SynDustry Fuse. Produce. Use.
Utilization of artificial endosymbiosis to abolish land grabbing through the production of terpenoid derived chemicals
The term "land grabbing" describes the acquisition of land, mainly in developing and newly industrialized countries through foreign investors to plant crops for food production as well as for the production of valuable secondary plant substrates, for example pharmaceuticals or biofuels derived from terpenoids . Although production of secondary plant substrates through microorganisms is possible in general, it is mostly either inefficient or extremely expensive in terms of research . This is mainly due to the different properties of various microorganisms, where some are more suitable than others for the production of a desired substrate. In addition, this often goes beyond the utilization of traditional model organisms in microbiology, such as S. cerevisiae and E. coli. As mentioned before, it requires great effort in terms of engineering one of these organisms to make the production of especially these secondary plant substrates feasible.
To make this production through microorganisms more interesting and therefore solve the issue of land grabbing for this purpose, our project "Syndustry – Fuse. Produce. Use" combines the naturally given advantages of various model organism strains. For this, we created an artificial endosymbiosis between different organisms, mainly S. cerevisiae and E. coli. The organisms can be specialized to overcome bottlenecks for improvement of biotechnological productions or can even grant possibilities for productions that have not been established to date. The process to make this possible can mainly be divided into three parts: establishing a dependency between the organisms, implementation of a production pathway and the actual fusion of the organisms.
Since the biological safety of our system would be relevant to the recipients and the environment, we also investigated in the behaviour of certain bacterial safety mechanisms, the kill switches. Instead of designing one of our own, we took advantage of the numerous kill switches already implemented in the iGEM database. Using these, we were creating a model describing their escape rate in terms of evolutionary stability seeing them as a genetic network. We did so in collaboration with the iGEM team of Lethbridge, who performed to experimental work for verification of our model.
Due to the multiplicity of kill switches designed in the past years of iGEM, we also created a simple and easy overseeable database of all kill switches either described or implemented. It contains all relevant information for the selection of a suitable kill switch, for example a classification regarding the redundancy of crucial compounds, such as inducer and toxin or a topology map.
Dependency. Keeps the system together.
In order to guarantee the fitness of the host organism as well as the invading cell, we established different exchange-based dependencies - a malonate based dependency with the invading E. coli cell as the malonate source and a protein based dependency complementing essential gene knockout.
Fusion. Brings the system together.
Since our whole project relies on the utilization of the principles of endosymbiosis for production purposes, we had to decide for a method to bring the organisms together. This was accomplished by modification and optimization of a protocol using polyethylene glycol (PEG).
Production Line. Novel system for modular synthesis.
Design of a production line that starts with limonene production in E. coli and export into S. cerevisiae. Limonene gets hydroxylated to the cancer drug perillyl alcohol and exported to the media.
Modeling. Evolutionary stability analysis of killswitches.
Quantitative work using mathematical modeling and numerics to study genetical killswitches. Treated as genetic regulatory networks, the stability of network topologies against evolution - selection and mutation - is studied.
-  Ajikumar, Parayil Kumaran, et al. "Terpenoids: opportunities for biosynthesis of natural product drugs using engineered microorganisms." Molecular pharmaceutics 5.2 (2008): 167-190.
-  Van Dien, Stephen. "From the first drop to the first truckload: commercialization of microbial processes for renewable chemicals." Current opinion in biotechnology 24.6 (2013): 1061-1068.