- AI creates a strain of E. coli with 19 amino acids, removing isoleucine from the ribosome
- It is the first organism to have fewer than 20 universal amino acids.
- Discovery supports theories about infancy and prepares for future of synthetic organisms in medicine
Researchers from Columbia University, the Massachusetts Institute of Technology and Harvard University have successfully used AI to create an entirely new version of the E. coli bacteria that removes one of the 20 amino acids considered the main building blocks of living organisms.
A study published in Science details the importance of this discovery, which uses AI and protein engineering to create a modified strain of E. coli with only 19 amino acids, specifically dispensing with isoleucine.
This is a major milestone not only for biology, but also for AI and research into the origins of life. Although some organisms already use more than 20 amino acids, scientists have never found anything containing fewer than 20.
AI has just enabled scientists to make a major genetic discovery
So far, they have only been able to hypothesize that primitive and primitive species might have used fewer amino acids in their genetic makeup. The following discovery turns this theory into a real possibility.
As for isoleucine, which is the favored amino acid among the 20, its chemical similarity to leucine and valine would have been a major factor in the decision, as it is the most replaceable.
But rather than trying to change the entire composition of the proteome (considered the collection of proteins within an organization), scientists sought to harness the ribosome, which is responsible for building these proteins in the first place. In the experiment, scientists were able to modify the 382 “building blocks” of isoleucine found in the ribosome, while still functioning as intended.
This is a unique study because until now, scientists have only been able to change 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 suggest amino acid substitutes, with the aim of preserving ribosome functions without using isoleucine.
Many AI-generated designs proposed sequences that humans might not have designed, with AI models able to analyze potentially successful combinations at a much faster rate than humans.
18 of the 50 strains of E. coli created from the process of replacing isoleucine with alternative amino acids continued to grow normally. The next step was to combine 21 of the rewritten ribosomal proteins into a single E. coli strain. coli, which, after some further adjustments, continued to grow (although more slowly than normal, unmodified strains).
Harris Wang, a systems and synthetic biologist at Columbia University, described completely removing an amino acid as “almost the hardest thing you can think of, because it’s the largest and most complex protein complex.”
What this discovery means for scientific research is that at least some fundamental biological systems can tolerate substantial disruptions to the genetic code. It also supports the argument that early life may have used fewer amino acids than modern organisms, opening new avenues for evolutionary theories.
However, beyond evolutionary biology, research also envisions a future in which personalized synthetic organisms can play targeted roles in specific tasks such as medicine and healthcare. Another conclusion is that modified organisms can become dependent on unusual chemicals not found in natural environments, thereby improving biological containment.
Longer term, it is possible that AI-assisted genetic modification will help researchers engineer organisms adapted to extreme environments, including space habitats where access to the full range of amino acids may be more limited.
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