Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Stopping Escape and Malfunction in Genetic Code Engineered Cells

Authors:

Anush Chiappino-Pepe1,2* (Anush_ChiappinoPepe@hms.harvard.edu), Felix Radford1,2, Bogdan Budnik1,2, Teresa Augustin1, Huseyin Tas1,2, Hana Burgess1, Michaël Moret1,2, Maksud M. Africawala1, Shova Topa1, Weicheng Fan3, Catherine Zeng3, Jenny M. Tam1,2, George M. Church1,2*

Institutions:

1Department of Genetics, Harvard Medical School; 2Wyss Institute for Biologically Inspired Engineering, Harvard University; 3Genscript, Inc.

Goals

The project engineered an ultra-safe strain of Escherichia coli for controlled growth and function, including production of peptides and proteins containing nonstandard amino acids.

Abstract

Engineered cells can address unmet needs for planetary health. To develop safe cell-based technologies, researchers need engineering strategies that allow control of cellular proliferation and function. Currently, bacteria used as platform technologies rely on a wild-type genetic code, which can result in horizontal gene transfer, escape, and loss of control of the designed programs. Genetic code engineering emerges as a promising alternative since it removes a set of codons and tRNAs from the genome, which should prevent translation of incoming DNA. However, the team discovered a new mechanism of escape in bacteria with an engineered genetic code and characterized it with multiomics and protein language models, resulting in the development of an ultra-safe 61-codon E. coli strain. In this strain, researchers engineered a tRNA/aminoacyl-tRNA synthetase pair for the incorporation of a nonstandard amino acid and kill switches. This is the first organism that enables the production of proteins containing user-defined nonstandard amino acids while remaining tightly biocontained and bioisolated. This work is a headstart to develop ultra-safe living technologies and will allow researchers to decode and expand genome and protein designs.

Funding Information

This project has been funded with government support under DE-FG02-02ER63445 awarded by U.S. DOE and 2123243 awarded by the U.S. National Science Foundation. Dr. Church is a founder of companies in which he has related financial interests: ReadCoor, EnEvolv, and 64-x. For a complete list of Dr. Church’s financial interests, see also https://arep.med.harvard.edu/gmc/tech.html.