Slx5/Slx8-dependent ubiquitin hotspots on chromatin contribute to stress tolerance in saccharomyces cerevisiae

Chromatin is a tightly controlled cellular environment and protein association with chromatin is often regulated by post-translational modifications (PTMs), including modification with SUMO and ubiquitin. In the last decades, both these modifications and their corresponding enzymatic machineries have emerged as pivotal regulators involved in nuclear quality control, DNA repair and transcriptional regulation. More recently, SUMO-targeted ubiquitin ligases (STUbLs) were discovered to provide an important link between those pathways, as they recognize SUMOylated proteins and catalyze their ubiquitylation. However, many of the physiological functions of STUbLs and how exactly they recognize specific substrates, while SUMOylated proteins are highly prevalent on chromatin, remained elusive. In this study, my analysis of the genome-wide distribution of the yeast STUbL Slx5/Slx8 demonstrates a remarkably specific localization of Slx5/Slx8 to seven loci of strong ubiquitin accumulation, so-called “ubiquitin hotspots”. My data show that Slx5/Slx8 is recruited to ubiquitin hotspots by the uncharacterized transcription factor-like protein Ymr111c/Euc1. Slx5/Slx8 recruitment relies on a bipartite interaction between Ymr111c/Euc1 and Slx5, which involves the Slx5 SUMO-interacting motifs and a novel, uncharacterized substrate recognition domain of Slx5 directly interacting with Ymr111c/Euc1. Importantly, the Euc1–ubiquitin hotspot pathway and Slx5/Slx8 are required for the cellular response to various stresses like temperature shifts, in particular when general gene expression control is impaired by mutation of members of the H2A.Z and Rpd3L pathways. Thus, my data suggest that the STUbL-dependent ubiquitin hotspots shape chromatin during stress adaptation, and the bipartite recruitment mechanism exemplifies how specificity can be generated in the STUbL pathway. These findings can guide future research elucidating how different substrate recognition domains control the diverse STUbL functions, which range from the response to DNA damage to early embryonic development.