By rewriting the DNA of Escherichia coli so that the bacterium requires a synthetic amino acid to produce its essential proteins, two research teams may have paved the way to ensure that genetically modified organisms don’t escape into the environment. The life-or-death dependence of the newly engineered E. coli on synthetic amino acids makes it astronomically difficult for the genetically modified organism to survive outside the laboratory, explains Harvard Medical School’s George M. Church, who led one of the teams reporting the discovery in Nature (2015, DOI: 10.1038/nature14121).
That’s because no pool of synthetic amino acids exists in nature, he explains. A similar strategy was simultaneously published by Farren J. Isaacs and his colleagues at Yale University, also in Nature (2015, DOI: 10.1038/nature14095). The discoveries help construct improved containment barriers for genetically modified bacteria currently used in the biotech-based production of products as diverse as yogurt, propanediol, or insulin, Isaacs says. They also set the stage for expanding the use of genetically modified organisms in applications outside the lab, Isaacs adds. For example, he says, the bacteria could be used as the “basis for designer probiotics for diseases that originate in the gut of our bodies, or for specialized microorganisms that clean up landfills or oil spills.”
“There are all these ideas for using engineered cells [outside the confines of a lab], but the problem is that they’re not contained,” comments Christopher A. Voigt, a synthetic biologist at Massachusetts Institute of Technology. “This is the proof-of-principle work for addressing that problem.” To make the genetic firewall, both teams made changes to E. coli’s genome so that the bacteria’s protein production machinery inserts a nonnatural amino acid when it reads a specific three-base-pair codon. “They’ve extended the genetic code so that it can take a 21st amino acid,” explains Tom Ellis, a synthetic biologist at Imperial University, in London, who was not involved in the work. The two teams used different synthetic amino acids, but both groups selected mimics of phenylalanine, a bulky, hydrophobic amino acid.
Next, both teams scoured E. coli’s genome for essential proteins that the organism needed to survive. They looked for areas in those proteins where the synthetic amino acids might replace natural amino acids. Although both teams combined computational design and evolutionary biology to select which amino acid to replace in three essential proteins, Church’s team relied more on the former approach and Isaacs’ team on the latter.
Finally, they showed that when the engineered bacteria have access to a pool of the synthetic amino acids, they can build their essential proteins. With no access to the synthetic amino acids, protein production stalls and the bacteria die.
The teams performed extensive tests to see whether the newly engineered bacteria could evolve ways to sidestep the need for synthetic amino acids. Whenever the microbes managed the feat, the researchers tweaked the DNA until the bacteria depended solely on the synthetic amino acids.
Previous strategies for containing genetically modified bacteria seem “naive” in hindsight, Ellis says. These earlier strategies employed kill switches, which are “systems where the organism dies if some compound or environmental cue wasn’t given,” he adds. “Here the kill system is fully embedded in the heart of the bacteria.”
In theory, the strategy could be extended to other genetically modified organisms, such as plants, Voigt says. “It will probably be really hard, but not impossible,” he adds. According to Ellis, the next step is to get the platform working in yeast, which will be “an order of magnitude harder than bacteria.”
Another important step is to improve containment by ensuring that all DNA engineered into the organism relies on the synthetic amino acid, Ellis says. “If you accidentally spill the bacteria into the environment, it’s going to die,” he says. “But that DNA is left behind. The genetically modified genes could be incorporated into other bacteria through horizontal transfer,” he warns. “To alleviate all fears, we need to ensure that all genes you add to an organism—say for making insulin or biofuels—are also behind the genetic firewall and somehow encode the 21st amino acid.”
Via Dr. Stefan Gruenwald