Creating Synthetic Protein-Protein Interaction Networks and Implications for Endogenous Network Discovery

5/17/2018


Abstract:

Cells utilize networks that span both temporal and spatial organizations, encompassing many individual steps of regulation. While the regulatory regimes to build networks in synthetic biology has grown from solely transcription to also include protein or RNA modalities, circuits comprised solely of protein-protein interactions have yet to be produced. Here, I'll describe several mechanisms relying on phosphorylation-activated localization and effector actuation for building OR and NOT gates from protein-protein phosphorylation events and their subsequent composition to form fast acting networks for ultrasensitive chemical sensing and phenotypic cellular control. Design and optimization of these networks were enabled by the use of a modular assembly method for rapid construction and testing of network variants. The final protein network spanned 15 individual member species to form a toggle switch that could sense chemical inputs as low as 1.0s in duration and maintain state over cellular division events. Motivated by these synthetic network designs, I will then describe one avenue in which synthetic biology network results can elucidate natural biological networks, i.e., synthetic biology-inspired discovery.

Key Points:

  • To create large (15-protein member) networks comprising solely protein-protein interactions, a toolkit for reliably assembling and fixed protein expression is necessary.
  • Formation of individual protein devices to implement the OR and NOT gates can be achieved by the creation of fusion proteins that are activated by phosphorylation, resulting in localization and effector domain actuation.
  • Protein-protein networks formed from synthetic interactions allows ease of implementation of complex cellular behavior that require fast information processing while also furthering our understanding of endogenous network composition and signal transduction.

Presenters

Deepak Mishra

Deepak Mishra, Sc.D.,
Postdoctoral fellow, MIT

Deepak is a postdoc in the Weiss Lab at the Center for Synthetic Biology at MIT. He is a former NSF Graduate Research Fellow, Eni-MIT Energy Fellow, and Siebal Scholar. He received his B.S. with honors in Chemical Engineering with a Biomolecular Emphasis from Caltech in 2009, and his Sc.D. in Biological Engineering from MIT in 2016.