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Genome Synthesis Another Venter First: Will the Real phiX174 Please Stand Up?

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As if sequencing his own genome wasn’t saucy enough, J. Craig Venter has now synthesized a genome.

Calling the feat “an important advance toward the goal of a completely synthetic genome that could aid in carbon sequestration and energy production,” Venter’s Institute for Biological Energy Alternatives revealed in November that a team there built a synthetic 5,386 base-pair bacteriophage phiX174. Ultimately, Venter says, they aim to synthesize an entire cellular genome.

IBEA’s 70-something-year-old scientific director Hamilton Smith and 60-ish microbiology professor Clyde Hutchison, visiting from the University of North Carolina, pulled all-nighters in the lab and took breaks at nearby apartments to complete the project in eight days from oligonucleotide delivery.

They used short oligos and a technique called polymerase cycle assembly that, like polymerase chain reaction, produces double-stranded gene sequences from single-stranded templates. PCA links bases together without amplifying. “Imagine you are playing with Legos and half are melted, degenerated, or broken,” Venter explains. “We try to find a clean piece of Lego and melt them together until you have a larger structure.”

For comparison, Venter notes that while polio scientists took three years to construct a 7,000 letter polio virus with only one ten-thousandth of the activity of the original virus, “we’ve been able to make things on the order of 5,000 letters in a single step … and 100 percent active.”

Venter says IBEA will not commercialize or file patents on PCA: “We’d rather wait till the next stage when there’s a clear-cut application: for instance if we have something that produces hydrogen that might hold some value.” How will other scientists get access to the PCA technology? “By reading our paper,” Venter says.

The paper, co-authored by Hamilton, Hutchison, Venter, and IBEA’s Cynthia Pfannkoch, is in press at the Proceedings of the National Academy of Sciences and under review by the US Department of Energy, whose Genomes to Life Program funded the work. DOE Secretary Spencer Abraham credits the team with creating “this phage from scratch with almost perfect accuracy in just days instead of months” and with bringing the DOE “closer to our goal of developing microbes that can be used to address energy department goals.”

Abraham appointed University of Utah genetics professor Ray Gesteland to head a new subcommittee of the department’s Biological and Environmental Research Advisory Committee to examine the benefits of IBEA’s research for energy missions. Gesteland will report back to Abraham by March.

Explaining the promise of the technology, Abraham explains: “With this advance it is easier to imagine, in the not-too-distant future, a colony of specially designed microbes living within the emission-control system of a coal-fired plant, consuming its pollution and its carbon dioxide, or employing microbes to radically reduce water pollution or to reduce the toxic effects of radioactive waste.”

Says Venter, “The ability to construct synthetic genomes may lead to extraordinary advances in our ability to engineer microorganisms for many vital energy and environmental purposes.”

— Adrienne J. Burke

 

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