For all the excitement surrounding the gene-editing tool CRISPR, it is not that efficient or precise. It’s hard to make many changes at once. My lab has set the record so far — making 62 modifications to the genome of a single cell — but we have compelling applications that need a greater number of simultaneous changes. Now, however, we have the technologies required to make this feasible.
‘Codon recoding’ is a completely generic way to make any organism resistant to most or all viruses and requires tens of thousands of precise changes per cell. Each codon, a section of DNA three bases long, such as TTG, corresponds to a specific amino acid, such as leucine, or a translational signal (start, stop and so on). Given that there are six codons for the leucine, we can switch any one for another, taking advantage of the redundancy built into the genetic code. Once done with those swaps, we delete the gene for the leucine transfer RNA (tRNA) that matches up with the swapped-out codons, so the cell can no longer recognize that sequence.
Now, when a virus infects a cell that has all of these codons recoded, it cannot translate its proteins from its messenger RNA because of the missing tRNA, and the virus will die. Viruses are not that robust; it doesn’t take much to throw them out of whack.
To make multiple, precise changes at once, we use the multiplexed automated genome engineering (MAGE) technique. Short segments of genetic material containing the precise base-pair changes you want to make are introduced into cells that are prevented from making DNA-mismatch repairs. After a few rounds of cellular replication the changes are incorporated fully into the bacterial genome.
Theoretically, this can be done in every organism for which viruses are a problem — microorganisms used in the dairy industry and agriculturally important plants and animals. In addition, researchers could make virus-resistant pigs whose organs can be used for transplants, and virus-resistant human cells to use for producing pharmaceuticals and vaccines.
What is really gee whiz here is that you have the potential to make an organism resistant to all viruses — even viruses that have never been studied. But there are many other things that recoding can accomplish. Pamela Silver at Harvard Medical School and Daniel Gibson at Synthetic Genomics in La Jolla, California, have collaborated to develop another recoding technology to improve vaccine strains of Salmonella typhimurium.
Researchers could also recode an organism to incorporate non-standard amino acids in proteins to enable chemistries that don’t exist in current organisms: amino acids that fluoresce, resemble nucleic acids or form unusual bonds. Whole new dimensions of biochemistry emerge when you are not limited to the universal and ordinary 20 amino acids. Jason Chin’s lab at the MRC Laboratory of Molecular Biology in Cambridge, UK, is using this approach to make precise alterations at the molecular level of well-known proteins in fruit flies.
Last, but not least, recoding provides a potent strategy for bio-containment. If a virus-resistant organism were to escape, even if they weren’t ‘bad’ for the environment, they would take over natural niches and ‘win’. Using one of these non-standard amino acids, you can engineer an organism that can grow only if it is given that certain nutrient. The result is an ‘escape-proof’ strategy for experimental organisms used in the laboratory.