Understanding Specificity in the Ubiquitin Ligase HACE1

Objective

Ubiquitination is a pivotal regulator of eukaryotic protein functions, governing myriad cellular pathways. Its deregulation causes manifold human diseases, yet our incomplete understanding of the underlying structural mechanisms has limited therapeutic efforts. Within the ubiquitination machinery, ubiquitin ligases (E3s) present major specificity determinants, as they select substrates for modification and decorate them with ubiquitin signals. These signals frequently comprise ubiquitin chains of various linkage types, each associated with distinct functional outcomes for the modified substrate. To understand how ubiquitin ligases select and modify substrates with specificity is, therefore, pivotal to understand and efficiently manipulate the ubiquitin system. To address this key question, my project focuses on the human HECT-type E3 HACE1, an important, yet poorly characterized neurodevelopmental regulator and tumour suppressor. I will structurally recapitulate linkage-specific ubiquitin chain formation by HACE1 on its physiological substrate RAC1 by cryo-EM, complemented by structure-guided mutagenesis and functional analyses in vitro and in cells. Moreover, I will develop new technologies to identify HACE1 substrates in cells, using tailored, mechanism-based crosslinking strategies. Capitalizing on my expertise in unnatural amino acid incorporation, I will insert a photoactivatable lysine-reactive amino acid at the E3 active site for covalently capturing of substrates based on proximity, followed by their mass spectrometry-based identification. This strategy may later be adapted to other cysteine-reactive E3 classes. Taken together, my studies will advance our fundamental understanding of ubiquitin ligase specificities in a disease-relevant model system, while establishing innovative new tools for substrate identification in the ubiquitin system.