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Synthesizing a Genome from Scratch

Scientists say the results represent a new stage in synthetic biology.
January 25, 2008

In a technical tour de force, scientists at the J. Craig Venter Institute, in Rockville, MD, have synthesized the genome of the bacterium Mycoplasma genitalium entirely from scratch. The feat is a stepping stone in creating precisely engineered microbial machines capable of generating biofuels and performing other useful functions.

Synthetic genomes: Shown here is a circular piece of DNA synthesized from scratch–the first bacterial genome to be created this way.

“It really is groundbreaking that you can synthetically build a genome for a bacterium,” says Chris Voigt, a synthetic biologist at the University of California, San Francisco, who was not involved in the project. “It’s bigger by orders of magnitude than what’s been done before.”

Biologists creating genetically engineered organisms now routinely order pieces of DNA that are 10,000 to 20,000 base pairs long–big enough to incorporate the genes for a single metabolic pathway. That allows researchers to engineer microbes that can perform specific tasks, but the ability to synthesize entire genomes could grant a whole new level of control over biological design. (See “Tumor-KillingBacteria.”)

In the new study, scientists ordered 101 DNA fragments, encompassing the entire Mycoplasma genome, from commercial DNA synthesis companies. These fragments were designed so that each overlapped its neighboring sequence by a small amount; these overlapping stretches stick together, thanks to the chemical properties of DNA. Researchers then bound the fragments piece by piece, eventually generating the full 582,970 base pair Mycoplasma sequence. The findings were published Thursday in the online edition of Science.

“We consider this a second and significant step in a three-step process of our attempt to create the first synthetic organism,” says Craig Venter, president of the Venter Institute. Venter and his colleagues ultimately want to create a minimal genome–one with the least number of genes needed to sustain life. Pinpointing the minimal genome will both shed light on key cellular processes and provide a base for designing sophisticated synthetic organisms. “We ultimately want to design cells that could function in a robust fashion to make unique biofuels,” says Venter.

The researchers’ next step will be to show that the synthetic genome functions as it should. “We have the whole genome assembled in a tube, but we need to transplant it into the cell of a different species to show that it can reboot the cell,” says Hamilton Smith, a Nobel laureate who oversaw the project at the Venter Institute. Last year, Smith’s group transplanted the genome of one species of Mycoplasma into another, demonstrating that this type of transplant is possible. (See “Transplanting a Genome.”)

While the synthesis of a genome might be impressive from a scientific perspective, it is not yet a practical way to engineer microbes to make biofuels. Instead, several companies, including Synthetic Genomics, a biotech company founded by Venter to engineer microbes for energy, are using more traditional metabolic engineering techniques to generate fuel-producing bacteria. (See “Building Better Biofuels.”) “What we’re doing with synthetic chromosomes will be the design process for the future,” says Venter.

Others in the field are excited about that prospect. “Being able to synthesize genomes opens up a new world,” says Voigt. “You can build things on the scale of the genome.” For example, he says, scientists are now engineering bacteria to perform different steps in the conversion of biomass into ethanol–one strain to break down the biomass, another to make ethanol. But ideally, scientists could put those processes together to create one organism that could eat biomass and spit out fuel. (See “The Price of Biofuels.”) “That would require genome-scale design,” Voigt says.

He likens the current project, which required multiple steps to glue the fragments together, to the last computers designed before automated manufacturing and microfabrication techniques were introduced. Similar advances are needed for more ambitious genome-synthesis projects. “We still need to develop ‘one step’ genome construction methods in order to reduce the costs and turn time of genome construction,” says Drew Endy, a synthetic biologist at MIT.

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