Japan_IPAP: Expanding epiproteome signalling with a new synthetic ubiquitin code

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In addition to the genome, precise regulation of the proteome is now recognised to be a major contributor to organismal health and disease. Proteins of the proteome are regulated by various chemical modifications that together make up the epiproteome. One of the most important regulatory modifications of the epiproteome is made by the small conserved protein ubiquitin. Attachment of ubiquitin to substates serves many signalling roles, including regulation of substrate stability, cellular localisation, activity and conformation. Consequently, dysfunction of the ubiquitin system causes severe cellular stress and is a leading cause of developmental defects across different eukaryotes, including human pathologies such as neurodegenerative diseases, autoimmunity, cardiomyopathy, and genetic disorders like cystic fibrosis. So how does ubiquitin control so many different processes? Ubiquitin can be attached to substrates as a monomer or as an interlinked chain of ubiquitin molecules. In nature there are eight different ways in which ubiquitin can be attached to itself. These eight different topologies each serve as a platform for cellular signalling by associating with specific ubiquitin-binding domain proteins (UBDPs). Thus, distinct ubiquitin chain topologies can regulate different cellular processes. The importance of ubiquitin to health and disease has made it a major target for intervention strategies in biomedicine, pharmacology and in agricultural biotechnology. Consequently, synthetic ubiquitin variants and synthetic ubiquitinated proteins with novel properties have been engineered. However, engineering novel ubiquitin chain topologies that do not exist in nature has not yet been considered, yet offers the potential to generate completely new synthetic signalling platforms in vivo. Here we propose to build synthetic ubiquitin chain topologies that are completely novel and thus can be utilised as a unique cell signalling platform. To that end we will also use intelligent design to build new UBDPs that specifically recognise these synthetic chain topologies. Taken together, our approach has the potential to create new cellular signalling platforms to engineer solutions to combat disease in biomedicine and pharmacology, and mitigate the effects of climate change in agricultural biotechnology.