Ubiquitin-Proteasome System crosstalk with Metabolism

Introduction

Cellular metabolites are essential components of life processes, and their import, biosynthesis, and enzymatic conversion are regulated by a wealth of pathways. The ubiquitin-proteasome system (UPS) plays a major role in ensuring that key metabolic regulators are maintained at proper levels, to control concentrations of ions, carbohydrates, amino acids, cofactors, and lipids.

Regulation of Ubiquitination Enzymes

In particular, the activities and localization of critical ubiquitination enzymes (E3 ligases) and the proteasome must be tightly regulated to ensure that degradation is restricted to proteins that are unwanted, superfluous, or toxic, while sparing those proteins needed for ongoing metabolic functions.

Knowledge Gaps

Nonetheless, we have limited knowledge of fundamental structural and cellular mechanisms underlying this regulation, and the extent of crosstalk between E3 ligases and metabolic signals.

Project Aims

The main aim of this proposal is to decipher molecular principles underlying crosstalk between ubiquitination and metabolites at large.

Aim 1

By using time-resolved cryo EM, single-molecule biophysics, cell-based mutagenesis screens, and functional studies, we will provide insights into how E3 ligases regulate key mediators of glucose, ion, and lipid homeostasis.

Aim 2

To further increase knowledge of the breadth and depth of crosstalk between metabolic pathways and the UPS, we will use our toolkit of E3 ligases and probes to:

1. Define regulatory interactions between a wide swath of metabolites and E3 ligases.
2. Identify E3s activated upon switches in metabolic conditions.

Aim 3

Moreover, we will explore how E3 ligases and proteasomes are reorganized at an ultrastructural level inside cells to respond to starvation or nutrient-rich conditions.

Conclusion

Taken together, these interdisciplinary approaches will establish a framework to translate conceptual and technical advances across molecular, structural, cell biological, and systems levels, to broadly illuminate coordination between metabolic signals and the UPS.