The E. coli Genome Redesigned with 101,000 DNA Modifications

Unlike the natural evolution of life forms, our ability to create life has reached new heights. The genome of an E. coli bacterium has been meticulously redesigned via computer simulations, utilizing just 57 out of the 64 genetic codons. This synthetic genome was built from the ground up and introduced into living bacterial cells.

“This was a massive undertaking,” states Wesley Robertson from the Institute of Medical Research in Molecular Biology, Cambridge, UK.

The objective was to demonstrate the feasibility of this approach, with the 57 codons, termed Syn57, offering commercial applications. Future modifications could enable Syn57 to develop complete resistance to viral infections, a significant benefit for the industrial production of proteins used in pharmaceuticals, food, or cosmetics. Since viral proteins depend on their hosts to produce, altering the genetic code can lead to erroneous viral proteins.

Moreover, additional modifications permit Syn57 to synthesize proteins containing up to 27 amino acids, whereas natural proteins are limited to 20. These synthetic proteins hold potential for functions unattainable with conventional proteins.

A protein is essentially a sequence of amino acids arranged in a specified order determined by a gene. Each triplet of DNA bases, known as a codon, instructs the synthesis machinery on when to add the next amino acid or when to cease the protein assembly.

There are four DNA bases that combine to produce 64 distinct codons. However, organisms on Earth typically utilize only 20 amino acids, leading to considerable redundancy, with multiple codons corresponding to each amino acid.

If all instances of a specific codon for an amino acid were substituted with another codon for the same amino acid, that original codon could then be repurposed. For instance, it could code for non-natural amino acids or alternative chemicals, facilitating the creation of novel protein types.

Theoretically, only 21 unique codons are required, allowing for a biological organism to free up to 43 codons—one for each natural amino acid and one stop codon. However, this is not yet feasible, as increasing genetic alterations raises the likelihood of harmful unintended consequences.

Instead, biologists are taking a more measured approach. In 2011, an edit of 314 genes in E. coli aimed to free one codon.

Because executing thousands of genetic edits is so labor-intensive, Robertson and his team opted to synthesize the DNA from scratch. In 2019, they introduced Syn61, incorporating 18,000 changes across 4 million DNA bases, achieving the release of three codons in the E. coli genome. A derivative company named Constructive.Bio is working on commercial applications.

Currently, researchers are implementing 101,000 modifications to release seven codons within Syn57. This process necessitated testing small sections of the reconstructed genome on live bacterial cultures to identify and rectify harmful changes. This complex procedure was repeated with progressively larger genome fragments until the entire structure was reassembled.

“This marks a significant achievement, resulting from years of effort,” mentions Akos Nyerges at Harvard Medical School. Nyerges’ team is also working to release seven codons in E. coli via different codon reproductions. “Our journey with the 57 codons in E. coli is ongoing,” he adds.

While Syn57 is already fully established, its growth rate is significantly slower than that of typical strains. Enhancements in this aspect are essential for commercial viability. “We anticipate being able to improve the growth rates, making it more beneficial,” remarks Robertson.

For the time being, his focus will be on investigating the potential applications of Syn57 rather than attempting further codon releases. “There’s still a great deal to accomplish before contemplating even more compressed genetic codes,” he concludes.

The first synthetic genome bacteria were created in 2010, but their design aimed more at simplifying organisms than at codon recovery.