Post-translational modifications (PTM) by members of the Ubiquitin (Ub) family represent an efficient way to regulate protein function at several levels: to change their localisation, activity, their interaction with partner proteins or their stability at the right time and cellular compartment, according to the cell requirements. Defects in this homeostatic equilibrium result in pathologies such as cancer, neurodegeneration, inflammation or multiple infections.
For this reason, this research area has become very attractive for fundamental scientists as well as for the pharmaceutical industry (Pharma) aiming to identify potential targets for therapeutic intervention. Interestingly, Ub and Ub-Like (UbL) proteins can modify themselves, forming intricate and complex chains. This landscape was recently expanded with the discovery of the formation of heterologous chains among UbL molecules including SUMO or NEDD8 but also other PTMs such as phosphorylation, acetylation or ribosylation.
This unsuspected complexity of what is now called «The Ubiquitin Code», an unexplored universal language that needs to be deciphered to understand protein homeostasis and its associated pathologies. To decrypt this complex code requires joint collaborative multidisciplinary efforts at all levels, including the use of distinct molecular systems and model organisms and the latest technological developments to explore chemical, biochemical, molecular, pharmacological and clinical aspects of protein modification by members of the Ub family. UbiCODE represents an unprecedented effort to understand «The Ubiquitin Code» in an integrated manner.
Our key scientific challenge is to investigate how chain diversity is generated (written), regulated (edited), recognised (read) and connected with effector functions (interpreted) to regulate cellular plasticity. Our main hypothesis is that a better knowledge of the “writers”, “editors”, “readers” and “interpreters” of this new universal language will help us to understand the encoded message, which will be crucial to predict physiologic and pathologic processes.
Deadline 31 March 2018
Title of the Project: Dynamic Ub modification regulated and interpreted by endosomal sorting complexes.
Host institution: University of Liverpool
Supervisor: Sylvie Urbé
Deadline: 31 March 2018
Summary of the project
We seek to understand the modes of Ub chain recognition and editing associated with endo-lysosomal degradative pathways. The ESCRT-0 complex (HRS and STAM) engages ubiquitylated growth factor receptors for lysosomal sorting via five Ub binding domains, which combine to provide a unique topology for Ub chain interactions.
We propose to leverage stable cell lines we either have already made or will generate to identify ubiquitylated proteins interacting with GFP or APEX-tagged HRS/STAM and profile the preferred chain types that associate with the ESCRT-0 complex ± growth factors. We will also immunoisolate intact endosomes or use APEX mediated biotinylation to profile the endosomal ubiquitylation landscape.
Finally we will examine the influence of endosome associated de-ubiquitylases (DUBs) with differing chain specificities for their influence upon ESCRT capture of receptors, ESCRT-0 associated chain types and the endosome associated Ub profile.