Genetically modified E. coli dependent on synthetic nutrients

While genetically modified organisms (GMOs) have imparted many benefits on society - including churning out drug ingredients, helping produce biofuels, teaching scientists about human disease, and improving fishing and agriculture - they also have the potential to upset natural ecosystems if they were to escape.

Physical containment of GMOs is not foolproof, so attention has since turned to biocontainment: building in biological safeguards to prevent the organisms from surviving where they’re not meant to. In the case of Professor George Church of Harvard Medical School’s Wyss Institute, the secret was making an organism whose life was dependent on something only he and his group could supply.

In 2013, Church and his team created the world’s first genomically recoded organism - a strain of Escherichia coli with a radically changed genome. Writing recently in the journal Nature, the scientists reported that they had further modified the E. coli to incorporate a synthetic amino acid in many places throughout their genomes. Without this amino acid - which cannot be created by the organism or found anywhere in the wild - the bacteria are unable to perform the vital job of translating their RNA into properly folded proteins.

“We now have the first example of genome-scale engineering rather than gene editing or genome copying,” said Church. “This is the most radically altered genome to date in terms of genome function. We have not only a new code, but also a new amino acid, and the organism is totally dependent on it.”

The process built on the existing method of turning normally self-sufficient organisms like E. coli into auxotrophs - creatures which can’t make certain nutrients they need for growth. The team also made 49 genetic changes to protect against the possibility that the E. coli could acquire the ability to synthesise the nutrient over time. According to Church, the chance one of the bacteria could randomly undo all of those changes, without also acquiring a harmful mutation, is incredibly slim.

These criteria limited Church and his team to “a small number of genes”, he said. The group used computational tools to design proteins that might cause the desired “irreversible, inescapable dependency”. They took the best candidates, synthesised them and tested them in actual E. coli.

They ended up with three successful redesigned essential proteins - whose combined capacity was “more powerful than using them separately”, Church said - and two dependent E. coli strains. By targeting the proteins that drive the essential functions of the bacterial cell, the E. coli would be unable to flourish even if it did escape.

The group grew a total of 1 trillion E. coli cells, 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 Church.

Church’s team also made the E. coli resistant to two viruses, with more to follow. The modifications offer theoretically safer E. coli strains that could be used in biotechnology applications with less fear that they will be contaminated by viruses, or cause ecological trouble if they spill.

A separate group, led by a Farren Isaacs of Yale University (a long-time collaborator of Church’s), has meanwhile been able to engineer the same strain of E. coli to become dependent on a synthetic amino acid using different methods. The success of the two studies suggests scientists may one day develop something that, according to Church, “will be so biologically contained that we won’t need physical containment anymore”.

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