Biocontainment of genetically modified organisms by synthetic protein design

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.

doi:10.1038/nature14121

Biocontainment of genetically modified organisms by synthetic protein design

Journal Article · 20 January 2015 · Nature (London)

DOI:https://doi.org/10.1038/nature14121· OSTI ID:1347113

Mandell, Daniel J. ^[1]; Lajoie, Marc J. ^[2]; Mee, Michael T. ^[3]; Takeuchi, Ryo ^[4]; Kuznetsov, Gleb ^[5]; Norville, Julie E. ^[5]; Gregg, Christopher J. ^[5]; Stoddard, Barry L. ^[6]; Church, George M. ^[7]

Harvard Medical School, Boston, MA (United States). Dept. of Genetics; Office of Scientific and Technical Information (OSTI)
Harvard Medical School, Boston, MA (United States). Dept. of Genetics; Harvard Univ., Cambridge, MA (United States). Program in Chemical Biology
Harvard Medical School, Boston, MA (United States). Dept. of Genetics; Boston Univ., MA (United States). Dept. of Biomedical Engineering
Fred Hutchinson Cancer Research Center, Seattle, WA (United States). Division of Basic Sciences
Harvard Medical School, Boston, MA (United States). Dept. of Genetics
Fred Hutchinson Cancer Research Center, Seattle, WA (United States). Division of Basic Science
Harvard Medical School, Boston, MA (United States). Dept. of Genetics; Harvard Univ., Cambridge, MA (United States). Wyss Inst. for Biologically Inspired Engineering

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. In this paper, 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. Finally, this work provides a foundation for safer GMOs that are isolated from natural ecosystems by a reliance on synthetic metabolites.

View Accepted Manuscript (DOE)

Research Organization:: Harvard Univ., Boston, MA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: FG02-02ER63445

OSTI ID:: 1347113

Journal Information:: Nature (London), Journal Name: Nature (London) Journal Issue: 7537 Vol. 518; ISSN 0028-0836

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Improved sgRNA design in bacteria via genome-wide activity profiling Guo, Jiahui; Wang, Tianmin; Guan, Changge https://doi.org/10.1101/272377	posted_content	February 2018
A Framework for Predicting Design Failures in Engineered Genetic Codes Yu, Bea; Murphy, Matthew; Carr, Peter A. https://doi.org/10.1101/363812	preprint	July 2018
At the Interface of Chemical and Biological Synthesis: An Expanded Genetic Code Xiao, Han; Schultz, Peter G. Cold Spring Harbor Perspectives in Biology, Vol. 8, Issue 9 https://doi.org/10.1101/cshperspect.a023945	journal	July 2016
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A transatlantic perspective on 20 emerging issues in biological engineering Wintle, Bonnie C.; Boehm, Christian; Rhodes, Catherine Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.20852	text	January 2017
Alternative Biochemistries for Alien Life: Basic Concepts and Requirements for the Design of a Robust Biocontainment System in Genetic Isolation Diwo, Christian; Budisa, Nediljko Genes, Vol. 10, Issue 1 https://doi.org/10.3390/genes10010017	journal	December 2018
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An engineered bacterium auxotrophic for an unnatural amino acid: a novel biological containment system Kato, Yusuke https://doi.org/10.7287/peerj.preprints.1001	posted_content	April 2015
An engineered bacterium auxotrophic for an unnatural amino acid: a novel biological containment system Kato, Yusuke https://doi.org/10.7287/peerj.preprints.1001v1	preprint	April 2015
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