Slx5/Slx8‐dependent ubiquitin hotspots on chromatin contribute to stress tolerance

Abstract

Chromatin is a highly regulated environment, and protein association with chromatin is often controlled by post‐translational modifications and the corresponding enzymatic machinery. Specifically, SUMO ‐targeted ubiquitin ligases ( STU bLs) have emerged as key players in nuclear quality control, genome maintenance, and transcription. However, how STU bLs select specific substrates among myriads of SUMO ylated proteins on chromatin remains unclear. Here, we reveal a remarkable co‐localization of the budding yeast STU bL Slx5/Slx8 and ubiquitin at seven genomic loci that we term “ubiquitin hotspots”. Ubiquitylation at these sites depends on Slx5/Slx8 and protein turnover on the Cdc48 segregase. We identify the transcription factor‐like Ymr111c/Euc1 to associate with these sites and to be a critical determinant of ubiquitylation. Euc1 specifically targets Slx5/Slx8 to ubiquitin hotspots via bipartite binding of Slx5 that involves the Slx5 SUMO ‐interacting motifs and an additional, novel substrate recognition domain. Interestingly, the Euc1‐ubiquitin hotspot pathway acts redundantly with chromatin modifiers of the H2A.Z and Rpd3L pathways in specific stress responses. Thus, our data suggest that STU bL‐dependent ubiquitin hotspots shape chromatin during stress adaptation.

A SUMO-dependent pathway controls elongating RNA Polymerase II upon UV-induced damage

“…SUMOylated Rpb1 might serve as a recruiting factor for the STUbL Slx5-Slx8, but then target RNAPII subunits other than Rpb1 would become ubiquitylated, potentially explaining why no STUbL-dependent ubiquitylation was detected for Rpb1. STUbL-dependent ubiquitylation of proteins that are in complex with the SUMOylated STUbL-recruitment factor have been suggested in other cases and importantly for RNAPIII 55,59,60 giving precedence for this model. In contrast, previous work has shown that specifically Rpb1, but not other subunits become destabilized upon UV treatment 61 .…”

“…Such a sequential mechanism allows the opportunity to differentially recruit proteins containing ubiquitin-and/or SUMO-interacting motifs. For instance, Cdc48 together with its co-factor Ufd1 were shown to target both ubiquitylated and SUMOylated proteins and, strikingly, also STUbL substrates 46,60,74 . SUMOylation of stalled RNAPII might therefore be a first line of defense and help in recruiting repair factors.…”

“…SUMOylation of stalled RNAPII might therefore be a first line of defense and help in recruiting repair factors. Prolonged stalling may require additional means and involve Slx5-Slx8 and Cdc48, perhaps to segregate RNAPII from chromatin similar to its role in the release of chromatin-associated proteins or complexes 55,60,75,76 .…”

Nuclear Ubiquitin-Proteasome Pathways in Proteostasis Maintenance

“…The best characterized STUbLs are the yeast Slx5/Slx8 heterodimer and the mammalian RNF4 and RNF111. A recent study showed that yeast Slx5 and Slx8 are enriched at seven genomic loci termed “ubiquitin hotspots” [ 101 ]. Slx5/Slx8 are recruited to the ubiquitin hotspots by the sumoylated transcription factor-like protein Euc1, which is specifically bound to the sequence motif within these sites [ 101 ].…”

“…A recent study showed that yeast Slx5 and Slx8 are enriched at seven genomic loci termed “ubiquitin hotspots” [ 101 ]. Slx5/Slx8 are recruited to the ubiquitin hotspots by the sumoylated transcription factor-like protein Euc1, which is specifically bound to the sequence motif within these sites [ 101 ]. Ubiquitin signal at these loci was dependent on Slx5/Slx8, and was enriched in a cdc48 -mutant, indicating that Cdc48-complex is required to remove ubiquitinated proteins from the ubiquitin hotspots.…”