Synthetic lifeforms closer to reality after AI creates world’s first synthetic genome

WHY THIS MATTERS IN BRIEF

The creation of the world’s first fully synthetic genome by an AI is a major milestone in synthetic biology researchers quest to create the world’s first fully synthetic lifeforms.

 

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Scientists from ETH Zurich have announced a major breakthrough and a world first – for the first time anywhere they’ve managed to get an Artificial Intelligence (AI) algorithm to create an entire bacterial genome. The findings were published in the Proceedings of the National Academy of Sciences and will have significant implications for the field of synthetic biology. It also now means that Harvard and MIT’s goal of creating the world’s first artificial human after 2035, a project they’ve been working on for a couple of years now, is also increasingly feasible.

The new genome, named Caulobacter Ethensis 2.0, is not a living organism, yet, and only exists as a bundle of DNA. Nonetheless the achievement represents a giant leap towards creating so called Synthetic Life, and the world’s first truly Synthetic Lifeforms – the likes of which we’ll have never seen before.

 

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The new genome was derived from that of Caulobacter Crescentus, or simply Caulobacter, a naturally occurring bacteria found in spring water, rivers and lakes around the world. This harmless bacteria is commonly used as a model organism in the lab. Its genome contains 4,000 genes, however, most of this is considered “junk DNA” and only around 680 of these genes are actually needed to support the survival of the bacteria in the lab.

Moreover, this “minimal gene set” still contains some redundancies since several different combinations of amino acids and proteins assembled by DNA often have the same result. So, the scientists in question developed a computer programme to determine “the ideal DNA sequence” – an optimised genome that didn’t contain the junk, and didn’t contain the duplications.

The new algorithm managed to completely rewrite the bacteria’s genome as new sequences of DNA that didn’t resemble the original ones, but that still managed to perform the same biological functions, resulting in the “minimal gene set.”

 

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The latest research builds upon previous work of American genetics pioneer Craig Venter, who was the first to chemically synthesise the genome of a bacterium, although, the feat took 10 years to achieve. Whereas Venter and his team made an exact copy of their bacteria’s genome the new computer generated genome contains an entirely new set of genes generated by the algorithm.

Either way, creating a bacterial genome completely from scratch is not an easy task. A step-by-step approach is needed. So, starting with the minimal gene set of Caulobacter, the team at ETH Zurich first created 236 genome segments. Next, the segments were pieced together. While this might sound quite easy, the process is incredibly challenging since DNA molecules can stick to each other and often become twisted and tangled.

Nature also has built-in genetic redundancies, which means that many genes can encode for the same protein. In this case, the researchers re-wrote the genome ― using completely different genetic sequences ― and it was still capable of providing the same biological functions.

 

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To test out their artificial genes, the authors produced strains of bacteria with both the naturally occurring Caulobacter genome and segments of the new artificial genome. When they switched off the natural genes one-by-one, they found that 580 of the 680 artificial genes were functional. This suggests there is still some room for improvement before the algorithm can create a fully functional computer-generated genome that can be used to synthesise a living, synthetic bacterium.

Nevertheless, the scientists hope the algorithm will one day produce functioning synthetic micro-organisms for various bio-manufacturing applications like producing pharmaceutical molecules, vitamins, or even vaccines. But not without discussions, among scientists and society as a whole, on the appropriate uses, as well as potential abuses of the technology and how they can be prevented.

Source: PNAS

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