CBET-EPSRC: Developing Standardized Cell-Free Platforms for Rapid Prototyping of Complex Synthetic Biology Circuits and Pathways

Synthetic biology is an emerging field of engineering that aims to establish a systematic framework for the design of biological systems based on a 'bottom-up' approach for the reconstruction of complex bio-molecular systems. The application of an engineering approach to design is attractive, as many engineering parallels can be identified in living systems. However, biological systems are highly complex and dynamic and difficult to engineer. Rapid characterization of particular biological parts and devices requires new methods as existing methods are inefficient and error prone, and require extensive time-consuming experiments.

An alternative to current methods is the use ell-free systems for rapid characterization. Cell-free systems are cell extracts that contain all the machinery that allows biological parts to function and as such one can analyse many parts quickly without using living cells. This therefore speeds up the whole process. However, cell free systems can be variable and the results can be different between different researchers. The overall goal of this project is to further advance standardized cell-free systems using both computer models and new biochemical measurement tools. 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 project will benefit the emerging and interdisciplinary academic research field of synthetic biology. The development of standardised and robust cell-free TX-TL systems will enable a wide range of researchers to adopt TX-TL as a prototyping platform to enable the synthetic biology design cycle. In addition it will also allow researchers to explore TX-TL systems for implementing complex genetic circuit design including complex logic gates and oscillators including the development of mathematical models that describe their behaviour. In addition researchers interested in biosynthetic pathway and biosensor design will be able to utilise TX-TL systems for enzyme discovery, flux optimisation and biosensor implementation. Chemical biologists interested in the origins of life would also benefit from a more quantitative analyses of cell free reactions.

The project will also benefit biotechnology start-ups and diagnostic companies interested in biomanufacturing and bio-sensing. Recent ground breaking work by Jim Collins in the US led to a 'proof-of-concept' study that implemented cell free TX-TL extracts as paper-based biosensors in relation to 'point of care' diagnostics and disease detection. There is a growing expectation and excitement around TX-TL systems providing highly novel and attractive solutions for detection and sensing in many industrial sectors including healthcare, food manufacturing and environmental applications like pollution management and water quality. The proposed project will contribute fundamental knowledge to making cell free bio-sensing systems reproducible, reliable and robust and it is possible that aspects of the project could lead to commercialisation opportunities both in the UK and US.