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2010.06.14 – Original Source: MIT Technology Review

Last month, researchers at the J. Craig Venter Institute announced that they had made the first synthetic cell by piecing together a genome made from bottled chemicals and transplanting it into a recipient cell. The landmark accomplishment represents a new level of control over the substance of life at the molecular level and one that could lead to ways to make cells that produce vaccines in large quantities and cleaner fuels.

Though researchers emphasize that it will be years before scientists can demonstrate the true potential of these techniques to engineer life, they’re now using the experiments to increase the fundamental understanding of cell biology.

During a tour last week of the institute’s Rockville, MD, facilities, where the experiments are taking place, scientists explained that the synthetic cell was created as a result of a project to learn how to make a cell with the minimum number of genes possible to live. “The hope is that by understanding the basic principles of cellular life, we will be able to make cells make more stuff,” says John Glass, a professor at the institute. Cells designed to make a particular chemical will make it more efficiently if researchers can eliminate every other nonessential metabolic process. “I’ve always wanted to know how cells work, and now we have the tools,” he says.


Synthetic cells:
The bacterial colonies growing on these petri dishes contain a genome modified on a computer and then pieced together in the lab. Credit: Katherine Bourzac

One way to figure out what the minimal genome is would be to start with a microbe that’s easy to work with in the lab, such as yeast or E. coli, and knock out each gene one at a time. But this process takes a very long time. Instead, the Venter scientists start out with a genome sequence from a bacterium that already has a very small genome, alter it on the computer to add or delete genes, then synthesize it from chemicals, transplant it into a cell, and see how the changes affect the cell’s function. Building a genome in this manner speeds up the institute’s research on minimal genomes, says Daniel Gibson, associate professor at the Venter Institute.

The first step in making a synthetic cell is to design the genome. This process happens on the computer, with the sequence of 1,077,947 letters that make up the genome of the bacterium Mycoplasma mycoides. In their initial demonstration experiments, the researchers deleted 15 genes. And to create a watermark that distinguishes the synthetic genome from the natural one, they also made additions. The researchers encoded their names, a URL, a few quotes, and an e-mail address into the four-letter alphabet of DNA and added it to the genome.

It’s expensive and time-consuming today to synthesize long pieces of DNA in the lab. So the researchers used a computer program to chop the genome up into 1,100 pieces, each about 1,080 base-pairs, or letters, long. The computer program added sticky sequences at either end of each slice that would enable the pieces to be put back together again. Researchers then sent these 1,100 designs to a DNA-synthesis company.

Institute researchers then enlist yeast cells to stitch the 1,100 fragments into a single, circular piece of DNA that makes up the completed synthetic genome. Before the yeast can do their work, Gibson’s group must make the DNA fragments yeast-friendly. Gibson’s group first adds to each set of DNA fragments a short sequence of DNA that pulls the fragments into a loop and makes the fragments friendly to yeast cells that have been treated to make them amenable to gobbling up DNA.

Gibson combines the yeast cells in solution with ten types of DNA fragments, each of which make up a consecutive sequence of the Mycoplasma genome. The yeast cells do the work of putting the fragments back together. This process is repeated until the yeast are putting together larger and larger pieces of the genome. Eventually, some of the yeast cells will have put together a complete synthetic genome. After testing to verify that a colony has the entire bacterial genome, the researchers grow the yeast in a flask to allow them to multiply and produce the genome in large quantities.

The next step is to extract the complete synthetic bacterial genome from the yeast and transplant it into bacterial cells. Extracting the genome from yeast and transporting it is the trickiest part of the process. The mycoplasma genome is relatively small, but it’s a huge molecule. The shear force of water moving around the bare DNA molecules can pull it apart. So the researchers immobilize the DNA in a pellet of gel and take it to another lab, where the transplant recipient cells have been prepared. The recipient cells, of the species Mycoplasma capricolum, are a close relative of the cells whose genome is the basis of the synthetic genome. Through trial and error, the researchers have found that there is a particular part of the cells’ cycle of growth and division at which they are most likely to take up the foreign DNA.

Getting the recipient cells to take up the synthetic genome is in part a matter of chance. A researcher mixes the recipient cells with a chemical solution to make their surfaces fluid and sticky, then adds the cells to the DNA solution. Once mixed, the sticky cells begin fusing with one another. In order to maintain a spherical shape as their surface area is increasing, the cells take on volume from the solution around them. By chance, as they fuse, some of these megacells take in copies of the M. mycoides genome.

Left for about three hours, the cells with more than one genome will divide, creating a mixture of cell types. About one in 100,000 cells has the transplanted genome, which contains an antibiotic-resistance gene. When the cell solution is streaked on plates containing the antibiotic tetracycline, only those with the transplanted genome survive. Though they were initially of a different species, the M. mycoides genome takes over to create what the researchers call a synthetic cell.

The researchers will now use these techniques to gradually shrink the genome. They’re currently using software to design new genomes with various genes removed, then using their technique to synthesize and transplant them. “We can test a staggering amount of possibilities in an experiment,” says Glass. This allows them to determine in a matter of weeks rather than years what happens when, say, 10 genes in a particular pathway are expressed at varying levels or eliminated.

Developing these techniques took about $30 to $40 million in funding, mostly from the company Synthetic Genomics. The main cost of these experiments comes from the price of synthesizing DNA, which may go down as more researchers see the promise of these types of experiments. “Other groups aren’t doing this because of the cost and because the methods have been difficult, but I’d like to think we’re making the methods simple,” says Gibson. Boston University professor James Collins agrees. “As the costs come down you’ll see a number of labs begin to synthesize on this scale. If this technique is viewed as being useful, we’ll get there on the costs.”



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