Recoding of Bacterial Genome Produces Proteins with New Functions

Altered stop codon allows E. coli strain to incorporate nonstandard amino acids.

Image courtesy of the U.S. Department of Energy Genomic Science program,
Protein production occurs in two basic steps: transcription and translation. Transcription is the process of making messenger RNA (mRNA), a temporary copy of a gene’s DNA sequence. In translation, the nucleotide base sequence of mRNA is used to direct the synthesis of a protein’s sequence of amino acids. Researchers have successfully engineered a bacterium to produce proteins with new amino acids by altering its genome.

The Science

Along with the biological molecules they naturally synthesize, engineered bacteria are used in biotechnology to produce enzymes and other proteins. However, the spectrum of possible proteins that can be biotechnologically produced is limited by the 20 amino acids in the genetic code that are added one at a time to build a linear protein chain during translation. One way to expand the potential functions of engineered proteins is to add amino acids to the repertoire that can be incorporated into proteins. To achieve this, researchers altered the genome of the model bacterium Escherichia coli so that it no longer used one of its three stop codons, a set of three messenger RNA (mRNA) bases that signal the end of protein synthesis.

The Impact

This research—conducted by scientists at Harvard and Yale universities—has tremendous implications for engineering organisms to produce novel proteins that perform new functions needed in processes relevant to the DOE mission, including biofuel production.


Once the E. coli strain was recoded, the freed stop codon (UAG) was used to incorporate new amino acids by providing the necessary machinery—a modified transfer RNA (tRNA) that recognizes UAG and a special aminoacyl–tRNA synthetase, the enzyme that loads amino acids onto the tRNA. With these tools, the researchers showed that they can incorporate novel amino acids into a selected protein without affecting the rest of the bacterial proteins and while maintaining a normal cellular physiology. In addition, the recoded cells are less susceptible to viral infection, and the risk of transferring altered DNA to other organisms is minimized because the normal protein synthesis machinery will not work properly with the recoded genes from the recoded strain.


Farren J. Isaacs
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520

George M. Church
Department of Genetics, Harvard Medical School, Boston, MA 02115


Funding provided by the U.S. Department of Energy (DE-FG02-02ER63445), National Science Foundation (NSF; SA5283-11210), National Institutes of Health (NIH; NIDDK-K01DK089006, NIH-MSTP-TG-T32GM07205), Defense Advanced Research Projects Agency (N66001-12-C-4040, N66001-12-C-4020, N66001-12-C-4211), Arnold and Mabel Beckman Foundation, U.S. Department of Defense National Defense Science and Engineering Graduate Fellowship, NSF graduate fellowships, NIH Director’s Early Independence Award (1DP5OD009172-01), and the Assistant Secretary of Defense for Research and Engineering (Air Force Contract no. FA8721-05-C-0002).


Lajoie, M. J., et al. “Genomically recoded organisms expand biological functions,” Science 342 (6156), 357–360 (2013). [DOI: 10.1126/science.1241459].

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