Mandell and colleagues (2015), in a very recent paper in Nature, describe their successful efforts to take the concept of synthetic biology and applied it to biocontainment of bacteria (E. coli), building in synthetic amino acids as safeguards should they be released into the environment either inadvertently or deliberately.
Genetic technologies are being applied to create genetically engineered (GE) organisms for many applications including the production of biofuels, crops with novel traits, human therapeutics, fermentation products and also for insect pests.
However, where you require the GE organism to be contained, for example with drug production or some biofuels, there are some public concerns about how they may affect the environment if they escape containment and let the ‘genie out of the bottle’.
To address these concerns GE organisms are currently regulated and before commercialization have to pass stringent safety and efficacy standards and review from the relevant regulatory agencies.
The concept of biocontainment of bacteria is not new and several methods have been developed, mainly around kill switches to destroy bacteria if they escape or making an organism reliant on an essential nutrient (auxotrophs).
These methods work but they are relatively easy for a bacterium to evolve resistance. With kill switches there are a number of known mechanisms to switch off the killing mechanism and with auxotroph’s there can be numerous mechanisms of overcoming the auxotrophy, including either making or scavenging the essential nutrient from the environment.
Mandell et al (2015) created auxotrophic bacterial strains but instead of changing the organism to require a natural amino acid they developed a synthetic amino acid, producing a ‘synthetic auxotrophic’ strain. This has a potential advantage that the amino acid is not found in the natural environment so the ability to overcome this auxotrophy is far less likely.
To develop the synthetic amino acid (in this case biphenylalanine) they used computational design, mass spectrometry to confirm insertion and then X-ray crystallography to check structure of the resulting protein.
They found that to reduce potential frequencies to the levels reported (virtually zero) they had to insert only around 32-49 base pair substitutions out of a 4.6Mb genome.
This is a relatively low number of changes compared to other systems where complete genes are replaced or edited; they also did not delete any essential genes or produce any toxic products. The work showed that they could almost eliminate escape through mutagenesis, the scavenging nutrients and horizontal gene transfer.
This all sounds useful for the biocontainment of GE bacteria but is this relevant to other engineered organisms including those used for the control of insect pests?
There are already many genetically engineered crops in the market that have gone through the regulatory process and been proven safe for commercial use, e.g. over 90% of the world’s soya is genetically engineered.
In Brazil, commercial approval has been granted for the use of GE Ae. aegypti (OX513A) which uses switchable system utilising tetracycline antibiotics, so in this system the ‘genie is contained in the bottle’. The synthetic auxotrophy system itself is complicated to develop requiring a lot of research, including the design of appropriate synthetic amino acids, checking how they function in the proteins they are expressed i.e. that they do not affect the protein activity, and whether mechanisms for them to be overcome exist.
Mandell et al (2015) reported that in some of the redesigned proteins they observed higher levels of escape than others. So overall this is likely to be an over-complicated and redundant system to introduce into GE organisms that are already considered safe to release into the environment. In addition, supplying the synthetic amino acid to the GE organism in the environment, as you would with GM crops to allow them to grow, presents its own challenges and safety issues.
Applications where this could be useful are where the GE organism needs to be inherently contained i.e. in therapeutic drug production or if the GE organism could be inherently unsafe but the risks outweigh the benefits. An example being a targeted therapeutic bacterial delivery system for the treatment of cancer with toxic chemicals and where you would not want the bacteria spreading outside of the patient.
But as genetically engineered crops and insects already go through stringent regulatory processes to evaluate safety and are designed to be safe this technology is redundant. In addition regulatory agencies would be required to assess not only beneficial GE traits but also the environmental impact of additional gene changes and the introduction of synthetic amino acids into cultivation or rearing systems. Therefore, the widespread deployment may have practical and regulatory draw backs.
This could be a useful technology in closed systems, where the GE organism might carry undesirable genes into the environment. This is a paper worth reading to see clever and sophisticated applications of genetic technologies.
Daniel J. Mandell, Marc J. Lajoie, Michael T. Mee, Ryo Takeuchi, Gleb Kuznetsov, Julie E. Norville, Christopher J. Gregg, Barry L. Stoddard & George M. Church 2015 Biocontainment of genetically modified organisms by synthetic protein design Nature 518, 55–60 (05 February 2015) doi:10.1038/nature14121