First functional synthetic bacterial genome announced

By John Timmer

Craig Venter, who has been a prominent figure in genome research, has been using Science magazine as a host for updates on his latest project: building a bacterium that runs off a genome engineered for specific tasks. As of early 2008, his research group had managed to assemble the entire genome of a small bacterium in a yeast cell, starting with nothing but mail-order DNA. At the time, it seemed like just a short step from there to having that DNA running a cell. That short step took a year and a half, and there were some stumbles along the way.

For starters, the original bacterial genome that the team had assembled came from an extremely slow-growing strain, which complicated the process of growing out cells with the replacement genome. So they switched to a related species, Mycoplasma capricolum. M. capricolum turned out to have a defense system against foreign DNA based on a restriction enzyme that cut any DNA originating in yeast into small pieces; the researchers eventually found the gene responsible and deleted it from the genome of the bacterium.

There were also issues with contamination from the yeast's own linear chromosomes, which the authors found a clever solution for. Instead of trying to separate huge DNA molecules out on a gel, they simply formed the gel around the DNA. The fibers of the gel actually extended through the circular bacterial chromosome, trapping it in place so that when a current was applied, the yeast chromosomes flowed out of the gel, leaving purified bacterial DNA behind.

The last (and perhaps most annoying) problem they faced was an assembly error: their million-base artificial chromosome contained a single base deletion that just happened to reside in an essential gene called dnaA. By gradually transferring smaller pieces of chromosome, they narrowed the problematic region of the genome down until they identified and corrected this issue. With that fix, the authors were finally able to get the genome into a host cell, and have it replace the original one.

Ultimately, this is just another step on the way to a designer genome, one with a specific set of genes that rewire the bacterium's metabolism to produce a specific biomolecule, digest a toxin, or something of that nature. We're still not there yet, although it seems likely that some of the solutions developed during this work will speed the process in the future. Still, the number of things that went wrong here suggest that the synthetic genome approach won't necessarily be the quick-and-easy route to designer organisms that some have expected.