Ubiquitin-specific Protease 11 (USP11) Deubiquitinates Hybrid Small Ubiquitin-like Modifier (SUMO)-Ubiquitin Chains to Counteract RING Finger Protein 4 (RNF4)

Ivo A Hendriks,Joost Schimmel,Karolin Eifler,Jesper V Olsen,Alfred C.O Vertegaal

doi:10.1074/jbc.m114.618132

Abstract

Ring finger protein 4 (RNF4) is a SUMO-targeted ubiquitin E3 ligase with a pivotal function in the DNA damage response (DDR). SUMO interaction motifs (SIMs) in the N-terminal part of RNF4 tightly bind to SUMO polymers, and RNF4 can ubiquitinate these polymers in vitro. Using a proteomic approach, we identified the deubiquitinating enzyme ubiquitin-specific protease 11 (USP11), a known DDR-component, as a functional interactor of RNF4. USP11 can deubiquitinate hybrid SUMO-ubiquitin chains to counteract RNF4. SUMO-enriched nuclear bodies are stabilized by USP11, which functions downstream of RNF4 as a counterbalancing factor. In response to DNA damage induced by methyl methanesulfonate, USP11 could counteract RNF4 to inhibit the dissolution of nuclear bodies. Thus, we provide novel insight into cross-talk between ubiquitin and SUMO and uncover USP11 and RNF4 as a balanced SUMO-targeted ubiquitin ligase/protease pair with a role in the DDR.

Highlights

Ring finger protein 4 (RNF4) is a ubiquitin ligase targeted to SUMOylated proteins
These SUMOylated targets are ubiquitinated by RNF4, which can lead to the degradation of these proteins by the proteasome [26, 50, 51]
Using an unbiased proteomic approach, we have identified ubiquitin-specific protease 11 (USP11) as a ubiquitin protease to co-purify with RNF4, with the ability to process hybrid SUMO-ubiquitin polymers

Summary

Background

RNF4 is a ubiquitin ligase targeted to SUMOylated proteins. Results: USP11 co-purified with RNF4 and can remove ubiquitin polymers attached to SUMO chains. Ring finger protein 4 (RNF4) is a SUMO-targeted ubiquitin E3 ligase with a pivotal function in the DNA damage response (DDR). Analogous to the ubiquitin system, a set of E1, E2, and E3 enzymes mediates the conjugation of SUMO to target proteins, and a set of SUMO-specific proteases is responsible for the reversible nature of this post-translational modification [2, 3]. The SUMO system and the ubiquitin system are linked together via the SUMO-targeted ubiquitin ligases (STUbLs), responsible for ubiquitinating SUMOylated proteins They were first identified in Schizosaccharomyces pombe as Rfp and Rfp and in Saccharomyces cerevisiae as the Slx5-Slx complex [23,24,25]. Around 100 mammalian deubiquitinating enzymes exist, with different substrate specificity, subcellular localization, and protein-protein interactions [36, 37] It is not clear how the activity of the STUbLs is balanced. We report the identification of a ubiquitin-specific protease with the ability to counteract RNF4

Experimental Procedures

Results

Discussion