Team:UCL/Project/Xenobiology

The wide use of genetically modified organisms causes concerns on how they will interact in the natural environment. In particular could the genetically modified 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?
Since the early days of genetic engineering we had to reflect on biosafety strategies to control these risks, and synthetic biology is bringing these concerns to another level: the more we tinker with biology, the more our biosafety needs to be bullet-proof.

Xenobiology 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 new XNAs, genetic codes and cofactors different 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 environmentnor will be able to use bacterial communication systems.

We explored this possibility with the longer term vision of creating an X. coli which lives is metabolically dependent on 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 non-biological life safe enough?

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:

1. Restriction enzyme systems: autodestruction of the transformed plasmid when task ended
2. Semantic containment: different meaning of stop codon, other bacteria will read as stop e.g. amber codon
3. Auxotrophy: knock-out of biosynthesis of a key naturally produced compound that needs to be provided in the media
4. Suicide system: bacteria die when finished its task/changes environment e.g. toxin/antitoxin where the bacteria stops producing antitoxin when triggered hence dies

Xenobiological strategies

The safety mechanism embedded is into the system on three different levels:

1. Genetic Firewall: Use of XNAs, incompatible with other organisms and synthetic nucleotides not found in nature
2. Semantic Firewall: Genetic code has a different meaning than the natural code, all the codons code for a different amino acid from the standard table and could code for non-natural amino acids as well
3. Metabolic Firewall: A Synthetic auxotrophy that uses a xenobiotic compound as key cofactor/amino acid which the bacteria is unable to produce or find in the natural enviroment

Designing Xeno-Coli

We aim to engineer the bacteria to utilise the synthetic dyes - a completely xenobiotic compound - as the key cofactor in respiration, substituting quinones in the electron transport chain.
Our X. coli will therefore only be able to survive in the presence of azodyes, a particular environment only found in the wastewater of the textile indutry that it is aimed to degrade. The biosafety strategy is embedded into the system, and tighly linked to the survival of the xenobiological organism.