American and Brazilian researchers presented the results of observations of the evolution of cells with artificially synthesized minimal genome. Over two thousand generations, they have regained their adaptability to external conditions, but have not been able to increase in size.

In 2010, the staff of the Institute of J. Craig Venter received the first cell with a completely artificial genome. To do this, they removed their own DNA from the bacterium Mycoplasma mycoides and replaced it with a slightly modified ONE synthesized in the laboratory. It consisted of about a million pairs of nitrogenous bases and contained 901 genes. The cell was named JCVI-syn1.0. After that, the researchers set out to find out what minimum set of genes a cell needs for independent survival and reproduction, and began to supply cells with increasingly stripped-down genomes. How this happened is described in detail in the material "Living Wage", published in 2016, when a version of JCVI-syn3.0 was created with a minimum genome, which consisted of only 473 genes. This was not enough for stable reproduction and convenience of experiments, and several genes had to be added. The current version of JCVI-syn3B, which is discussed in the new work, contains 493 genes. To date, it is an organism with the smallest known genome capable of growing in a pure laboratory culture.

J. T. Lennon from Indiana University with colleagues from the J. T. Lennon Institute. Craig Venter and other scientific centers in Brazil and the USA compared the level of accumulation of mutations in organisms with minimal and non—minimal genomes - JCVI-syn3B and JCVI-syn1.0. In order to minimize the influence of natural selection, they were pre-acclimatized in a standard liquid nutrient medium and sequentially grew several monoclonal populations from one selected cell. It turned out that the average number of mutations per nucleotide per generation is almost indistinguishable: 3.25 × 10-8 versus 3.13 × 10-8 (p = 0.667). This is the highest level of mutation accumulation ever recorded in cellular organisms, which corresponds to the existing ideas that with a smaller genome, the mutation rate is higher (and in M. mycoides it is high initially).

General distribution of mutations by type (insertions, deletions, single-nucleotide substitutions) it also turned out to be similar (χ22 = 4.16; p = 0.125). However, the composition of single-nucleotide mutations, which accounted for 88 percent of the total, in JCVI-syn3B and JCVI-syn1.0 was different. In both types of cells, the replacement of guanine or cytosine with adenine or thymine occurred much more often than vice versa, but the degree of this imbalance was different: 30 times with a non—minimal genome and 100 times with a minimal one. This is probably due to the lack of the ung gene in the latter, which is responsible for the excision of incorrectly embedded uracil in the DNA.

Having found out this, the researchers set up an evolutionary experiment, observing 2,000 generations in a population of more than 10 million cells. During such a period, each nucleotide of their genome had to mutate more than 250 times, which creates unlimited genetic diversity for adaptation to the environment. Thus, all other things being equal, the potential difference in natural selection pathways between populations in JCVI-syn3B and JCVI-syn1.0 is due only to artificial genome truncation. It turned out that initially it leads to a decrease in the maximum growth rate by about half. However, this indicator grows linearly over time, and by the end of the experiment, the adaptability of cells in the two groups was almost equal, and if we evaluate it relatively, cells with a minimal genome evolved 39 percent faster, and the genetic patterns of their evolutionary paths differed.

The most pronounced feature of JCVI-syn3B was that during the evolution of their cells did not increase in size, which usually happens when there is an abundance of nutrients (JCVI-syn1.0 cells during this time increased by an average of 85 percent in diameter and tenfold in volume). Epistatic effects of mutations in the FtsZ gene of the prokaryotic homologue of tubulin, which regulates cell division and morphology, were responsible for this.

The obtained results demonstrate that natural selection is able to quickly increase the adaptability of the simplest autonomously growing organisms, and the minimization of the genome opens up the possibility of involving key genes in the evolutionary process, which usually evolve slowly, the authors write.

The article was published in the journal Nature
photo: The device of the previous version of the cell with the minimum JCVI-syn3A genome during division © David S. Goodsell, RCSB Protein Data Bank

Source: Oleg Lischuk

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