Ubiquitination is a fundamental post-translational modification (PTM) crucial for a wide range of cellular processes, including protein degradation, localization, quality control, DNA repair, cell signalling, and immune responses. Traditionally, ubiquitin attaches to lysine residues via isopeptide bonds. However, recent advances have uncovered a novel form of ubiquitination - non-canonical ubiquitination - where ubiquitin binds to serine, threonine, and other hydroxyl-containing biomolecules through ester bonds. This dynamic and less stable modification challenges established paradigms and opens up new possibilities for interactions with other PTMs, such as phosphorylation and glycosylation, which could have far-reaching consequences on cell biology. Investigating non-canonical ubiquitination promises to deepen our understanding of cellular mechanisms and identify new therapeutic targets for diseases linked to dysfunctional ubiquitination. By deciphering the code of non-canonical ubiquitination, we aim to identify novel therapeutic targets for diseases associated with its dysfunction.

The De Cesare Lab’s mission is to understand the functional landscape of non-canonical ubiquitination and its impact on health and disease. Our lab has pioneered the identification of several non-canonical ubiquitin conjugating enzymes (E2s) - UBE2Q1, UBE2Q2, and UBE2QL1 - that mediate ubiquitin attachment to non-lysine residues [1]. Notably, UBE2Q1 knockout mice exhibit infertility due to defective embryo implantation, highlighting the critical role of these non-canonical E2s in early developmental processes and reproductive biology [2]. Additionally, altered expression of UBE2Qs has been observed in various human cancers, raising important questions about their roles in human health and disease.

This PhD project will address the following key questions:

1. How does non-canonical ubiquitination affect cellular processes and human health, including links to infertility and cancer?
2. What are the substrates and functional roles of non-canonical E2s (UBE2Q1, UBE2Q2, UBE2QL1) in different cellular contexts?
3. Does non-canonical ubiquitination interact with or regulate other PTMs such as phosphorylation and glycosylation?

This project offers flexibility to align with the student's specific interests and incorporates a range of advanced methodologies, including MALDI-TOF [3] and Liquid Chromatography (LC) Mass Spectrometry (MS), protein biochemistry, structural biology, molecular biology and cell biology.

This comprehensive training will provide the student with valuable skills across multiple disciplines, preparing them for successful careers in both academic and industrial settings.

References

[1] Syed Arif Abdul Rehman et. al., Discovery and characterization of non-canonical E2 conjugating enzymes Science Advances 10 1-18 doi:10.1126/sciadv.adh0123 PMID: 38536929

[2] Grzmil P et. al., Embryo implantation failure and other reproductive defects in Ube2q1-deficient female mice. Reproduction. 2013 Jan 8;145(1):45-56. doi: 10.1530/REP-12-0054. PMID: 23108111.

[3] De Cesare V et. al., High-throughput matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry-based deubiquitylating enzyme assay for drug discovery. Nat Protoc. 2020 Dec;15(12):4034-4057. doi: 10.1038/s41596-020-00405-0. Epub 2020 Nov 2. PMID: 33139956.