Biocontainment of genetically modified organisms by synthetic protein design

• Published in: Nature (London) 2015-02, Vol.518 (7537), p.55-60
• Main Authors: Mandell, Daniel J., Lajoie, Marc J., Mee, Michael T., Takeuchi, Ryo, Kuznetsov, Gleb, Norville, Julie E., Gregg, Christopher J., Stoddard, Barry L., Church, George M.
• Format: Article
• Language: English
• Subjects: 101/58; 119/118; 13/31; 38/1; 38/77; 42/70; 45/23; 631/114; 631/181/735; 631/208; 631/61; Amino acids; Amino Acids - chemistry; Amino Acids - metabolism; BASIC BIOLOGICAL SCIENCES; Biological Evolution; biotechnology; Codon - genetics; computational biology and bioinformatics; Containment of Biohazards - methods; Design; E coli; Ecosystem; Escherichia coli - enzymology; Escherichia coli - genetics; Escherichia coli - growth & development; Escherichia coli - metabolism; Escherichia coli Proteins - biosynthesis; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; Gene Transfer, Horizontal - genetics; Genes; Genes, Essential - genetics; Genetic Code - genetics; Genetic engineering; Genetic Engineering - methods; Genetically modified organisms; genetics; Humanities and Social Sciences; Metabolites; Microbial Viability - genetics; molecular evolution; multidisciplinary; Mutation; Mutation - genetics; Organisms; Organisms, Genetically Modified - genetics; Organisms, Genetically Modified - metabolism; Proteins; Safety; Science; Selection, Genetic; Synthetic Biology - methods
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/nature14121

Genetically modified organisms (GMOs) are increasingly deployed at large scales and in open environments. Genetic biocontainment strategies are needed to prevent unintended proliferation of GMOs in natural ecosystems. Existing biocontainment methods are insufficient because they impose evolutionary pressure on the organism to eject the safeguard by spontaneous mutagenesis or horizontal gene transfer, or because they can be circumvented by environmentally available compounds. 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 non-standard amino acids for survival. 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. This work provides a foundation for safer GMOs that are isolated from natural ecosystems by a reliance on synthetic metabolites. Essential enzymes in genetically modified organisms are computationally redesigned to functionally depend on non-standard amino acids, thereby achieving biocontainment with unprecedented resistance to escape by evolution or by supplementation with environmental metabolites. Two routes to safer GMOs Two manuscripts published in this issue of Nature describe independent approaches towards generating an organism dependent on unnatural amino acids, a development which could find applications for biocontainment and exploration of previously unsampled fitness landscapes. George Church and colleagues redesigned essential enzymes in an organism ( Escherichia coli ) with an altered genetic code to make it metabolically dependent on non-standard amino acids for survival. The resulting genetically modified organisms (GMOs) cannot metabolically circumvent their biocontainment mechanisms and show unprecedented resistance to evolutionary escape. The few escapees are rapidly outcompeted by unmodified organisms. Using multiplex automated genome engineering, Farren Isaacs and colleagues construct a series of genomically recoded organisms whose growth is restricted by the expression of essential genes that depend on exogenously supplied synthetic amino acids. They constructed synthetic auxotrophs with advanced orthogonal barriers between engineered organisms and the environment, thereby creating safer GMOs.