Researchers have rebuilt an entire genome from scratch, they report online today in Science. Although the team has yet to demonstrate that this DNA can substitute for the real thing, the work paves the way for customized bacteria that could efficiently produce drugs, biofuels, and other molecules useful to humankind.
Ever since his group decoded the genome of Mycoplasma genitalium, a parasitic bacterium that lives in the human urogenital tract, sequencing maverick J. Craig Venter has wanted to remake the bug's genome in the lab. At just under 600,000 bases, M. genitalium sports the smallest known genome for a free-living organism, and Venter hoped that an artificial genome could be modified to turn the bacterium into a living chemical-manufacturing plant.
Last year, Venter and his colleagues developed a technique for replacing M. genitalium's genome with another natural genome from a different species (Science, 3 August 2007, p. 632). But synthesizing the M. genitalium genome from the ground up proved challenging, in part because long strands of DNA are quite fragile.
Japanese researchers have built a large genome from two existing bacterial chromosomes. But Venter, Hamilton Smith, and their colleagues at the J. Craig Venter Institute in Rockville, Maryland, started with short pieces of DNA that a company had manufactured base by base. About 6000 bases long, these pieces represented overlapping bits of the microbe's only chromosome. Some of the pieces also contained "watermarks": a few extra or different bases here and there that distinguish an artificial chromosome from a natural one.
To link the pieces, Smith and Venter's team used enzymes that allowed them to join longer and longer DNA strands until they had just four, each representing one-quarter of the genome. Finally, the team inserted these quarters into yeast, which copied and combined them into a complete chromosome. The researchers sequenced their newly constructed genome and, except for the watermarks, it matched M. genitalium's exactly. The work is "a technical tour de force" and a "monumental effort," says yeast biologist Jef Boeke of Johns Hopkins University School of Medicine in Baltimore, Maryland. However, to be sure this genome works as it should, the researchers must still put it into a DNA-less M. genitalium, notes Eckard Wimmer, a molecular virologist at Stony Brook University in New York state: "Proof is biological function, and that's missing in this paper."