THE language of life has been rewritten. A bacterium has had its genome recoded so that one of its genetic words has been freed up to impart a different meaning, allowing the creation of proteins that don't exist in nature.
The work has been described as the first step towards a new biology because the techniques used should open the door to reinventing the meaning of several words simultaneously. This could lead to novel types of biomaterials and drugs with exotic properties. It also raises the tantalising possibility of integrating these genetically recoded organisms (GROs) into living organisms – to create virus-resistant plants or animals, for example.
To understand how the recoding was achieved, we need to zoom down to what happens inside cells when proteins are made. First, an enzyme called RNA polymerase converts our DNA code into RNA. Then the cell's protein-production machinery, the ribosome, reads the four letters of the RNA code in sets of three letters called codons. The three-letter "words" indicate which amino acid – the building blocks of proteins – the ribosome should add next to its growing chain of peptides.
There are 64 ways of combining the four letters (U, A, G and C) into groups of three, and 61 of these codons are used to encode the 20 amino acids found in nature. So some of the codons encode the same amino acid – a phenomenon called redundancy. The three combinations left over, UAG, UAA and UGA, act like a full stop or period – telling the ribosome to terminate its production process. When this happens, a release factor binds and triggers the release of the peptide chain, so it can be folded into a protein.
A team of synthetic biologists led by Farren Isaacs at Yale University has now rewritten these rules. They took Escherichia coli cells and replaced all of the UAG stop codons with UAAs. They also deleted the instructions for making the release factor that usually binds to UAG, effectively rendering UAG meaningless (see diagram).
The swap was done by placing bacterial cells in a water bath with viral enzymes and fragments of single-stranded DNA. The strands were identical to the DNA the team wanted to alter in the E. coli, except with the stop codons substituted. When a jolt of electricity was applied, pores in the bacterial cell membranes opened and let the bits of DNA float in. The next time the cells divided, the viral enzymes incorporated the altered DNA fragments. Not every codon was replaced on the first hit, so the team knitted together the genomes of many bacteria to create one with a completely recoded DNA genome.
The next step was to assign a new meaning to UAG during protein production. The team did this by designing molecules called transfer RNAs and accompanying enzymes that would attach an unnatural amino acid – fed to the cell – wherever they spotted the UAG codon. Many such amino acids have been created by biologists and they have even been substituted into simple organisms such as fruit flies. But until now, the new cell machinery competed with the old. This made the process inefficient and meant that sometimes unnatural amino acids would be inserted into other proteins as well. By reintroducing UAGs at specific locations, as the Yale team have done, unnatural amino acids can be added into proteins at will (Science, doi.org/pb8).
"We now have an organism that has a new code, and we can reliably and efficiently open up the chemical diversity of proteins," says Isaacs.
For example, artificial amino acids could be added that give proteins unusual properties, such as the ability to bind to metals – resulting in novel adhesives. Or enzymes could be developed that are activated only in the presence of other molecules – which could be useful for drugs.
"The genetic code is conserved for all of life, so this is a fundamental step forward," says Philipp Holliger of the MRC Laboratory of Molecular Biology in Cambridge, UK. He says that because so much of the genetic code is redundant, there might be other codons that could be reassigned to expand the chemistry of living organisms.
Isaac's team are already on the case. In separate experiments, they picked 13 other codons and substituted them for alternatives with the same function across 42 different E. coli genes. Even though 24 per cent of the genes' DNA had changed, the proteins the cells produced seemed identical to the originals (Science, doi.org/pb9). The next step would be to endow these freed up codons with new meaning.
"This has great potential for the future to not just replace one codon here and there, but to replace loads of them and have completely new types of biopolymers made in cells," says Holliger. "It's a first step down the road to a new biology."
