Localized K63 ubiquitin signaling is regulated by VCP/p97 during oxidative stress

ABSTRACT: Under stress conditions, cells reprogram their molecular machineries to mitigate damage and promote survival. Ubiquitin signaling is globally increased during oxidative stress, controlling protein fate and supporting stress defenses at several subcellular compartments. However, the rules driving subcellular ubiquitin localization to promote these concerted response mechanisms remain understudied. Here, we show that K63-linked ubiquitin chains, known to promote proteasome-independent pathways, accumulate primarily in non-cytosolic compartments during oxidative stress induced by sodium arsenite in mammalian cells. Subcellular ubiquitin proteomic analyses of non-cytosolic compartments revealed thousands of proteins ubiquitinated during oxidative stress and involved in pathways related to immune signaling and translation control. Moreover, subcellular proteome analyses also revealed proteins that are recruited to non-cytosolic compartments under stress, including a significant enrichment of helper ubiquitin-binding adaptors of the ATPase VCP that processes ubiquitinated substrates for downstream signaling. We further show that VCP recruitment to non-cytosolic compartments under arsenite stress occurs in a ubiquitin-dependent manner mediated by its adaptor NPLOC4. Additionally, we show that VCP and NPLOC4 activities are critical to sustain low levels of non-cytosolic K63-linked ubiquitin chains, supporting a cyclical model of ubiquitin conjugation and removal that is disrupted by cellular exposure to reactive oxygen species. This work deepens our understanding of the role of localized ubiquitin and VCP signaling in the basic mechanisms of stress response and highlights new pathways and molecular players that are essential to reshape the composition and function of the human subcellular proteome under dynamic environments.

INSTRUMENT(S): Orbitrap Fusion Lumos, Orbitrap Astral, Orbitrap Exploris 480

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Gustavo Monteiro Silva  

PROVIDER: MSV000094932 | MassIVE | Tue Jun 04 17:37:00 BST 2024

SECONDARY ACCESSION(S): PXD052838

REPOSITORIES: MassIVE