Developing Standardized Cell-Free Platforms for Rapid Prototyping of Synthetic Biology Circuits and Pathways

The goal of this project is to further advance standardized cell-free systems from engineered E. coli and other organisms for use in prototyping synthetic circuit and pathway designs. Such standardized systems will both explore the boundaries of cell-free prototyping and characterization, and enable more detailed understanding of key mechanisms, accelerating the usage and broader utility of cell-free systems in industry and academia. The long term vision for this project is to establish cell-free systems as a platform for implementation of synthetic biological circuits, pathways, and systems, where modular and complex biomolecular systems can be engineered in a systematic fashion. This project seeks to overcome some of the current limitations of cell-free systems through a combination of experimental characterization and computational modeling.

Current participants: Additional participants:

Collaborators: Paul Freemont (Imperial College London) Past participants: Zoila Jurado (Alumni, CMS) Joe Meyerowitz (Alumni, BMB) Ayush Pandey (Alumni, CDS) Xinying (Cindy) Ren (Alumni, CDS)

Objectives

The main objectives of this project are:

• Development of well-understood, standardized TX-TL reaction systems that are suitable for prototyping circuits and pathways for a variety of cells
• Characterization and modeling of complex synthetic biology components, circuits, and pathways using TX-TL that enable forward engineering
• Development of new biochemical indicator components for use in TX-TL systems to achieve better understanding and more predictive models

References

• A chemical reaction network model of PURE. Zoila Jurado, Ayush Pandey, Richard M. Murray. BioRxiv preprint, 2023.
• BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts. William Poole, Ayush Pandey, Zoltan Tuza, Andrey Shur, Richard M. Murray. PLoS Computational Biology, 18(4), e1009987, 2022.
• Characterization of Integrase and Excisionase Activity in Cell-free Protein Expression System Using a Modeling and Analysis Pipeline. Ayush Pandey, Makena L. Rodriguez, William Poole, Richard M. Murray. ACS Synthetic Biology, 12(2):511–523, 2023.
• Robustness guarantees for structured model reduction of dynamical systems with applications to biomolecular models. Ayush Pandey, Richard M. Murray. International Journal on Robust and Nonlinear Control (IJRNC), 1-29, 2022.
• Robustness Guarantees for Structured Model Reduction of Dynamical Systems. Ayush Pandey, Richard M. Murray. IEEE Conference on Decision and Control (CDC), 2021.
• Model Reduction Tools For Phenomenological Modeling of Input-Controlled Biological Circuits. Ayush Pandey, Richard M. Murray. 2020 Winter q-bio.

Agency: NSF Grant number:

Start date: 1 Jul 2019 End date: 30 Jun 2023

Support: 1 graduate student Reporting: Annual reports