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Summary The formation of insoluble inclusions in the cytosol and nucleus is associated with impaired protein homeostasis and is a hallmark of several neurodegenerative diseases. Due to the absence of the autophagic machinery, nuclear protein aggregates require a solubilization step preceding degradation by the 26S proteasome. Using yeast, we identify a nuclear protein quality control pathway required for the clearance of protein aggregates. The nuclear J-domain protein Apj1 supports protein disaggregation together with Hsp70 but independent of the canonical disaggregase Hsp104. Disaggregation mediated by Apj1/Hsp70 promotes turnover rather than refolding. A loss of Apj1 activity uncouples disaggregation from proteasomal turnover, resulting in accumulation of toxic soluble protein species. Endogenous substrates of the Apj1/Hsp70 pathway include both nuclear and cytoplasmic proteins, which aggregate inside the nucleus upon proteotoxic stress. These findings demonstrate the coordinated activity of the Apj1/Hsp70 disaggregation system with the 26S proteasome in facilitating the clearance of toxic inclusions inside the nucleus., Graphical Abstract, Highlights • Nuclear Hsp40 Apj1 mediates proteolytic clearance of intra-nuclear protein inclusions • Apj1 supports Hsp104-independent disaggregation in vitro and in vivo • Apj1 competes with Hsp104 in disaggregation, supporting turnover instead of refolding • Inside the nucleus, Apj1 functions in quality control of nuclear and cytoplasmic proteins, den Brave et al. show that the Hsp40 chaperone Apj1 promotes Hsp70-dependent disaggregation of intra-nuclear protein aggregates. This Hsp104-independent disaggregation activity promotes proteolytic turnover and competes with substrate refolding. Co-ordinated disaggregation with turnover protects against potential toxicity of solubilized proteins.

Summary The AAA+ ATPase VCP regulates the extraction of SUMO and ubiquitin-modified DNA replication factors from chromatin. We have previously described that active DNA synthesis is associated with a SUMO-high/ubiquitin-low environment governed by the deubiquitylase USP7. Here, we unveil a functional cooperation between USP7 and VCP in DNA replication, which is conserved from Caenorhabditis elegans to mammals. The role of VCP in chromatin is defined by its cofactor FAF1, which facilitates the extraction of SUMOylated and ubiquitylated proteins that accumulate after the block of DNA replication in the absence of USP7. The inactivation of USP7 and FAF1 is synthetically lethal both in C. elegans and mammalian cells. In addition, USP7 and VCP inhibitors display synergistic toxicity supporting a functional link between deubiquitylation and extraction of chromatin-bound proteins. Our results suggest that USP7 and VCPFAF1 facilitate DNA replication by controlling the balance of SUMO/Ubiquitin-modified DNA replication factors on chromatin., Graphical abstract, Highlights • VCP and USP7 control the SUMO/ubiquitin landscape during DNA replication • VCP is recruited by FAF1 to chromatin-associated SUMO/ubiquitylated proteins • FAF1 recognizes both SUMO and ubiquitin on target proteins • The control of DNA replication by VCPFAF1 and USP7 is evolutionarily conserved, Chromatin at DNA replication forks is SUMO-rich and ubiquitin-poor. Franz et al. report that FAF1 is a dual reader of SUMO and ubiquitin targeting VCP to extract DNA replication factors from chromatin in C. elegans and human cells. Together with USP7, VCPFAF1 controls the SUMO/ubiquitin landscape during replication.