Adventures of a Wetware Hacker

GENETICS:
Replacement Genome Gives Microbe New Identity

Elizabeth Pennisi

For decades, molecular biologists have genetically modified microbes and other kinds of cells by adding short DNA sequences, whole genes, and even large pieces of chromosomes. Now, in a feat reported in a paper published online by Science this week (www.sciencemag.org/cgi/content/abstract/1144622), one group has induced a bacterium to take up an entire 1.08-million-base genome in one gulp. In doing so, microbiologist John Glass and his colleagues at the J. Craig Venter Institute in Rockville, Maryland, have transformed one bacterial species into another.

"This is a significant and unexpected advance," says molecular biologist Robert Holt of the Michael Smith Genome Sciences Centre in Vancouver, Canada. But the advance remains somewhat mysterious. Glass says he doesn't fully understand why the genome transplant succeeded, and it's not clear how applicable their technique will be to other microbes. Nonetheless, "it's a necessary step toward creating artificial life," says microbiologist Frederick Blattner of the University of Wisconsin, Madison.

Glass and his colleagues are among several groups trying to build a microbe with the minimal gene set needed for life, with the goal of then adding other useful genes, such as ones for making biofuels. In anticipation, Glass and colleagues wanted to develop a way to move a complete genome into a living cell.

As a proof of principle, they tried transplanting the single, circular chromosome of Mycoplasma mycoides large colony (LC) into a close relative, M. capricolum. Both of these innocuous goat pathogens lack the cell walls typical of many other bacteria, eliminating a possible impediment to genome transfer.

At the Venter Institute, Carole Lartigue and her colleagues first added two genes to M. mycoides LC that would provide proof if the transfer of its genome worked. One gene conferred antibiotic resistance, and the other caused bacteria expressing it to turn blue. Lartigue removed the modified chromosome from M. mycoides LC, checked to make sure she had stripped off all proteins from the DNA, and then added the naked genome to a tube of M. capricolum. Within 4 days, blue colonies appeared, indicating that M. capricolum had taken up the foreign DNA. When they analyzed these blue bacteria for sequences specific to either mycoplasma, the researchers found no evidence of the host bacterium's DNA.

Microbial geneticist Antoine Danchin of the Pasteur Institute in Paris calls the experiment "an exceptional technical feat." Yet, he laments, "many controls are missing." And that has prevented Glass's team, as well as independent scientists, from truly understanding how the introduced DNA takes over the host cell.

Glass suspects that at first, both genomes are present in M. capricolum. But when one of those double-genomed microbes divides, one genome somehow goes to one daughter cell and the other to the second. By exposing the growing colony to an antibiotic, the researchers selected for cells that contain only the M. mycoides LC genome.

Species makeover. Blue signals successful genome transfer in these bacterial colonies. CREDIT: NACYRA ASSAD-GARCIA/JCVI

Other researchers are not sure the strategy will work on bacteria with cell walls. And Danchin expects it will be difficult to swap genomes among bacteria that aren't as closely related. Regardless, George Church of Harvard University questions the need for genome transplantation; instead of starting with a minimal genome, he's making useful chemicals by simply adding customized genes to existing species' genomes.

Nonetheless, Markus Schmidt of the Organisation for International Dialogue and Conflict Management in Vienna, Austria, predicts that the mycoplasma genome swap will force more discussions about the societal and security issues related to synthetic biology. "We are one step closer to synthetic organisms," he says.

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