Scientists Reduce Genome of Synthetic Cell Down To Genes Essential for Life

Researchers led by J. Craig Venter, founder and CEO of the J. Craig Venter Institute, have designed and built a minimal bacterial genome containing only the genes necessary for life. Comprising just 473 genes, it represents a genome smaller than that of any autonomously replicating cell found in nature to date.

The study, published in the 25 March issue of Science, advances the team's research published in 2010, in which they built and booted up the first self-replicating, synthetic bacterial cell, providing proof of principle that genomes can be designed in the computer, chemically made in the lab, and transplanted to a recipient cell to produce a new, self-replicating cell controlled only by the synthetic genome.

After their 2010 achievement, the team — led by Venter and Clyde Hutchison, Distinguished Professor at the J. Craig Venter Institute — set about their ultimate objective: to synthesize a cell containing only the genes necessary to sustain life in its simplest form, an effort that could help scientists understand the function of every essential gene in a cell, and also more easily manipulate cells to perform jobs such as creating clean water or new biofuels.

"This new paper is important not only for what it has achieved in providing a tool to investigate the core functions of life," said Science Deputy Editor Valda Vinson at a 23 March AAAS press event, "but also for development of the methodology, which could be applied to construct cells with various desired properties."

To do this latest work, Venter, Hutchison and colleagues again turned to Mycoplasma, bacteria possessing the smallest known genomes of any autonomously replicating cells. In 2010, the researchers had synthesized the genome of Mycoplasma mycoides. Here, they designed hypothetical minimal versions of this synthetic genome in eight different segments, each of which could be tested in order to accurately classify constituent genes as essential or not. (This represents a more systematic approach than applied in past efforts to ascertain essential genes in a cell.)

Of the 473 genes in the minimal cell, 79 have no assigned functional category. The remaining genes can be divided into four major groups.| Hutchison et al., Science (2016)

During the researchers' design-build-test process, they also sought to identify quasi-essential genes, those needed for robust growth but not absolutely required for life.

In a series of experiments, Venter, Hutchison and colleagues inserted transposons (or foreign genetic sequences) into numerous genes to disrupt their functions and determine which ones were necessary to overall bacterial functioning. They whittled away at the synthetic, reduced genome, repeating experiments until no more genes could be disrupted and the genome was as small as possible.

Critically, analysis revealed that some genes initially classified as "non-essential" do in fact perform the same essential function as a second gene; thus, one of the pair of genes needs to be retained in the minimal genome.

"We've come up with a lot of metaphors to explain this," Venter said during the press event, then providing one of his favorites: "If you know nothing about airplanes and you're looking at a 777 trying to find out functions of parts by removing them, and you remove the engine from the right wing, the airplane can still fly and land," he said, "so you might say that's a non-essential component. But you don't really discover the essentiality until you remove the second one. And that's what's happened over and over again [here], where we would have what appeared to be a non-essential component until we removed its counterpart. The process and sorting out all these unknown genes is why this process took about four years longer than we initially estimated that it would."

The final version of the minimal genome was dubbed JCVI-syn3.0 and represents a versatile, self-replicating, biological organism that might be a better starting point for scientific and engineering goals than continuing to study natural systems, the researchers say.

Their minimal genome lacks all DNA-modifying and restriction genes. In contrast, almost all genes involved in reading and expressing the genetic information in the genome, as well as in preserving genetic information across generations, are retained.

Interestingly, the precise biological functions of roughly 31% of the JCVI-syn3.0 genes remain undiscovered. "This shows that despite our efforts, there are still aspects of biology we don't understand," Venter said.

Venter noted that one of the biggest lessons he took from this work, and in particular the finding of the role of the quasi-essential genes, was that scientists need to have more of a genome-centric and less of a gene-centric view of biology. "Life is much more like a symphony orchestra than a piccolo player. There is not the gene for X kind of phenomenon that everybody was kind of wishing for as reductionist biology," he said. "And we're applying the same philosophy now to our analysis of the human genome, where we're finding most human conditions are affected by variations across the entire genome."

[Credit for associated teaser image: Flickr/ Stuart Caie/ CC BY 2.0]