Concerted Action of the Ubiquitin-Fusion Degradation Protein 1 (Ufd1) and Sumo-Targeted Ubiquitin Ligases (STUbLs) in the DNA-Damage Response

Abstract

In eukaryotes many players in the DNA-damage response (DDR) catalyze protein sumoylation or ubiquitylation. Emphasis has been placed on how these modifications orchestrate the sequential recruitment of repair factors to sites of DNA damage or stalled replication forks. Here, we shed light on a pathway in which sumoylated factors are eliminated through the coupled action of Sumo-targeted ubiquitin ligases (STUbLs) and the ubiquitin-fusion degradation protein 1 (Ufd1). Ufd1 is a subunit of the Cdc48-Ufd1-Npl4 complex implicated in the sorting of ubiquitylated substrates for degradation by the proteasome. We find that in fission yeast, Ufd1 interacts physically and functionally with the Sumo-targeted ubiquitin ligase (STUbL) Rfp1, homologous to human RNF4, and with the Sumo E3 ligase Pli1, homologous to human PIAS1. Deleting a C-terminal domain of Ufd1 that mediates the interaction of Ufd1 with Rfp1, Pli1, and Sumo (ufd1ΔCt 213-342) lead to an accumulation of high-molecular-weight Sumo conjugates and caused severe genomic instabilities. The spectrum of sensitivity of ufd1ΔCt 213-342 cells to genotoxins, the epistatic relationships of ufd1ΔCt 213-342 with mutations in DNA repair factors, and the localization of the repair factor Rad22 in ufd1ΔCt 213-342 cells point to ufd1ΔCt 213-342 cells accumulating aberrant structures during replication that require homologous recombination (HR) for their repair. We present evidence that HR is however often not successful in ufd1ΔCt 213-342 cells and we identify Rad22 as one of the high-molecular-weight conjugates accumulating in the ufd1ΔCt 213-342 mutant consistent with Rad22 being a STUbL/Ufd1 substrate. Suggesting a direct role of Ufd1 in the processing of Sumo-conjugates, Ufd1 formed nuclear foci colocalizing with Sumo during the DDR, and Sumo-conjugates accumulated in foci in the ufd1ΔCt 213-342 mutant. Broader functional relationships between Ufd1 and STUbLs conceivably affect numerous cellular processes beyond the DDR.

Pli1PIAS1 SUMO Ligase Protected by the Nuclear Pore-associated SUMO Protease Ulp1SENP1/2

“…We and others recently proposed a cooperative role for STUbL and Cdc48 (p97) AAA ϩ ATPase in the proteasomal degradation of SUMO conjugates, at a global level (44,45). Consistent with this proposal, mutations in the Cdc48 cofactor Ufd1 (ufd1-1) or in the 19S proteasome regulatory subunit Mts3 (mts3-1) also stabilized Pli1 in nup132⌬ cells (Fig.…”

“…In addition, Cdc48-Ufd1-Npl4 was recently identified as a cofactor for STUbL in managing global SUMO conjugate levels (44,45). However, evidence for a cooperative role in degrading a specific substrate was lacking.…”

“…As in fission yeast (44,45), budding yeast Cdc48 also acts as a SUMO-targeted segregase that removes sumoylated DNA repair factors from chromatin (59). Given this degree of functional conservation, it seems likely that the human STUbL RNF4 and p97 cooperate in the remodeling of chromatin e.g.…”

Ubiquitin-dependent and independent roles of SUMO in proteostasis

“…Yeast Ufd1 exhibits a COOH-terminal SIM motif, which enables a noncovalent interaction between SUMO and the CDC48-Ufd1-Npl4 complex (90). Yeast Ufd1 mutants displayed subnuclear foci of accumulated SUMO-conjugates, indicating a role of Ufd1 in the degradation of SUMOylated proteins (64, 90). Furthermore, the CDC48-Ufd1-Npl4 complex was shown to physically interact with STUbLs (64).…”

“…Yeast Ufd1 mutants displayed subnuclear foci of accumulated SUMO-conjugates, indicating a role of Ufd1 in the degradation of SUMOylated proteins (64, 90). Furthermore, the CDC48-Ufd1-Npl4 complex was shown to physically interact with STUbLs (64). These observations strengthened the idea that STUbL-induced proteasomal targeting of SUMO-conjugates could be facilitated by the segregase activity of CDC48, especially within the chromatin context where proteins might be “stuck” to the DNA and specific forces are needed to extract them.…”