Intending to make the world safe from genetically modified organisms gone rogue, scientists from Harvard Medical School and Yale University have devised what may be the ultimate in biocontainment: genomic recoding. The technique, a radical form of genetic engineering, has been used to render a strain of Escherichia coli dependent on an amino acid that does not occur naturally. Were the E. coli to escape into the open environment, it would soon expire, deprived of a synthetic nutrient available only in specially formulated laboratory cultures.

Genomic recoding is a timely advance. To date, most genetically engineered organisms have been vessel-bound, serving as tiny chemical factories. By and large, these organisms require finely tuned environments to survive. They are simply too feeble to survive in the microbial wild. Yet genetically engineered organisms are being prepared to leave the cozy confines of the laboratory and clean up the environment or unwind disease processes.

More robust bugs require more stringent safeguards. Such safeguards have been described in a pair of papers that appeared January 21 in the journal Nature. One paper, prepared by Harvard scientists led by George M. Church, Ph.D., is entitled, “Biocontainment of genetically modified organisms by synthetic protein design.” Another paper, prepared by Yale scientists led by Farren J. Isaacs, Ph.D., is entitled, “Recoded organisms engineered to depend on synthetic amino acids.”

“Here we computationally redesign essential enzymes in the first organism possessing an altered genetic code (Escherichia coli strain C321.ΔA) to confer metabolic dependence on nonstandard amino acids for survival,” wrote the Harvard team. “The resulting GMOs cannot metabolically bypass their biocontainment mechanisms using known environmental compounds, and they exhibit unprecedented resistance to evolutionary escape through mutagenesis and horizontal gene transfer.”

The approach described by the authors goes beyond existing biocontainment methods in a couple of respects. It does not merely engineer organisms to cease making a naturally occurring nutrient. (Such organisms may simply start scavenging the nutrient from the environment.) And it does not rely on a “kill switch,” which can essentially become jammed. What’s more, in creating E. coli dependent upon a synthetic nutrient, the Harvard team introduced 49 genetic changes, drastically lowering the probability that the bacterial could randomly undo all of those changes without also acquiring a harmful mutation.

The Yale team, which also engineered E. coli to become dependent on a synthetic amino acid, described their approach as follows: “Using multiplex automated genome engineering, we introduced in-frame TAG codons into 22 essential genes, linking their expression to the incorporation of synthetic phenylalanine-derived amino acids.

“We constructed synthetic auxotrophs dependent on [synthetic amino acids] that were not rescued by cross-feeding in environmental growth assays. These auxotrophic GROs possess alternative genetic codes that impart genetic isolation by impeding horizontal gene transfer and now depend on the use of synthetic biochemical building blocks, advancing orthogonal barriers between engineered organisms and the environment.”

Another study by the Yale team appeared January 21 in Nucleic Acids Research (“Multilayered genetic safeguards limit growth of microorganisms to defined environments”). It described the use of overlapping safety measures—engineered riboregulators that tightly control expression of essential genes, and an engineered addiction module based on nucleases that cleaves the host genome—to restrict viability of E. coli cells to media containing exogenously supplied synthetic small molecules.

The authors noted that the new code paired with artificial amino acids will allow scientists to create safer GMOs for use in open systems, which include improved food production, designer probiotics to combat a host of diseases, and specialized microorganisms that clean up oil spills and landfills. “This is a significant improvement over existing biocontainment approaches for genetically modified organisms,” explained Dr. Isaacs. “This work establishes important safeguards for organisms in agricultural settings, and more broadly, for their use in environmental bioremediation and even in medical therapies.”

With respect to escape rate measurements, the Harvard team cited encouraging results. It grew a total of 1 trillion E. coli cells from various experiments, and after two weeks none had escaped. “That's 10,000 times better than the National Institutes of Health's recommendation for escape rate for genetically modified organisms,” said Dr. Church.

“As part of our dedication to safety engineering in biology,” he added, “we're trying to get better at creating physically contained test systems to develop something that eventually will be so biologically contained that we won't need physical containment anymore.”

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