Containing Genetically Modified Bacteria

At a Glance Researchers altered the genomes of bacteria to make them unable to survive without a synthetic nutrient.

This technique may prove effective for preventing genetically modified bacteria from surviving in the wild.

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Genetically modified organisms (GMOs) are widely used in research and for making pharmaceuticals and other products. However, use of genetically modified bacteria outside of the lab has been limited by concerns that they—and the sometimes novel genes they carry—could escape into the wild.

Scientists have attempted to solve this problem in a variety of ways, including the creation of bacteria that depend on nutrients they can’t make themselves. But these bacteria might survive in the wild by receiving those nutrients from natural organisms.

One potential solution would be to create genetically engineered bacteria that are dependent on nutrients not found in nature. Researchers previously changed the genetic code of bacteria to allow them to incorporate synthetic amino acids (sAAs) into their proteins. A team led by Dr. Farren Isaacs of the Yale School of Medicine set out to make such “genomically recoded organisms” (GROs) dependent on sAAs for survival. Their work was supported by the Defense Advanced Research Projects Agency, NIH’s National Institute of General Medical Sciences (NIGMS), and others. The study appeared on February 5, 2015, in Nature.

Each set of 3 nucleotides in a DNA strand, called a codon, directs the cell to add a specific amino acid to a growing chain to form a protein. The team modified the genome of Escherichia coli so that the TAG codon directed the bacteria to incorporate sAAs into proteins.

The researchers introduced these TAG codons into 22 essential genes. They then compared the growth of these bacterial strains in the presence and absence of sAAs to find those with the lowest “escape frequencies”—that is, those least able to grow without the sAA. In a series of experiments, they were able to construct strains with very low escape frequencies by combining TAGs from the strains with the lowest escape frequencies.

To eliminate any rescue by natural amino acids, the team chose 4 of these essential genes dispersed throughout the genome. They then introduced TAG codons into carefully chosen sites known to be involved in functional protein–protein interactions. One strain with 3 of the TAG codons was able to grow well when provided the sAA, but showed no detectable growth without it.

“This is a significant improvement over existing biocontainment approaches for genetically modified organisms,” Isaacs says. “This work establishes important safeguards for organisms in agricultural settings, and more broadly, for their use in environmental bioremediation and even in medical therapies.”

Another team led by Dr. George Church of Harvard Medical School published a study in the same issue of Nature describing a similar result. Such research may lead to new beneficial proteins and organisms that are designed with multiple safeguards.

— by Brandon Levy and Harrison Wein, Ph.D.