Team:Evry Paris-Saclay

VIRAL TALK

Our project aims to build a synthetic intercellular communication system. In natural ecosystems, there already exist several mechanisms which bacteria utilize to interact among themselves for latency, reproduction, or survival. Bacteria can produce signaling molecules that are sensed by others of their species, or even of other species, to trigger a molecular response. These communication systems can be engineered to regulate and automatize industrial bioprocesses. An important feature that would help achieve this goal is the orthogonality of the signaling molecules. The more specific the send-sense system is, the more efficiently the response of the targeted microorganism can be engineered.

We find the recently described phage communication system to be a good candidate for synthetic cell-cell interaction (Zohar et al., 2017 Nature 541, 488-493). The system uses a secreted peptide called “arbitrium” to control phage-mediated bacterial lysis. The principal genes in charge of this regulated lysis have been validated in phage Phi3T and B. subtilis. However, to our knowledge there are 17 orthologous genes that encode similar peptides and their receptors, which have not yet been characterized. A key part of our project goals is to characterize a library of these different arbitrium peptides and their receptors for orthogonality. This will help identify unique peptide-receptor pairs that do not exhibit cross-talk for future use in engineering of unambiguous cell-cell communication. Additionally, we will test and expand the use of the peptide-based communication system from Bacillus to E. coli, a more widely used model bacterium. This will benefit many academic and industrial projects by enabling multiple parallel channels of communication between cells.

The newly validate communication system will be also be integrated into a co-culture of two different species of bacteria. Co-culturing more than one microorganism has been used as a strategy for mainly industrial process. It has been shown that the engineered co-culture displays robustness, tolerance for toxic metabolic waste and resistance to stress conditions (Goers et al., 2014, J R Soc Interface 11, 20140065). Moreover, engineered co-cultures can be used for many other applications such as biocatalysis or bioremediation, bioproduction of high-valued compound with metabolic engineering, complex protein expression, among others.

An engineering-ready specific communication system like ours could also be useful within the framework of distributed biological computing. Instead of implementing complex molecular circuits in one cell, it would enable bioengineers to implement simpler circuits in multiple cells of a consortium and integrate circuit outputs later. This would make building large-scale circuits easier to implement, more modular and less noisy, while reducing the expression burden on individual cells (Macía et al., 2012 Trends Biotechnol 30, 342-349). In practical terms, the envisioned bacterial communication system would have numerous benefits, some of them relevant to the fields of biomedicine (Kim et al., 2018, bioRxiv 308734), bioengineering and bioremediation (Macia & Sole, 2014, PLoS ONE 9, e81248). It would also enable new ways of engineering multicellular biomaterials, such as biofilms or tissue architectures (Macia & Sole, 2014, PLoS ONE 9, e81248).