USP7 and VCPFAF1 define the SUMO/Ubiquitin landscape at the DNA replication fork.

Domenic Pilger,Guillermo de la Vega-Barranco,Pablo Valledor,Antonio Galarreta,Vanesa Lafarga,Emilio Lecona,Patricia Ubieto-Capella,André Franz,Thorsten Hoppe,Fabian den Brave,Oscar Fernandez-Capetillo,Alejandro Fernández-Llorente

doi:10.1016/j.celrep.2021.109819

Abstract

SummaryThe 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.

Highlights

The duplication of genomic information requires an elaborated fine-tuning of multiple protein activities at the chromatin throughout DNA replication to ensure genome integrity (Burgers and Kunkel, 2017; Gaillard et al, 2015; Lecona and FernandezCapetillo, 2014)
Genetic interaction between CDC-48/VCP and MATH33/USP7 Our recent findings showed that CDC-48 regulates the association of DNA replication factors with chromatin in cooperation with its cofactors UFD-1, NPL-4, and UBXN-3 (CDC48UFD-1:NPL-4:UBXN-3) (Mouysset et al, 2008; Franz et al, 2011, 2016)
Depletion of math-33 in cdc-48.1(lf) mutants resulted in decreased embryonic survival (Figure 1B), indicating that the synthetic lethality of math-33(RNAi) in the ubxn-3(lf) mutant is related to its function as a cofactor of CDC-48

Summary

Introduction

The duplication of genomic information requires an elaborated fine-tuning of multiple protein activities at the chromatin throughout DNA replication to ensure genome integrity (Burgers and Kunkel, 2017; Gaillard et al, 2015; Lecona and FernandezCapetillo, 2014). Proteomic analyses of the replisome revealed an overall higher concentration of SUMO compared to low levels of ubiquitin around active replication forks, suggesting that group SUMOylation of replication factors sustains efficient DNA replication (Dungrawala et al, 2015; Lopez-Contreras et al, 2013; Psakhye and Jentsch, 2012) In this context, the modification by SUMO could be restricting the ubiquitylation of replication factors by direct competition on the same lysine residues (Moldovan et al, 2007) or serve as a mark for the timely ubiquitylation of modified proteins by SUMO-targeted ubiquitin ligases (STUbLs) (Tatham et al, 2008; Uzunova et al, 2007). We have recently described that the chromatin-bound SUMO-ubiquitin equilibrium

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