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iGEM Freiburg 2022 presents
chAMBER
Our project is mostly a foundational advance: we created a compartmentalisation toolbox that can be used by future iGEM teams and researchers worldwide to localize in their compartment of choice their proteins of interest. Nonetheless, we did have an application with potential consequences for the real world: the production in E. coli of the pigment indigo, the antileukemia compound indirubin, and the sugar trehalose. Our aim was to test if encapsulation of some of the enzymes of the pathway into nanocompartments would boost production. We also tested if incorporation of a non-canonical amino acid at a selected position in one of the proteins forming the shell would have a positive effect and if the usage of genome-reduced strains would also improve product yield. We had some quite encouraging results! This led us to think that, in the future, our platform could be effectively implemented in the real world for the production of the above-mentioned valuable compounds, and many more.
What should we consider when implementing our project in the real world?
In Germany, releasing genetically modified organisms (GMOs) in the wild is generally prohibited. Our GMO would, however, remain contained in a bioreactor and would not have to come in contact with the outside environment. For this reason, we do not deem it necessary to include a kill switch in the design in case we were to implement our project in the real world. Moreover, we would use laboratory, non-pathogenic E. coli strains, which would likely not be able to outcompete wild-type strains. Therefore, we think that implementing our project in an industrial plant would not require extensive work to meet higher safety than what we have done so far.
However, there is another aspect of biosafety to consider. While producing indigo from bacteria does not pose many safety problems –since the pigment is used on fabric and is not given orally or intravenously to people– the situation is very different for drugs, which are then given to patients. In this case, we would need to spend considerable time implementing the appropriate pipeline to eliminate endotoxins (LPS) that could cause septic shock.
For a real-world implementation, we would likely integrate the pathway and the genes for the compartments into the genome to prevent genetic instability. We would also need to screen more strains to find the most suitable one. When producing drugs, one possibility would be to use probiotic strains; yet, these strains are not as established as E. coli as chassis. We would have to find the right tradeoff between spending time (and money) to genetically manipulate a probiotic strain and establish a pipeline to make the drug pure enough to be used in patients.
We would also likely exchange the chemical inducers we have used so far with light since this is cheaper, more easily applicable, and leads to less contamination. We know that in dense bioreactors, the light might have difficulties penetrating; nonetheless, we believe new solutions continue to emerge given that optogenetics as technology is becoming increasingly popular.
Indigo is a very popular pigment since it durably dyes fabric without staining or washing out since it is not water-soluble. The next step in our project is to stain fabric with our biosynthesised Indigo to prove our sustainably produced dye works like synthetically produced Indigo. For a real-world application, we would also need to perform tests with fabric after extensive washings, for instance. Perhaps further optimisation of the synthesis or purification pathway would be necessary to improve the dye properties of our Indigo.
Even if we do believe that producing goods in a sustainable, more ecologically-friendly way is necessary to keep climate change at bay in the future, we are aware that the economy runs the planet in one way or another. If a pair of jeans dyed with our bioproduced indigo would cost ten times as much as a conventional jeans dyed with chemical dyes, we would either have to run a strongly convincing advertising campaign to gain customers, or we would have strongly push the price of our products down to be competitive on the market. In the future, the possibility to grow E. coli using waste products as a carbon source could already be an excellent solution to reduce the overall production price and follow a circular economy model. When producing drugs or food additives, such as indirubin and trehalose, we would have to consider the costs of the purification from bacterial debris. Further work might have to be done to develop more economical methods to eliminate endotoxin than the current ones based on expensive antibodies.
An important aspect to consider is obtaining the green light from the future potential users of our products. In this respect, we have already done a questionnaire and spoke to people in our city and found out that they would have no objections in wearing clothes stained with a pigment produced by GMOs. While we do not know what the public thinks of GMO-based medication, we know that before going to the market with our products, we would have to invest time (and money) for an advertising campaign based on clear communication to the public about the science behind our product. We realised that, most often, fear comes from ignorance. Therefore, clear explanations of the work on this project should already help get acceptance.
As with most synthetic biology projects, it is important to consider that our scientific innovation may be used by people with the intention to damage rather than benefit society. Dual use is a problem that should not be disregarded, as it could pose a true danger to society. While trehalose, indigo and indirubin are not toxic and do not pose any danger to humans or society (quite the opposite, they have very beneficial properties for human health), our platform chAMBER could potentially be used to boost the production of harmful compounds. Unfortunately, any new tool developed in the field of synthetic biology bears the potential for dual use. In some cases, the software can be installed to automatically check DNA sequences and notify when hits are found for enzymes known to produce toxic substances. Nonetheless, if the DNA is synthesised in-house, such checks can be easily bypassed. Therefore, when implementing our project in the real world, we would create a working atmosphere where all employees are aware of the danger and keep an eye on each other.