of ubiquitinated protein (Funakoshi et al, 2002;Saeki et al, 2002;Tsuchiya et al, 2017), Ubqlns have been implicated in the degradation of specific classes of proteins, most strikingly hydrophobic and/or transmembrane proteins (Suzuki and Kawahara, 2016), aggregates (Hjerpe et al, 2016), and mislocalized mitochondrial proteins (Itakura et al, 2016;Whiteley et al, 2017). While these reports implicate different potential functions of Ubqlns, some of their apparent functional diversity may be due to the multiplicity of Ubqln isoforms.…”

Pleiotropic roles of the ubiquitin-proteasome system during viral propagation

“…Therefore, there are eight possible positions for the second Ub to attach (including the amine group at the N-terminus), and the functional diversity of this modification is expanded by polyubiquitination. The best-characterised K48-linked polyubiquitination is commonly involved in Ub-dependent proteolysis [14]. Other linkage types, such as K63, serve as signals for the regulation of protein endocytosis, sorting, cellular trafficking, and innate immune signalling [15,16].…”

Cytosolic N‐Glycans: Triggers for Ubiquitination Directing Proteasomal and Autophagic Degradation

“…VCP is an ATPase that segregates ubiquitinated substrates from protein complexes or membranes, and its function is best understood in the ERAD pathway . RAD23 contains ubiquitin‐associated (UBA) domains for binding of ubiquitin chains and a ubiquitin‐like (UBL) domain for proteasome association, and functions a shuttling factor between the VCP–NPL4–UFD1 complex and the proteasome . It is unclear whether the deglycosylation activity or some additional function of NGLY1 is necessary for development.…”