Smallest genomed-bacterium addresses big questions

Among the insights to be had from the "minimal genome" cell that was reported Thursday is just how relative the term minimal is – a fact freely acknowledged by its creators.

"There's no such thing as a true minimal genome," J. Craig Venter told reporters at a press conference announcing the "Design and synthesis of a minimal bacterial genome," which is both the gist of the work and the title of the paper reporting it. "Every genome is context-specific, so it . . . depends on the chemicals in the environment it has available to it."

But if it is not the only possible minimal genome, Venter and his colleagues have nevertheless published the first minimal genome – a genome in which every gene is necessary for survival or robust growth.

Venter, who is a genomics pioneer, the founder and CEO of the J. Craig Venter Institute and co-founder and co-chief scientific officer of Synthetic Genomics Inc., and his co-authors reported their work in the March 25, 2016, issue of Science.

The bacterium, which they have named JCVI-syn3.0, or Syn3.0 for short, contains 473 genes in slightly more than a half million base pairs. That is roughly 50 genes fewer than Mycoplasma genitalium, which has the smallest known genome of any self-replicating organism. There are smaller viral genomes, but those cannot replicate themselves without infecting a host cell and co-opting its transcriptional and translational machinery.

One unexpected aspect of the minimal genome is that it still contains a large number of genes whose functions are unclear. The team classified 149 of the 473 genes in Syn3.0 as having an unknown function.

Co-author Clyde Hutchinson III, a distinguished professor at the J. Craig Venter Institute, noted that "our criteria for knowing the function are pretty stringent. So quite a few of those, we have a rough idea what they do. For example, we might know a gene is part of a transporter in the cell membrane to move some small molecule into the cell . . . but if we don't know what small molecule it moves, we're putting it in our not precisely defined category."

Nevertheless, Venter said, the work shows "how complex life is even in the simplest of organisms."

Those complexities, he pointed out, are vastly increased in the human genome, with its estimated 20,000 genes and possibly as many noncoding RNAs. "So I think these findings are very humbling in that regard."

M. genitalium was one of the first genomes Venter and his colleagues sequenced, in 1995. Together with its relatives Mycoplasma capricolum and Mycoplasma mycoides, it formed the basis of many of the J. Craig Venter Institute's synthetic biology feats, including the creation of the first fully chemically synthesized genome in 2010. (See BioWorld Today, May 21, 2010.)

From the beginning of the sequencing work, one of the team's goals was to find a minimal genome – a genome in which every gene was essential for life. Initial experiments, however, were notably unsuccessful – in part because the question of whether a gene is essential is not cut and dried.

Hutchinson used the example of nutrient availability to describe genes that can be essential or not, depending on both genetic and environmental circumstances.

M. genitalium can grow on either glucose or fructose, and "there's a transporter for each," he told reporters at the press conference. "And so if both sugars are present in the [media] and you knock out the glucose transporter, nothing happens. The cell still happily lives so you would say that's probably a non-essential gene."

But "if you knock out the fructose transporter as well, then the cell dies." Likewise, "if the cell only has glucose in the media and you knock out the glucose transporter, you would score it as an essential gene."

Venter said the team's approach was somewhat similar to removing components from an airplane to discover how it worked. Discovering synthetic lethal pairs of genes was akin to removing first one and then the second engine from a plane.

After removing one engine, Venter said, "the airplane can still fly and land, so you might say that's a non-essential component. And you don't really discover the essentiality until you remove the second one. And that's what's happened over and over again in biology, where we would have what appeared to be a non-essential component until we removed its counterpart."

To Venter, there is an important lesson in the frequent occurrence of synthetic lethals in even the smallest genomes.

Biology, he said, is currently "based on a gene-centric view of life. . . . I think we've shown that we need to have a genome-centric view of life, looking at functions across the genome.

"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."

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