HUMAN PRACTICES

Meeting with professionals

Applications

Education and public engagement

https://2018.igem.org/Team:Evry_Paris-Saclay/Public_Engagement

Integrated human practices

During our Human Practices research, we have realised two things. The first one is that there is a real need of new bacterial communication systems for researchers. According to this assessment, we have deeply investigated what kind of communication system would fit the most to current research and interests. The second thing we realised is that the general public has limited knowledge about biology, which make really hard for it to understand a foundational project as our. Therefore, we made great efforts on educating people about biology and synthetic biology.

Choosing the communication system

First of all, bacteria communicates through quorum sensing (QS) and there are basically two kinds of QS: AHL QS and peptide based QS [1]. When we met Jérôme Bonnet (link to Human Practices), he explained us that it would be very useful to characterise a large number of different sets of orthogonal communication molecules. Since peptides are easier to engineer than small molecules, we decided to focus on a peptide based QS. After we had engineered the system for a chassis, we expected to be able to generate several variant of it through directed evolution.

Besides, our communication system had to be as orthogonal as possible to avoid interferences, on one hand, with other variants of this communication system and, on another hand, with natural communications systems inside the cells. Therefore, we found the “Arbitrium” bacteriophage QS [2] to be a good candidate since the orthogonality would have been better using a bacteriophage system than a bacterial system.

Finally, while using the original “Arbitrium” system, we get a promoter which respond to an activator and a deactivator. Since the activator can be produced constitutively, the system finally looks like a promoter with an inhibitor. This kind of promoter can be really useful for logic gates construction. However, many labs and companies are used to work with promoters which can be activated to induce the production of some compounds, such as LacI/IPTG, pBad/Ara, TetR/tetracycline and LasR/Acyl-homoserine-lactone. Therefore, we decided to switch the system, using the original promoter as a operator for an E. coli promoter. Thus, we developed a promoter which respond to a constitutive inhibitor and a “de-inhibitor”.

Choosing the chassis

After we decided to work on the “Arbitrium” system, one question came up: which chassis would we use? We have thought during a long time to still work into B. subtilis, which is the host of the SPbeta bacteriophage group, to characterise a library of orthogonal QS into B. subtilis. However, our Human Practices research has revealed that most of labs and companies are working with E. coli. So we decided to adapt the “Arbitrium” system to fit E. coli chassis, which, as Gram negatives, are naturally not expressing peptide based QS. Then, the characterisation of a library of new QS into E. coli would have became possible.

Popularising the project

Through our Human Practices research, we realised that it was not possible to explain our project to the general public and make people interested about it because it was very abstract for them. So we managed to do two things. First, we have searched for a lot of applications (link to Applications) which can be reached with our new communication system, such as distributed logic gates, sensitive biosensors or gene regulation. Then, we have created many different media to educate the public about each of these applications. The orthogonality of a communication system is described through our video game (link), distributed logic gates are explained through our interactive rug (link) and other applications were described through many events we were involved in (link).

Collaborations

https://2018.igem.org/Team:Evry_Paris-Saclay/Collaborations

References

[1] Federle MJ, Bassler BL. Interspecies communication in bacteria. J Clin Invest (2003) 112, 1291-1299.

[2] Erez Z, Steinberger-Levy I, Shamir M, Doron S, Stokar-Avihail A, Peleg Y, Melamed S, Leavitt A, Savidor A, Albeck S, Amitai G, Sorek R. Communication between viruses guides lysis-lysogeny decisions. Nature (2017) 541, 488-493.