iGEM Berlin 2014: A remote control for E. coli

As the first iGEM team from Berlin, we decided to construct a simple BioBrick that enables synthetic biologists to remotely control the movement of E. coli. A seemingly simple and non-invasive mechanism for this remote control is the use of magnetic fields. By altering the iron homeostasis of E. coli, we want to increase the total iron level of the cytosol. By sequestering iron in a ferritin protein, iron crystals are formed and the cell is detoxified. We will work with other metal binding proteins such as metallothioneins and phytochelatin synthases in order to create ferromagnetic crystals. Furthermore, we will search for the optimal conditions which yield the most efficient formation of magnetic nanoparticles in E. coli. Once we have discovered the best way to magnetize E. coli bacteria, we will build and characterize suitable BioBricks that can be used to remote control the cellular movement of E. coli.

The following animaton visualizes the concept of using ferritin iron storage proteins as a magnetism mediating module.



This animation was developed by Florian Renner who is an science interested and very talented grafic designer based in munich. We thank Florian for his amazing job he did voluntarily for iGEM Berlin helping us to overcome the limitations of our budget.

As the first iGEM team from Berlin to take part in the competition, we decided to construct a simple BioBrick that enables synthetic biologists to remotely control the movement of the laboratory workhorse Escherichia coli. A seemingly simple and non-invasive mechanism for this remote control is the use of magnetic fields, which enable a vast variety of applications. In nature, these are already used by several mammals, as well as bacteria for orientation. Remote-controlled E. coli cells could be used as “bacteria-based nanorobots” in order to maneuver them live in the intestine - targeting diseased tissue or even tumors. Combined with BioBricks from other iGEM teams a local, site-directed treatment of intestine cancer is envisioned[1]. Therefore, we work with the probiotic E. coli strain Nissle 1917, which already has an 80 year history as a treatment for chronically inflamed intestine tissue and is sold commonly as “Mutaflor”[2]. Our experiments should enable us to construct simple BioBricks capable to produce a diverse set of nanoparticles, including quantum dots, magnetic nanoparticles, semiconductor nanoparticles, noble metal nanoparticles and many more[3]. For example, cheap and efficient production of magnetic nanoparticles could be used in hyperthermal cancer therapy. Subsequently, we would like to investigate if our method can also be adapted to the synthesis of rare earth metals, which despite their abundance are not mineable. This would offer an alternative to the environmental hazardous mining operations that are common today. A remote control for E. coli will enable a whole variety of application relevant for bioprocess engineering. Therefore one can imagine neglecting centrifugation for cell separation - simply use a magnet. Also, it should be possible to use high frequent oscillating magnetic fields for cell lysis or even use rotating magnetic fields for self-stirring cultures in bioreactors solving scale up limiting issues like tip speed. Nature is the world’s most skilled engineer and has naturally occurring magnetotactic bacteria such as Magnetospirrilium magneticum. Under certain conditions, these organisms form magnetosomes, which are chains of magnetite nanoparticles. These function as an intracellular compass for the cell and even allow them to orientate along earth’s weak magnetic field. As previous iGEM teams have shown, synthesizing fully functional magnetosomes in E. coli is highly difficult as more than 60 highly regulated genes are involved[4]. The Berlin iGEM team came up with an alternative strategy that does not rely on the formation of magnetosomes. By knocking out the iron efflux transporter gene FieF and the iron uptake suppressor Fur, we want to increase the total iron level of the cytosol. By sequestering iron in a ferritin protein, iron crystals are formed and the cell is detoxified. In order to create ferromagnetic crystals, we will use intensive high-throughput growth medium optimization to discover the best conditions for the formation of magnetic nanoparticles in E. coli. We will work with other metal binding proteins such as metallothioneins and phytochelatin synthases in order to achieve nanoparticle synthesis. Once we have discovered the best way to magnetize E. coli bacteria, we will build and characterize suitable BioBricks that can be used by any research lab or iGEM team in the world in order to remote control the cellular movement.

Involving the Community
Although there are several scientific institutions located in Berlin which are conducting research in synthetic biology, there has never been an iGEM team from Berlin before. This is even more surprising as Berlin with its vibrant bio-arts and diy-biology community seems to be the perfect location for successful iGEM projects. As an interconnected workforce, our team incorporates members from various scientific, cultural and creative backgrounds, which makes our team able to address complex issues from various persepctives. So far, iGEM Berlin consists of students from biotechnology, history, design, medicine, theoretical physics, informatics, and more. So far our diverse team has been able to make valuable connections into the bio-arts scene of Berlin, working together with think tanks such as the Hybrid Plattform, as well as EU advisor Markus Schmidt and his Biofaction AG. Supported by the Hybrid Plattform, we organized a science and design workshop event on the 8/9.08.2014. During this event we conducted a series of short presentations about synthetic biology, as well as about prototyping and speculative design. Participants from different backgrounds designed and constructed interactions, which deal with the idea of a biological modularity. The resulting interactions addressed currently debating issues about the future of syntheic biology applications. Surpisingly the participants focused on topics like performance enhancement, transhumanism, alternative materials and housing as well as standardiziation. By explaining the basic principles of synthetic biology and approaching synthetic biology with a limited complexity synthetic biological speculation became easily accessible and reached wide variety of people. In the beginning of September, we collaborated with the artists and scientists from the c-lab collectiv (UK) as well as the Artlaboratory - a berlin bio-arts space. In the Synthetic Biology Workshop artists and other people were introduced to synthetic biology and performed their own cloning experiment. The whole event came to an end in Berlins first Science Café event for synthetic biology organized by the iGEM Berlin Team. During this event, we had speakers from different backgrounds and we discussed chosen aspects of synthetic biology with participants openly over drinks and food. The artist Ping Lui from Cologne presented his speculative design of an oracle based on magnetotactic bacteria. Rüdiger Trojok, a infamous German biohacker presented his current project, Howard Boland shared his bioart projects and former iGEM involvement with us and Johann from our team gave a short presentation about iGEM and our project. These events were designed to have a high impact on the German understanding of synthetic biology and were a major success in Berlin. One of the current major issues in synthetic biology is the laws and regulations concerning patents. iGEM generally refuses patents and promotes the idea of open source biology. However, as the success and applicability of synthetic biology depend on industry investments, there has to be a compromise in policy regulations. To discuss this topic in detail we teamed up with patent lawyers from the Adares Patentanwältekanzlei as well as Biocommons (Creative Commons license model for Synbio) activist Rüdiger Trojok to discuss patenting and fundamental principles of intellectual property.
In summary, we used art events and practical workshops to confront the German public with issues of synthetic biology. Furthermore, our project of creating a remote control for E. coli bears various practical applications as well as expands the possibilities of future functional biological systems.

References
[1] https://2012.igem.org/Team:Penn/ProjectResults (11.07.2014)
[2] http://www.mutaflor.de/cms/ (11.07.2014)
[3] Park, T. J., Lee, S. Y., Heo, N. S. and Seo, T. S. (2010), In Vivo Synthesis of Diverse Metal Nanoparticles by Recombinant Escherichia coli. Angew. Chem. Int. Ed., 49: 7019–7024.
[4] https://2011.igem.org/Team:Washington/Magnetosomes/Magnet_Toolkit (11.07.14)