New publication by the Ulrich lab on how custom affinity probes reveal DNA-damage-induced, ssDNA-independent chromatin SUMOylation in budding yeast
Tröster V, Wong RP, Börgel A, Cakilkaya B, Renz C, Möckel MM, Eifler-Olivi K, Marinho J, Reinberg T, Furler S, Schaefer JV, Plückthun A, Wolf E, Ulrich HD (2025) Custom affinity probes reveal DNA-damage-induced, ssDNA-independent chromatin SUMOylation in budding yeast.Cell Rep., doi: 10.1016/j.celrep.2025.115353 Link
Abstract:
The small ubiquitin-related modifier SUMO regulates cellular processes in eukaryotes either by modulating individual protein-protein interactions or with relaxed substrate selectivity by group modification. Here, we report the isolation and characterization of designed ankyrin repeat protein (DARPin)-based affinity probes directed against budding yeast SUMO (Smt3). We validate selected DARPins as compartment-specific inhibitors or neutral detection agents. Structural characterization reveals a recognition mode distinct from that of natural SUMO interactors. In vivo application pinpoints Smt3’s essential function to the nucleus and demonstrates DARPin-mediated sensitization toward various stress conditions. A subset of selected clones is validated as SUMOylation reporters in cells. In this manner, we identify a DNA-damage-induced nuclear SUMOylation response that—in contrast to previously reported chromatin group SUMOylation—is independent of single-stranded DNA and the SUMO-E3 Siz2 but depends on Mms21 and likely reflects late intermediates of homologous recombination. Thus, Smt3-specific DARPins can provide insight into the dynamics of SUMOylation in defined subcellular structures.
Read the full paper here: https://doi.org/10.1016/j.celrep.2025.115353
