Lab creates viable synthetic cell with smallest-ever genome

A team of geneticists have created the simplest self-replicating cell known, a bacterium called JCVI-syn3.0 that marks a breakthrough in synthetic biology.

Dr Craig Venter, the team leader, was at the forefront of efforts to sequence the human genome in 2000, and spent the following ten years—and an estimated $40 million—working toward the creation of JCVI-syn1.0, the first synthetic life form. As a synthesis of the Mycoplasma mycoides genome and non-functional “watermarks” (including the names of the scientists involved) which were then implanted into a different bacterium, Syn1.0 was perhaps not the revolutionary new life form many considered it to be. Unlike its predecessor, however, Syn3.0 is not based on an existing genome: Venter describes it as constituting “a brand new, artificial species.” And, in a sharp contrast to the more than one million DNA bases that made up Syn1.0’s genome, 3.0 contains less than half that number.

In Venter et al.’s report in Science, they explain how mycoplasmas were identified as “the simplest cells capable of autonomous growth” in the 1980s, and so considered useful models for understanding the fundamental principles of life. Mycoplasma genitalium, a close relative of the bacterium that formed the basis for Syn1.0, has the smallest genome for an autonomous cell yet found in nature at just 525 genes—but many of those are unnecessary for survival under lab conditions, and only about 250 are conserved across other bacteria, so the team knew a simpler cell was theoretically possible.

Because of functional redundancies (i.e. when multiple genes encode proteins that play the same key role, such that no individual gene is necessarily conserved across all species), it is difficult to determine which genes are truly essential by comparative genomics alone. Venter and his colleagues have devoted two decades to a different approach, known as the design-build-test (DBT) cycle: picking apart bacterial genomes, mixing and matching sequences as they go, and seeing whether the cells they build can survive and reproduce.

They quickly found that sorting genes into the broad categories of “essential” and “non-essential” wasn’t actually that simple, in large part because environmental conditions dictate the necessity of different products. For the sake of streamlining, and in the hope of revealing a core set of environment-independent requirements for life, Venter’s team made these conditions as favourable as possible: the medium in which Syn 3.0 is cultured supplies nearly all of the nutrients it needs, so the genes it does have are predominantly to do with “cellular chores” like DNA replication and protein production. So-called “quasi-essential” genes, which the authors describe as “not absolutely critical for viability but… nevertheless required for robust growth,” also had to be reintroduced so that the cell could replicate quickly enough to be studied.

One of the most surprising elements of the study is that the functions of 149 of Syn3.0’s genes remain uncertain; the roles of 65 are completely unknown. As Venter put it, “We know about two thirds of essential biology. We are missing a third, which is a very important lesson.”

The genomics entrepreneur remains optimistic about the applications of his team’s findings. He and his partners at Synthetic Genomics believe that this is an important step toward complete computational modelling of the cell, so that new biofuels, drugs and industrial chemicals can be produced by custom-made organisms with greater efficiency in the future. As the authors concluded, “Application of our DBT cycle is limited only by our ability to produce designs with a reasonable chance of success. With increasing knowledge of the functions of essential genes… and with increasing experience in reorganising the genome, we expect that our design capabilities will strengthen.”

Photo: J Craig Venter Institute/Science