Recoded organism paves way to new genetic language of life

RecodedOrganismPavesWayToNewGeneticLanguageOfLife
Fully recoded life form may be two years away

Original source: New Scientist

A form of life that uses a fresh genetic “language” could be just a few years away. This comes after geneticists used a new technique to recode 5 per cent of the Salmonella bacterium’s genome, introducing a record number of engineered changes into a single organism.

Now the race is on to recode the entire genome and put the microbes to work.

Genome recoding is seen by many as the next big thing in genetic engineering. Among other things, it offers geneticists a way to engineer the proteins produced by organisms and give them new properties – allowing the creation of proteins that don’t exist in nature, and potential uses in new types of drugs and vaccines.

Standard proteins are built from 20 amino acids, which are in turn coded for by “codons” – runs of three DNA “letters” in the genetic code (TTT, TTC, and so on). It’s possible to produce 64 distinct codons, meaning there is a lot of redundancy in the system because amino acids are usually coded for by more than one codon. The amino acid leucine, for example, is produced by six different codons.

That redundancy could be used to our advantage. For instance, if an entire genome was recoded so that leucine was produced by just one codon, it would free up five others that could be reassigned to produce brand new amino acids beyond the 20 natural ones, potentially leading to new commercially useful proteins.

The novel amino acids are important for another reason: they are fundamentally alien to life on Earth. An organism with a fully recoded genome would, in effect, use a subtly different genetic “language” to everything else on the planet. Its DNA would be unable to function properly in other organisms, because they would be unable to read it.

This is a particularly useful trait in the microbial realm, in which cells are only too willing to “talk” to one another and share genetic information.

That process of DNA sharing is a problem for researchers who want to use genetically engineered bacteria in real-world applications, because society demands that any genetically modified organism doesn’t transfer those modifications to other organisms in the environment.

“Ideally, you would have a firewall between your bacterium and the other bacteria,” says Jeffrey Way at Harvard University’s Wyss Institute. Recoding the genome provides that firewall because the new code would be meaningless to natural life forms.

Mammoth task

It’s a mammoth task to recode one or more codons across an entire genome. However, a team led by Way and his colleague Yu Heng Lau – both members of Pamela Silver’s laboratory at the Wyss Institute – thinks it might be no more than a few years away from achieving the feat. Working with a strain of Salmonella, the team has already made more than 1550 codon changes in 176 genes.

The researchers decided to free up two codons that code for leucine, TTA and TTG, by replacing them with CTA and CTG codons, which also code for leucine. They designed the new Salmonella DNA on a computer and paid a commercial supplier to build it.

Such suppliers typically provide DNA in short strands, 1-4 kilobases long. To build longer stretches, the geneticists inserted the DNA fragments into yeast cells, which can naturally assemble them into strands 20 kb long.

Then came the crucial step – one that the team thinks might be key to making genome recoding much quicker. The researchers used a new technique to replicate each modified 20-kb DNA strand inside the yeast and produce large quantities at the level of micrograms. Then they inserted modified DNA into the Salmonella.

The hope was that the bacteria would then do some of the geneticists’ work for them. When bacterial cells divide and replicate their DNA, they may incorporate a new strand of DNA if it happens to be present in the cell.

What’s more, if that new strand of DNA has a near-identical sequence to a particular region of the bacterial genome, some of the bacteria should even incorporate the new DNA in that region. This process is known as recombineering, which is a form of “crossing over” between similar DNA strands that occurs naturally in all organisms.

Geneticists have used recombineering to insert new DNA sequences in the past, but those were typically only about 3-4 kb rather than 20 kb long. “We were initially unsure if this was feasible,” says Lau. “But it actually worked well enough for our purposes.”

It took roughly two days to insert a particular 20 kb section. After that, the team could give the Salmonella engineered DNA corresponding to the next 20 kb of the genome’s DNA sequence and wait for the bacteria to incorporate it, and so on.

Efficient tool

The approach offers an efficient way to design and assemble recoded genomes, says Marc Lajoie at the University of Washington in Seattle, a member of a team using a different method to recode E. coli. “I think their method will provide a complementary tool for existing efforts to synthesise radically recoded organisms,” he says.

Way says it might be no more than a couple of years before the team has applied the technique across the entire Salmonella genome, which will involve changing more than 33,000 codons in total. At that point, the microbe could find uses in vaccine development, he says.

Many bacterial vaccines are made using dead microbes because of the risk that living ones would swap genetic material with others in the human body. Because recoded bacteria would be unable to communicate with other microbes, it should be possible to use them to create “live” vaccines – which can be far more effective.

“That’s an example of a real-world use of this technology,” says Way. “Salmonella would be a perfect bacterium to work with.”

Journal reference: bioRxiv, DOI: 10.1101/115493