Synthetic and structural biology of Rab GTPase networks

Introduction

Eukaryotic cells are characterized by their compartmentalization into hundreds of different membrane-bound organelles with unique biochemical identities. Small GTPases of the Rab family play a central role in this organization, but how they are able to generate spatiotemporal order in the complex cellular environment is currently not known.

Current Understanding

Most previous studies on Rab GTPases have either relied on describing their behavior in living cells or in highly reductionist biochemical assays. However, neither of these two approaches can explain the dynamic activity patterns of Rab GTPases associated with their cellular functions.

Regulatory Networks

It has become clear that Rab GTPases are controlled in sophisticated regulatory networks with emergent, self-organizing properties. To obtain a mechanistic understanding of these Rab GTPase systems, new experimental assays are now required.

Proposed Methodology

In this proposal, we will use a “bottom-up” synthetic biology approach to rebuild the biochemical networks of Rab GTPases from purified components and demonstrate their self-organization into spatiotemporal activity patterns in vitro.

Experimental Techniques

We will combine these reconstitution experiments with cryo-electron microscopy to elucidate the structures of membrane-recruited Rab GTPase regulators. Finally, we will use microfabrication and laser lithography to prepare a mimic for the compartmentalized cell and find out how Rab GTPase signaling systems sense and process preexisting geometric and biochemical cues as in the living cell.

Expected Outcomes

This project will provide novel, quantitative information from different scales, from the emergent ensemble behavior down to the molecular structure of protein complexes. Together, this data will reveal how signaling systems of Rab GTPases control membrane identities in space and time, thereby improving our understanding of the intracellular organization of the eukaryotic cell.