To understand this, the team of biotechnology entrepreneur Craig Venter has made a minimum genome of 473 genes. The cell that carries it is viable, but the function of a third of these genes is unknown! A cluster of artificial cells with a minimal genome, the most abundant cells are approximately one micrometer in diameter.
Tom Deerinck and Mark Ellisman of the National Center for Imaging and Microscopy Research at the Uni Nature have produced genomes of all sizes. The human DNA contains about 20,000 genes formed by nearly 3 billion base pairs, which is very little compared to Paris japonica, a herbaceous plant from Japan, which accounts for 150 billion base pairs. Conversely, some bacteria have at most a few thousand genes. Hence the question that has challenged geneticists for several decades, how many genes are needed to produce a viable cell capable of replicating? It is part of this enigma that the team of Craig Venter, co-founder of the Institute which bears his name, in La Jolla, California, has solved. It has synthesized a cell capable of replicating with only 473 Genoa.
It is an essential step in synthetic biology, a field of research, one of the objectives of which is to build new biological systems to understand the mechanisms of living things. Many teams have embarked on the quest for a minimal genome. For Craig Venter and his team, the adventure began in 1995, when they sequenced the genome of Mycoplasma genitalium, a bacteria living in the human urinary tract and which has only 517 genes. It is one of the organisms capable of self-replication with the smallest genome (the DNA of a virus can be even smaller, but the virus must parasitize a cell and divert its functions to replicate).
In 2010, Craig Venter's team succeeded in synthesizing a replica of the genome of Mycoplasma mycoides (a ruminant parasite which has the advantage for researchers of replicating faster than M. genitalium) and substituting it for genetic material, 'a cell from another species of mycoplasma. The artificial genome, with 901 genes, was an almost faithful copy of a genome existing in nature, but this experiment demonstrated the possibility of chemically synthesizing DNA on a large scale and injecting it into a cell to produce a viable organism. The researchers then used this synthetic genome as the basis for determining the genes essential or superfluous for the life of the cell.
The researchers first selected and inactivated themselves the genes which seemed to them useless, from knowledge on the functioning of the cell, but the approach proved ineffective. The team, therefore, opted for a different path, the “trial, and error” method. Biologists cut the genome of M. mycoides into eight segments of similar size, which could be assembled in different combinations, partial or complete. By then testing the viability of the cell with the recombinant genome, the researchers eliminated, by successive tests, the non-essential genes.
They assembled the small pieces by transferring them to yeast and then to the E. coli bacteria. Once ready, the artificial genome was implanted in M. capricolum cells. The manipulation did not work the first time, reports Science. We had to try several combinations until finding an error on a single basis, which delayed operations by three months.
The end result is a synthetic cell, named JCVI-syn3.0, comprising 473 genes. Among them, 41% participate in the expression of the genome, 18% in the structure and functions of the membrane, 17% in metabolism, and 7% in the preservation of genetic information. Certain genes could be classified by studying their structure, but their biological action in the cell could not be identified. The function of certain other genes, however, is completely unknown. In total, 149 genes have an unknown role, which represents almost a third of the genetic material! However, these genes are necessary; without them, the cell is not viable. For Jack Szostak, a biochemist at Harvard University, "the most interesting thing about this result is everything we don't know."
The discovery of Craig Venter's team is, therefore, rich in education and shows that there is still much to discover the functions essential to life. In addition, stripped of maximum complexity, the JCVI-syn3.0 cell will be able to serve as the basis for many fundamental works. Biochemists will use it as a platform to study specific functions that they can add one by one. Starting from such a minimal cell could also prove very useful in the study of evolution.
However, one should not see in JCVI-syn3.0, the universal minimum cell. From a bacterium other than M. mycoides, the minimal genome could have been very different. François Képès, director of research at the Institute of Systems Biology and Synthesis (iSSB, Genopole, UEVE, and CNRS) and director of the Epigenomics Program at Genopole, underlines that “certain almost universal principles could emerge from such approach. For this, we should not make a viable genome, but a series in order to test by comparison certain hypotheses on what makes a genome functional, which makes it stable, etc.”
JCVI-syn3.0 is a new species, a pure product of synthetic biology. Beyond his interest in fundamental research, Craig Venter's ambition is to exploit the industrial potential of synthetic biology by creating tailor-made cellular functionalities allowing the production of useful components for the pharmaceutical or chemical sector. However, the JCVI-syn3.0 strain is not economically interesting; its doubling time is three hours and requires a rich and very expensive medium.
In addition, the approach consisting of starting from a minimal cell is today competed by the very recent CRISPR-Cas9 method (whose inventors, Emmanuelle Charpentier and Jennifer Doudna, have just received the L'Oréal-UNESCO For Women and Science 2016 ), which makes it possible to modify the genome of a cell at will and whose perspectives are just as numerous. Whatever the winner, more than ever, and ethical reflection is essential to supervise the use of such tools.