- AI creates a strain of E. coli with 19 amino acids, removing isoleucine from the ribosome
- This is the first organism to have fewer than 20 of the universal amino acids
- The discovery supports early life theories and lays a future for synthetic organisms in medicine
Researchers from Columbia University, the Massachusetts Institute of Technology and Harvard University have successfully used AI to create a brand-new version of the bacteria E. coli that does away with one of the 20 amino acids that are considered the primary building blocks of living organisms.
A study published in Science details the significance of this discovery, which uses AI and protein engineering to create a modified strain of E. coli with just 19 amino acids, making do specifically without isoleucine.
This is a major milestone not just for biology, but also across AI and research into the origins of life. While some organisms have already been seen to employ more than 20 amino acids, scientists have never found anything with fewer than 20.
AI just enabled scientists to make a major genetic discovery
Until now, they have only been able to theorize that early, primitive species may have employed fewer amino acids in their genetic make-up. The discovery that follows next turns that theory into a genuine possibility.
As for isoleucine being the amino acid of focus within the selection of 20, its chemical similarity to leucine and valine is said to have been a major factor in the decision due to it being the most replaceable.
But rather than trying to change the entire make-up of the proteome (seen as the entire collection of proteins within an organization), the scientists looked to tap into the ribosome, which is responsible for building those proteins in the first place. Under the experiment, the scientists were able to change the 382 isoleucine ‘building blocks’ found in the ribosome with it still working as expected.
This makes it a first-of-its-kind study, because until now, scientists have only been able to edit the genetic code of bacteria, yeast and other organisms by adding amino acids – not removing them.
The experiment worked by using AI protein language models to predict alternative protein structures and offer up amino acid substitutes, with the goal of preserving the ribosome’s functions without using isoleucine.
Many of the AI-generated designs offered up sequences that humans might not have designed, with the AI models capable of analyzing potentially successful combinations at a far greater pace than humans.
18 of the 50 E. coli strains created from the process of replacing isoleucine with alternative amino acids went on to grow normally. The next stage was to combine 21 of the rewritten ribosomal proteins into one strain of E. coli, which after some additional tweaks, went on to grow (albeit more slowly than regular, unmodified strains).
Columbia University systems and synthetic biologist Harris Wang described totally eliminating an amino acid as “almost the hardest thing you could think about, because it’s the biggest, most complicated protein complex.”
What the discovery means for scientific research is that at least some core biological systems can tolerate substantial genetic code disruption. It also supports the argument that early life may have used fewer amino acids than modern organisms, offering up new perspectives for evolutionary theories.
However, beyond evolutionary biology, the research also lays out a future where customized, synthetic organisms can play focused roles across specific tasks such as medicine and healthcare. Another conclusion is that modified organisms may become dependent on unusual chemistries not found in natural environments, therefore improving biological containment.
Looking much further ahead, it’s possible that AI-assisted genetic modification could help researchers to design organisms for extreme environments, including space habitats where access to the full range of amino acids may be more limited.
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