We provide a summary of the major achievements achieved during the project:
1) [Month 12] We produced collections of biological parts for the precise control of transcription, translation, RNA and protein stability in bacteria (Guiziou et al, Nucleic acids Research, 2016).
2) [Month 24] We have designed a complete framework for the automated design of recombinase logic gates within multicellular systems. We generated a reduced library of computational modules distributed into different cellular subpopulations which are then composed in various manners to implement all desired logic functions at the multicellular level. Our design platform is broadly accessible via a web server taking truth tables as inputs and providing corresponding DNA designs and sequences (available at:
Guiziou et al, ACS Synthetic Biology, 2017(s’ouvre dans une nouvelle fenêtre).
3) [Month 28] We have engineered the first set of programmable transmembrane receptors using a synthetic binder as a sensing domain. These receptors open the road to novel sensing modalities, in particular towards the detection of ligand for which no receptor is found in nature (Chang et al., ACS Synthetic Biology, 2017). One patent application was also deposited.
4) [Month 44] We have implemented a systematic framework for engineering reliable recombinase logic devices by hierarchical composition of well-characterized, optimized recombinase switches. We apply this framework to build a recombinase logic device family supporting up to 4-input Boolean logic within a multicellular system. This work enables straightforward implementation of multicellular recombinase logic and will support the predictable engineering of several classes of recombinase devices to reliably control cellular behavior Guiziou et al, Nature Communications, 2019).
5) [Month 48] We have designed a workflow to expand the range of molecules detectable by cell-free biosensors capable of functioning in a variety of complex media, including human urine, in which they can be used to detect clinically relevant concentrations of small molecules. This work provides a foundation to engineer modular cell-free biosensors tailored for many applications (Voyvodic et al, Nature Communications, 2019)
6) [Month 52] We have generated combinations and permutations of recombination sites, genes, and regulatory elements, for a total of 4 Billion designs supporting the implementation of 2-, 3-and 4-input logic functions. We provide a user-friendly interface, called RECOMBINATOR (
Guiziou et al., BiorXiv, 2019(s’ouvre dans une nouvelle fenêtre).
7) [Month 64] We implemented robust, scalable history-dependent programs by distributing the computational labor across a cellular population. Our design is based on standardized recombinase-driven DNA scaffolds expressing different genes according to the order of occurrence of inputs. These multicellular computing systems are highly modular, do not require cell-cell communication channels, and any program can be built by differential composition of strains containing well-characterized logic scaffolds. We developed automated workflows that researchers can use to streamline program design and optimization. (Zuniga et al., Nature Communications, 2020).
8) [Month 76] We have shown that novel, clinically relevant sensing modalities can be introduced into bacterial biosensors in a modular fashion. To do so, we have leveraged our synthetic receptor platform to detect bile salts, a biomarker of liver dysfunction, by repurposing sensing modules from enteropathogenic Vibrio species. We then engineer a colorimetric bacterial biosensor detecting pathological bile salt levels in serum from patients having undergone a liver transplant, providing an output detectable by the naked eye. The EMeRALD technology enables functional exploration of natural sensing modules and rapid engineering of synthetic receptors for diagnostics, environmental monitoring, and control of therapeutic microbes. (Chang et al., Nature Communications, 2021). Two patent applications were deposited.
