On March 15, Nature reported a breakthrough in which George Church's team designed a strain of E. coli that is immune to any known virus infection and for the first time developed a built-in safety measure to prevent modified genetic material from escaping into natural ecosystems. A related article titled "A swapped genetic code prevents viral infections and gene transfer."
(Source: Nature)
"We can't say it's completely antiviral, but so far, based on extensive laboratory experiments and computational analysis, we haven't found a virus that can destroy it." Akos Nyerges, the first author of the article, said.
The article states, "This study may provide a general strategy to make any organism resistant to many or all natural viruses and prevent the inflow of genetic information into and out of GMOs." ”
"We expect this result to have an impact on the safe use of GMOs in open environments."
Exchange genetic code and mistranslate viral proteins
In October last year, the Cambridge team published the research results in Science "aiming to obtain a safe antiviral bacteria", which genetically reprogrammed E. coli, reduced the naturally occurring 64 codons to 61 codons, deleted the two sets of codons TCG and TCA corresponding to serine (there are six sets of codons corresponding to serine in nature), and also removed the corresponding tRNAs in an attempt to disrupt the self-replication after virus invasion.
(Source: Science)
It is envisaged that the missing codon would prevent the virus from making proteins on demand, thus achieving an antiviral effect.
However, Akos Nyerges and others found a loophole, and some viruses introduce their own tRNAs to bypass the lost codon and still be able to replicate themselves.
This result shows that simply removing codons is not enough.
Since "delete" doesn't work, let it be "mistranslated".
George Church's team added new tRNAs to their place, translating the codons TCG and TCA, which originally correspond to serine, into leucine, an amino acid that is physicochemically different from natural serine.
▲Figure 丨The genetic code of amino acid exchange provides a variety of viral resistance. a, TCA and TCG codons in modified E. coli are reassigned to leucine. b, Schematic diagram of engineering E. coli virus infection (Source: Nature)
In this way, when the virus injects its own genetic code, the TCG and TCA in it will be mistranslated and cannot achieve the purpose of hijacking the cell.
Of course, the virus is also equipped with its own tRNAs that can still accurately convert TCG and TCA to serine. But the researchers provided evidence that the tRNAs they introduced could defeat viral counterparts.
The researchers say that by demonstrating effective serine-to-leucine reprogramming, this study makes biological containment possible at the gene, operon and entire chromosomal levels.
"While this work may make bacteria immune to all viruses, it's still possible that something could disrupt protection." However, overcoming the exchange codon would require the virus to produce dozens of specific mutations simultaneously, which is very, very unlikely for natural evolution. ”
Two safeguards to prevent gene escape
Studies have also shown that exchanging genetic codes prevents viruses from replicating while also preventing synthetic genetic information from escaping into other organisms.
This work consists of two separate safeguards.
The first safeguard prevents horizontal gene transfer. Horizontal gene transfer, also known as horizontal gene cloning or lateral gene transfer, refers to the process by which organisms transmit genetic material to other cells rather than their offspring, such as ligation, transduction, and transformation.
In modified E. coli, the researchers used the introduced tRNAs to change TCG or TCA to all corresponding leucine. If another organism integrates any modified fragment into its genome, the organism's native tRNAs will revert TCG and TCA to their serine counterparts, resulting in junk proteins without any evolutionary advantage.
▲Figure 丨Adding synthetic genetic information to the genetic code encoding leucine of the TCR codon can prevent horizontal gene transfer (Source: Nature)
For the second fail-safe measure, the team engineered the bacteria themselves to make it impossible to survive outside of a controlled environment by making E. coli dependent on a lab-made amino acid that is not present in the natural environment.
Overall, this study achieves unprecedented resistance to gene transfer, proving that it is possible to exchange the genetic code of organisms.
The authors also point to potential limitations of this work, including the viral diversity of the samples and the inability of viral resistance assays to sample the multi-step, long-term evolutionary process of viruses.
At present, adaptive laboratory evolution has greatly improved the doubling time of organisms with altered genetic code, which can help improve the development of modified E. coli in the direction of industrial applications.
The authors also look forward to exploring codon reprogramming as a tool to induce bacteria to produce medical synthetics as an alternative to expensive chemical reactions.
Further application prospects include the use of this strategy to prevent the release of transgenes during bioremediation and to provide control for the open culture of engineered photoautotrophs for carbon sequestration; and enabling safe microbial engineering and vaccine production.
Reference Links:
1.https://www.nature.com/articles/s41586-023-05824-z
2.https://www.science.org/doi/10.1126/science.add8943