First bacterial genome created entirely with a computer

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Caulobacter crescentus is a harmless bacterium that lives in freshwater around the world (electron microscopic image). Credit: ETH Zurich

All the genome sequences of organisms known worldwide are stored in a database belonging to the National Center for Biotechnology Information of the United States. To date, the database has an additional entry: Caulobacter ethensis-2.0. It is the first genome of a living organism, fully computer generated, developed by scientists from ETH Zurich. However, it should be noted that although the genome of C. ethensis-2.0 has been physically produced as a very large DNA molecule, there is still no corresponding organism.

C. ethensis-2.0 is based on the genome of a well-studied and harmless freshwater bacterium, Caulobacter crescentus, a naturally occurring bacterium found in spring waters, rivers and lakes around the world. It does not cause any disease. C. crescentus is also a model organism commonly used in research laboratories to study the life of bacteria. The genome of this bacterium contains 4000 genes. Scientists have previously demonstrated that only about 680 of these genes are essential for the survival of the species in the laboratory. Bacteria with this minimal genome are viable in the laboratory.

Beat Christen, professor of experimental systems biology at ETH Zurich, and his brother Matthias Christen, chemist at ETH Zurich, took as starting point the minimal genome of C. crescentus. They began chemically synthesizing this genome from scratch into a continuous ring chromosome. The task is seen as a feat: the chemically synthesized bacterial genome introduced 11 years ago by American genetic pioneer Craig Venter is the result of 10 years of work by 20 scientists, according to media reports. The cost of the project would have totaled $ 40 million.

Streamline the production process

While the Venter team was making an exact copy of a natural genome, researchers at ETH Zurich have radically altered their genome using a computer algorithm. Their motivation was twofold: first, to make the production of genomes much easier and secondly, to answer the fundamental questions of biology.

To create a DNA molecule the size of a bacterial genome, scientists must proceed step by step. In the case of the Caulobacter genome, scientists at ETH Zurich synthesized 236 segments of the genome, which they then reconstituted. "The synthesis of these segments is not always easy," explains Matthias Christen. "DNA molecules not only have the ability to stick to other DNA molecules, but depending on the sequence, they can also twist into loops and knots, which can hinder the production process or make the manufacturing impossible, "explains Matthias Christen.

Simplified DNA sequences

To synthesize the segments of the genome in the simplest possible way, then to gather all the segments in the simplest way, the scientists radically simplified the sequence of the genome without modifying the real genetic information (at the level of the protein). There is plenty of room for genome simplification because biology has built-in redundancies to store genetic information. For example, for many protein components (amino acids), there are two, four or more possibilities of writing their information in DNA.

The algorithm developed by the scientists at ETH Zurich optimally exploits this redundancy of the genetic code. Using this algorithm, the researchers calculated the ideal DNA sequence for the synthesis and construction of the genome, which they eventually used for their work.

the Caulobacter ethensis-2.0 genome in a micro tube. Credit: ETH Zurich / Jonathan Venetz

As a result, scientists have introduced many small changes in the minimal genome, which are impressive in their entirety: more than one-sixth of the 800,000 DNA letters of the artificial genome have been replaced, compared to the "natural" minimal system. ". genome. "Thanks to our algorithm, we have completely rewritten our genome in a new sequence of DNA letters that no longer resembles the original sequence, but the biological function at the protein level remains the same," explains Beat Christen. .

The rewritten genome is also interesting from a biological point of view. "Our method is a litmus test to determine if we, biologists, have a good understanding of genetics, and it also allows us to highlight any gaps in our knowledge," says Beat Christen. Of course, the rewritten genome can only contain information that researchers have really understood. Any additional "hidden" information that is in the DNA sequence and has not yet been understood by the scientists would have been lost in the creation of the new code.

For research purposes, scientists have produced strains of bacteria that contain both the natural genome of Caulobacter and segments of the new artificial genome. By deactivating certain natural genes in these bacteria, researchers were able to test the functions of artificial genes. They tested each artificial gene in a multi-step process.

In these experiments, the researchers found that only about 580 of the 680 artificial genes were functional. "With the knowledge we have gained, we will be able to improve our algorithm and develop a fully functional version 3.0 of the genome," says Christen.

"Even though the current version of the genome is not yet perfect, our work shows that biological systems are built so simple that in the future we can develop computer-based design specifications based on our goals. and then build them, "says Matthias Christen. And this can be accomplished in a relatively simple way, as Beat Christen points out: "What took ten years with the approach of Craig Venter, our small group realized with our new technology in one year with manufacturing costs. 120,000 Swiss francs "

"We believe that it will soon be possible to produce functional bacterial cells with such a genome," said Beat Christen. Such a development would have great potential. Possible future applications include synthetic microorganisms that could be used in biotechnology for the production of pharmaceutically active complex molecules or vitamins, for example. The technology can be used universally for all microorganisms, not just for Caulobacter. Another possibility would be the production of DNA vaccines.

"As promising as research results and possible applications may be, they require an in-depth discussion of society about the purposes for which this technology can be used and, at the same time, how abuse can be avoided" says Beat Christen. It is still unclear when the first bacterium with an artificial genome will be produced – but it is now clear that it can and will be developed. "We need to use the time we have for intensive discussions between scientists, as well as throughout society, and we are ready to contribute to this discussion with all the expertise we have."