iGEM Berlin 2014: A remote control for E. coli
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)

  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.

  3.1 Basics
Advantages and basic principles of using magnetic fields
In order to control E. coli remotely, we decided to use magnetic fields because of a few key reasons. First, magnetic fields allow to control the cells by an external force field which means that cells do not have to be directly treated or media conditions have to be changed as it is the case in many chemotaxis assays. Second, magnets are widely spread and electro magnets easily built as you can see in this video: https://www.youtube.com/watch?v=wzXRFp0DDrU The accessibility and safety of magnetic fields opens up the field for new innovation and ideas using remote controlled bacteria. Third, magnetic fields do have a high energy density and are way more viable to transfer energy than other energy fields like electrical fields. However, the magnetic moment of an atom is the product of of the atoms orbital angular momentum and its electron spins. Atomic magnetism is based on unfilled electron orbits. Nobel gases and alkyl halogenide are non-magnetic or “diamagnetic”. Other elements like metals may have an increased magnetic moment as long as their electron orbit are unfilled, meaning they are unbound. Mn2+, Fe3+ have a magnetic moment of about 5 µB, Cr2+, Mn3+, Fe2+ and Co3+ have a magnetic moment of 3 µB. [http://www.diss.fu-berlin.de/diss/servlets/MCRFileNodeServlet/FUDISS_derivate_000000000626/2_f-Kapitel1.pdf?hosts=]
Because of the variety of atomar magnetic properties, magnetism can be divided into different forms by looking at apparent forces and effects. There is diamagnetism, antiferromagnetism, paramagnetism, ferrimagnetism, superparamagnetism and Ferromagnetism. Ferromagnetic forced are about 1000 times stronger than super paramagnetic forces. However, it turns out that creating ferromagnetic particels or residues is very difficult (see magnetite formation in magnetospirrilium bacteria). Also note that in a lot of biological papers, people tend to mix e.g. super paramagnetism with ferromagnetism [Various magnetic Nanoparticles Paper].
Magnetic properties are depended on the crystal structure of a metall particle. The magnetic moment is proportional to the aligment of the electron spins within an component. If electron spins are alignt magnetism can be observed. However on a nanoscale real ferromagnetism can only be noted after a critical particle size of 128 nm.[An-Hui Lu, An-Hui; E. L. Salabas; Ferdi Schüth (2007). "Magnetic Nanoparticles: Synthesis, Protection, Functionalization, and Application". Angew. Chem. Int. Ed. 46 (8): 1222–1244] This is due to thermal fluctations that prevent the alignment of electron spins and therefore prevent the development of sufficient magnetic moments. Because of this phenomena all meassurements for magnetism are usually conducted at very low temperatures.
All magnetic effects that are observed for particles between 1 nm to 100 nm are considered superparamagnetic. Superparamagnetic nanoparticles only show magnetic effects when an external magentic field is applied. This field aligns the electron spins in the particle resulting in an magnetic moment mediated by an external magnetic field. [Picture Atomarer Magnetismus]

3.2 Iron Homeostasis, E. coli Nissle and Knockouts
As an essential element for almost all life iron is often necessary for the activity of certain proteins but can also be problematic because of its toxicity and poor solubility. Organisms have evolved to regulate their iron effectively and as iron in an organism is usually supplied in a limited condition pathogens evolved iron aquisation systems to outcompete other microorganism. A very efficient iron aquisition system, which bacteria inlcuding E. coli use are siderophore mediated transport pathways. [Simon C. Andrews, Andrea K. Robinson, Francisco Rodriguez-Quinones; School of Animal and Microbial Sciences, University of Reading, Reading RG6 6AJ, UK; 2003] Iron E.coli Link

3.3 Ferritin Strategy
Ferritins as scaffolds for magnetic nanoparticle synthesis
In order to protect themselves against radical stress as well as the lack of co-factors, organisms evolved a high regulated and stable iron acquisition system, also known as iron homeostasis. [Iron Homeostasis of E. coli] To put it in a nutshell iron is taken up by iron transporters or siderophore mediated mechanism and is transporters through the outer membrane into the periplasm, in the periplasm it “changes” transporters and is transported through the inner membrane into the cytoplasm. It always gets released as Fe2+ into the cytoplasm. In order to protect themselves against superoxide formation by the Fenton-Reaction a lot of organisms evolved iron storage proteins. One of the superfamily of these proteins is called ferritin. These ferritins are highly symmertrical protein nanocages synthesizing iron concentrates required for cells to make cofactors of iron proteins. Through their ability to cage in biominerals they were the first and most obvious scaffolds for the synthesis of magnetic nanoparticles. These natural metal storage homomers form solid particles inside of their protein shell. Ferritins are ubiquitous in nature and protect the cell from redox stress through iron overload and from iron deficiency. They consist of 24 protein subunits which can consists of a heavy (catalytical active) and light chain (catalytical inactive but stabilizing). Caged ferritin minerals can have diameters as larg as 8-12 nm with thousands of iron and oxygen atoms. Between species ferritins have different affinity for phosphate. Phosphate is low in animal ferritin iron minerals (Fe:P = 8:1) whereas in bacterial and plant ferritins iron minerals are usually occurring in higher relations (Fe:P = 1:1).[1] Mössbauer studies on the superparamagnetic character of bacterioferritins (bfr) revealed that the phosphate concentration in a ferritin iron mineral reduces superparamegntic effects heavily due to replacement of the iron bridges between the iron atoms with phosphate. As these bridges have a lower exchange constant the order temperature is reduced further. [2] The hollow ferritin nanocages are used in the chemical industry as scaffolds for synthesis of magnetite particles as well as for delivery of magnetic resonance imaging (MRI) contrast agents, drug delivery and catalysis.
[1]
Ferritins for Chemistry and for Life.
Elizabeth C Theil, Rabindra K Behera, Takehiko Tosha Children's Hospital Oakland Research Institute, University of California, Berkeley ; Department of Nutritional Science and Toxicology, University of California, Berkeley. Coordination Chemistry Reviews (Impact Factor: 11.02). 01/2013; 257(2):579-586. DOI: 10.1016/j.ccr.2012.05.013
[2] Mössbauer studies of superparamagnetism in E. coli; Hawkins, C.; Williams, J. M. Journal of Magnetism and Magnetic Materials, Volume 104, p. 1549-1550

iGEM Berlin Ferritin Library
During our summer we collected a variety of ferritin-coding sequences from bacterial and mammalian sources. As ferritins are common among all organisms we categorized our ferritins in three major groups. (Table)
3.4 Inclusion body Strategy
By talking to the Fussenegger group from the ETH Zurich, who published the superparamagnetism paper about ferritins we got the tip to look for another strategy as they experienced the limitations of ferritins. [1] For this reason, we came up with a different strategy. Park et al came up with a different strategy for the synthesis of biogenic nanoparticles in E. coli. [2] A strategy where they produced impressive results showing one strategy to synthesize a whole array of diverse nanoparticles with E. coli. (See Figure 1) Two heavy metal binging proteins were combined and co-expressed on one plasmid. Peptides called phytochelatins are produced in fungus and plants to detoxify the cell from harmful heavy metals. Structurally phytochelatins are (gamma-Glu-Cys)n-Gly (n=2-7) peptides and function as metal ion accumulators through formation of peptide-metal conjugates. In this study the phytochelatin synthase from Arabidopsis thaliana (Columbia leave) was used (ATPCS). The other peptid that was used in combination with ATPCS was a metallothionein from Pseudomonas Putida KT2240 strain (PPMT). Metallothioneins are low-molecular proteins with a high content of cysteine and bind well cadmium, zinc, nickel and copper. For expression of ATPCS a trc promotor was used while PPMT was expressed using a T5 promotor. After co expressing both proteins in an standard E. coli strain(DH5alpha) for 4 h the culture broth was centrifuged and fresh metal rich LB media added. (1 – 5 mM of corresponding final metal concentration (see table 1.). After further incubation at 37°C for about 6 - 12 hours the cultures and the biogenic synthesized nanoparticles can be harvested. Park et al reported further that by incubating these ATPCS and PPMT co-expressing in 1.0 mM FeSO4 and MnCl2 magnetic nanoparticles where obtained and cell moved by high magnetic fields (see figure 2).

[1] Kim T, Moore D, Fussenegger M. Genetically programmed superparamagnetic behavior of mammalian cells. J Biotechnol. 2012 Dec 31;162(2-3):237-45. doi: 10.1016/j.jbiotec.2012.09.019. Epub 2012 Oct 2. PubMed PMID: 23036923.
[2] 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. doi: 10.1002/anie.201001524
[3] Wu CM, Lin LY. Immobilization of metallothionein as a sensitive biosensor chip for the detection of metal ions by surface plasmon resonance. Biosens Bioelectron. 2004 Nov 1;20(4):864-71. PubMed PMID: 15522603.

3.5 Magnetic modelleing (Andres)

  Results, jo!