Valosin-containing protein (VCP)–Adaptor Interactions are Exceptionally Dynamic and Subject to Differential Modulation by a VCP Inhibitor

Abstract

Protein quality control (PQC) plays an important role in stemming neurodegenerative diseases and is essential for the growth of some cancers. Valosin-containing protein (VCP)/p97 plays a pivotal role in multiple PQC pathways by interacting with numerous adaptors that link VCP to specific PQC pathways and substrates and influence the post-translational modification state of substrates. However, our poor understanding of the specificity and architecture of the adaptors, and the dynamic properties of their interactions with VCP hinders our understanding of fundamental features of PQC and how modulation of VCP activity can best be exploited therapeutically. In this study we use multiple mass spectrometry-based proteomic approaches combined with biophysical studies to characterize the interaction of adaptors with VCP. Our results reveal that most VCP-adaptor interactions are characterized by rapid dynamics that in some cases are modulated by the VCP inhibitor NMS873. These findings have significant implications for both the regulation of VCP function and the impact of VCP inhibition on different VCP-adaptor complexes.

Wnt-Dependent Inactivation of the Groucho/TLE Co-repressor by the HECT E3 Ubiquitin Ligase Hyd/UBR5

“…Our evidence based on dominant-negative VCP/p97 and two distinct VCP/p97 inhibitors ( Figure 6 ) implicates this ATPase in the Wnt-dependent inactivation of Ub-TLE. Intriguingly, a recent proteomic screen for NMS-873-induced VCP/p97-associated proteins identified TLE1 and TLE3 as the only Wnt signaling components, along with VCP/p97 adaptors and other putative substrates ( Xue et al., 2016 ), consistent with our notion of Groucho/TLE as a substrate of this ATPase. VCP/p97 regulates the folding of ubiquitylated proteins, to promote their segregation from large structures, such as endomembranes, and also from large protein complexes, including DNA repair and chromatin complexes ( Dantuma et al., 2014 , Xia et al., 2016 ).…”

VCP /p97 cooperates with YOD 1, UBXD 1 and PLAA to drive clearance of ruptured lysosomes by autophagy

“…We next asked whether they can bind p97 at the same time and therefore first analyzed proteins co‐immunoprecipitating with UBXD1. Because p97‐cofactor complexes can dissociate quickly after cell lysis (Xue et al , ), we used stable cells expressing the ATPase‐deficient trapping mutant p97‐E578Q (p97‐EQ) at near endogenous levels in addition to p97‐wt cells. Indeed, UBXD1 co‐precipitated p97 and also co‐isolated PLAA in the p97‐EQ background (Fig D).…”

Composition and Regulation of the Cellular Repertoire of SCF Ubiquitin Ligases

“…It is unclear whether post-lysis SR exchange is a problem for other CRL complexes, but we suspect that it is considering that Cand1 binds other cullins (Bennett et al, 2010; Chua et al, 2011; Liu et al, 2002; Min et al, 2003; Zheng et al, 2002). Although SR exchange is a facilitated process, in the case of the p97 network rapid equilibration of cofactors is mediated by their high intrinsic k on and k off (Xue et al, 2016). This problem is likely to be widespread and may affect other heteromeric enzymes that undergo dynamic remodeling, like protein phosphatase 2A (Kong et al, 2009).…”