02 April 2019

Another minimal genome

Scientists have rewritten and synthesized the bacterial genome

Vera Mukhina, N+1

A group of researchers from the Swiss Higher Technical School of Zurich adapted the minimal genome of the bacterium Caulobacter crescentus to facilitate its de novo synthesis. To do this, the researchers replaced about every sixth letter of DNA, but so that the amino acid sequences of proteins remained the same. After these manipulations, it turned out that only 580 genes out of 680 retained their functionality. The work is published in the journal Proceedings of the National Academy of Sciences (Venetz et al., Chemical synthesis rewriting of a bacterial genome to achieve design flexibility and biological functionality).

The study was based on information about the minimum set of genes required for Caulobacter crescentus.


The usual genome of this harmless freshwater bacterium consists of four thousand genes, but in previous studies it turned out that only a small part of them is vital for its survival in laboratory conditions – about 680 sites, including protein- and RNA-coding sequences, as well as regulatory sites.

The minimal genome of this bacterium is a ring molecule, the length of which is approximately 800,000 nucleotide pairs, which is very much for de novo synthesis (that is, not based on another DNA or RNA matrix). In 2009, researchers from Craig Venter's laboratory synthesized the genome of another bacterium in this way for the first time, and it took them about forty million dollars and ten years of work. Despite the constant improvement of methods, synthesizing long DNA molecules is still quite difficult, expensive, and not every sequence can be synthesized in the usual commercial way. Special problems arise with GC-rich DNA and with repeats that like to tangle into secondary structures.

To simplify the task, Jonathan Venetz and his colleagues decided to modify the minimal genome so as to facilitate synthesis as much as possible, in particular by optimizing the GC composition. To do this, they had to thoroughly rework the sequence using the previously developed Genome Calligrapher software and replace approximately every sixth "letter" in it. Despite the fact that the genome was made almost anew, all the protein sequences encoded in it remained the same. This happened due to the degeneracy of the genetic code, due to which the same amino acid of a protein can be written into DNA using different codons.

The genome was stitched together from 236 separately synthesized segments, looped and planted to bacteria instead of the usual genome. According to scientists, it cost them about 120 thousand dollars. Comparing the work of genes in the conventional and synthetic genome, the researchers found that only 580 of the 680 genes were functional. This is due to the fact that not only protein sequences are recorded in the bacterial genome, but also regulatory sites and RNA molecules, for which maintaining the correct conformation is very important. Apparently, not all of them were known in advance, and therefore underwent "optimization", which broke them.

With this result in hand, the authors plan to create a third, fully functional version of the bacterial genome, in which the errors of the second version would be corrected. They hope that non-working sections of the genome will be able to tell about previously unknown elements of the minimal genome of Caulobacter.

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