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Team:UCL/Project/Xenobiology
From 2014.igem.org
The ultimate safety tool
“Any technological advance can be dangerous. Fire was dangerous from the start, and so (even more so) was speech - and both are still dangerous to this day - but human beings would not be human without them.” - Isaac Asimov
Since the early days of genetic engineering, our ability to manipulate living organisms had to face the invevitable risks of any new technology. We cannot predict all the possible risks of our inventions and, as scientist, we have the responsibility to implement all the safety measures against known and unknown outcomes.
The Asilomar conference first addressed these concerns, which Synthetic Biology is bringing to another level: as our tinkering with Biology increases, the unknowns of this technology expand and oblige us to further reflect on the safety measures we need to implement.
Xenobiology is the part of synthetic biology that mostly implements the term "synthetic" by creating organisms that are unable to survive in the natural environment and necessitate an artificial intervention from man to exist. It aims to create a synthetic "man-made" version of Biology that respects the definition of life, but is based on entirely different mechanisms to function.
The biochemistry of a xeno-organism uses different materials from the ones explored by Biology and is therefore incompatible with other forms of life. This allows a much higher level of control: a xeno-organism will not be able to find the xenocompounds in the natural environment, and will not be able to use bacterial communication systems.
We explored this possibility with the longer term vision of creating an X. coli which lives only because of azo dyes. An alien form of life, different from the one we know, will merge synthetic chemistry with synthetic biology - allowing the remediate the damage that the first one caused and making the remediating agent dependent on the toxic compounds. This system would be completely incompatible and invisible to regular biology, now we can ask: is alien life safe enough?
Biosafety in Synthetic Biology
The wide use of genetically modified organisms causes concerns on how they will interact in the natural environment. In particular could the genetically modiefied microbes escape our constrains, and outcompete the organisms found in the natural ecosystem? Could the DNA we inserted into a specific bacteria be transmitted, with unknown spread of information?
Leak of Bacteria
Containing engineered microorganisms has been the main concern of genetic engineers.The leak of any form of life into a new environment could destabilise the environment, and the same problem applies to synthetic forms of life. Any new organism could outcompete the natural species and undermine the equilibrium of an ecosystem.
Physical containment can be addressed with auxotrophic strains, sterilisation of tools and materials used in experiments together with a conscious waste disposal.
Nevertheless, as the image shows, the possibility - even if remote - of an accident is always present and any biosafety measure should take into account the worst case scenario.
Leak of DNA
The leak of bacteria is not the only risk involved in the use of GE organisms. The information encoded into the GE is new and has been artificially designed for that specific microorganism. We assume that it will not have any other effect than the ones we predicted, but we also have to remember that our knowledge is limited and we moderate any unknown risk.
DNA can also leak from the microorganisms and it is possible that other bacteria can take up that information and start behaving accordingly. We could give a selective advantage (e.g. antibiotic resistance?) to some specific bacteria and our control over the consequences would come close to zero.
Even if the evidence for leak of GE strains of bacteria shows that they are strongly disadvantaged in the natural environment, we don't know how the spread of DNA could affect other species, in particular as the level of engineering becomes higher and higher.
Biological vs. Xenobiological strategies
Biosafety strategies have so far explored biology to implement clever control mechanisms to control. They investigated various strategies that allow to kill bacteria when needed or that hinder genetic information to spread among different organisms. Our biosafety strategy is exploring the regions outside of Biology, with the ultimate goal of bringing Biology to a parallel domain where it does not interact with our own one. Why tinkering with our same Biology when we can create a new on, at the same time biology and technology, that we can control at a much higher level?
Biological strategies
The biosafety mechanism is added to the system as additional layers of protection, the most explored are:
- Restriction enzyme systems:
- Semantic containment e.g. amber codon
- Suicide system e.g. toxin/antitoxin
- Auxotrophy
Xenobiological strategies
The safety mechanism embedded is into the system on three different levels:
- Genetic Firewall: Use of XNAs, incompatible with other organisms and synthetic nucleotides not found in nature
- Semantic Firewall: Genetic code has a different meaning e.g. amino acids correspond to different codons
- Metabolic Firewall: A Synthetic auxotrophies that uses a xenobiotic compound as key cofactor/amino acid
Silence quinones production in E. coli
- Identified ispB: both ubiquinone and menaquinone (the two quinones in e. coli)
- Prepared a gene silencing strategy as a first proof of concept
Xenoquinone from azo dyes
- analyse a library of azo dye breakdown product most similar to quinones (software) - identify and prepare the specific one for substitution (chemist)
Xenoquinones as permissive condition
Directed evolution on E. coli
Reference:
- Wright, O., Stan, G.-B., and Ellis, T. (2013). Building-in biosafety for synthetic biology. (Review) Microbiology, 159, 1221-1235. http://www.ncbi.nlm.nih.gov/pubmed/23519158
- Okada, K., Minehira, M., and Zhu, X. (1997). The ispB gene encoding octaprenyl diphosphate synthase is essential for growth of Escherichia coli. Journal of Bacteriology, 179, 3058–3060. http://www.ncbi.nlm.nih.gov/pubmed/9139929
- Søballe, B. , Poole, K. R. (1999). Microbial ubiquinones: multiple roles in respiration, gene regulation and oxidative stress management. (Review) Microbiology, 145, 1817-1830. http://www.ncbi.nlm.nih.gov/pubmed/10463148
- Schmidt, M (2010). Xenobiology: A new form of life as the ultimate biosafety tool Bioessays, 32, 322-331. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2909387/
- Malyshev, D.A., Dhami, K., Lavergne, T. et al. (2014). A semi-synthetic organism with an expanded genetic alphabet Nature, 509, 385-388. http://www.nature.com/nature/journal/v509/n7500/full/nature13314.html
