While scientists have long had the ability to edit individual genes, it is a slow, expensive and hard to use process.
Now researchers at Harvard and MIT have developed technologies, which they liken to the genetic equivalent of the find-and-replace function of a word processing program, that allow them to make large-scale edits to a cell’s genome. The researchers say such technology could be used to design cells that build proteins not found in nature, or engineer bacteria that are resistant to any type of viral infection.
DNA consists of long strings of “letters” (A, C, G and T) – or nucleotides – that code for specific amino acids. The genetic code consists of three-letter ‘words’ called codons, which are formed from a sequence of three nucleotides, such as ACT, CAG. The new technology is possible because all living organisms use the same genetic code to translate those letters into amino acids, which are then strung together into proteins. While most codons specify an amino acid, there are a few that tell the cell when to stop adding amino acids to a protein chain. It was one of these “stop” condons that the researchers targeted in their research.
To make edits to the genome of E. coli, they combined a technique previously unveiled in 2009, called multiplex automated genome engineering (MAGE), with a new technology dubbed conjugative assembly genome engineering (CAGE).
Dubbed an “evolution machine” for its ability to accelerate targeted change in living cells, MAGE locates specific DNA sequences and replaces them with a new sequence as the cell copies its DNA. This allows scientists to precisely control the types of genetic changes that occur in cells as the targets are replaced, while the rest of the genome remains untouched.
The researchers used MAGE to replace the TAG codon with another stop codon, TAA, in living E. coli cells. They chose the TAG codon because, with just 314 occurrences, it is the rarest in the E. coli genome. To make the process more manageable, they first used MAGE to engineer 32 strains of E. coli, each of which has 10 TAG condons replaced.
To combine those strains and eventually end up with one that has all 314 edits, they then developed CAGE, which allows them to precisely control a naturally occurring process called conjugation that bacteria use to exchange genetic material. The CAGE method resembles a playoff bracket, with the researchers inducing the cells to transfer genes containing TAA condons at increasingly larger scales.