The strains chosen for this analysis were grouped into a 16S rRNA based phylogenetic tree using E. coli BL21 (DE3) as the outgroup. The number of negative effectors indicates the total number of copies present in an organism’s genome for the top 20 proteins shown to have the greatest negative effect on cell-free protein expression.
We have succeeded in producing cell-free extracts from several different organisms as a proof of concept in our ability generate extracts from non-traditional hosts. We have begun a more systematic study of which organisms are most likely to be useful for generating durable extracts that can be used for advanced sensing and protyping needs.
The two primary goals for this project are to (1) increase the number of organisms and portable parts available for synthetic biologists for design, prototyping, and implementation of cell-free biomolecular circuits and pathways in a rapid, systematic, and predictable way and (2) improve the durability, sensitivity, and robustness of cell-free detection systems. The use of a diverse set of organisms and parts can provide access to durable biological functionality in varied field operating conditions, to a broad array of new outputs and improved scale-up for biological circuits and pathways, and to new modes for detection and diagnostics.
We are working to accomplish these goals by focusing on the following specific objectives:
Develop high-throughput, cell-free methods for measuring and modeling key parameters of transcriptional and translational processes of biological parts in a diverse set of organisms.
Perform a demonstration of the utility of these models by moving parts and circuits from one organism to another with a repeatable and predictable outcome.
Demonstrate expanded capabilities for detection and diagnostics of chemical and biological signals in simulated or real field operating conditions, with the goal of increasing sensitivity, specificity, and output signal strength of cell-free biological detectors.
Distribute the tools and techniques to the synthetic biology community for broader use.