The faithful transmission of the genetic information is essential. In cells, this process is perpetually challenged by endogenous or exogenous agents. Due to this constant exposure, chromatin-adjacent proteins can become covalently crosslinked on the DNA, and form stable structures called DNA-protein crosslinks, or DPCs. The repair of these highly toxic lesions received great research attention during the last decade. While canonical repair pathways have the potential to act on DPCs, the most effective way to repair these adducts occurs by means of dedicated proteases, of which yeast Wss1 (known as SPRTN in higher eukaryotes) is the best described.

This manuscript presents four studies conducted in the budding yeast Saccharomyces cerevisiae, each of which aimed to decipher mechanisms governing DPC recognition and clearance. The first study identifies the protease Ddi1 as an important player in the repair of DPCs. The second study focuses on the role of post-translational modifications, especially how SUMOylation coordinates DPC repair pathways. As the repair of DPCs relies, to some extent, on the segregase Cdc48 (known as VCP/p97 in mammals), the third study aimed to develop the knowledge about how Cdc48 is involved in DPC repair. It specifically shows that the Cdc48 adaptor Ubx5 is assisting Wss1 in DPC processing by targeting Cdc48. Finally, the regulation of Ddi1 is expected to be crucial for its function, in order to avoid unwanted proteolysis. The last study therefore intended to define how Ddi1 is targeted to DPCs. In the process, ubiquitination by the cullin Rtt101 emerged as an important S-phase-dependent regulatory event of DPC repair.