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A Machine That Speeds Up Evolution

A genome-wide approach to genetic engineering greatly speeds the manufacture of bacteria for making drugs and biofuels.
March 17, 2009

Rather than changing the genome letter by letter, as most genetic engineering is done, George Church and his colleagues have developed a new technology that can make 50 changes to a bacterial genome nearly simultaneously–an advance that could be used to greatly speed the creation of bacteria that are better at producing drugs, nutrients, or biofuels.

Better bugs: Using a specially designed machine (shown here), scientists can rapidly engineer up to 50 genetic changes in bacteria, dramatically speeding the quest to design bacterial factories capable of efficiently producing drugs, biofuels, and other chemical products.

“What once took months now takes days,” says Stephen del Cardayré, vice president of research and development at LS9, a biofuels company based in South San Francisco of which Church is a founder. LS9 soon plans to use the technology–called multiplex-automated genomic engineering, or MAGE–to accelerate development of bacterial cells that can produce low-cost renewable fuels and chemicals.

In the traditional stepwise approach to genetic engineering, scientists tinker gene by gene with a cell’s metabolic system, attempting to rev up some reactions and dampen others. But this method is slow and unpredictable. A cell’s metabolism consists of millions of intricately intertwined reactions, so making a specific change to a gene involved in one reaction may not produce the desired outcome, or may trigger harmful side effects.

Instead, Church and his collaborators attack the genome on a broad scale. They design numerous genetic changes targeting genes throughout the genome, and then implement them all at once, looking for the resulting bacterial strain that can best produce the desired product. “It allows you to make modifications to the genome much more rapidly than the traditional one-step processes we have,” says Kristala Jones-Prather, a metabolic engineer at MIT who was not directly involved in the research.

Under the MAGE technology, scientists first generate 50 short strands of DNA, each containing a sequence similar to a gene or gene regulatory sequence in the target bacterial genome, but that has been updated in some way–incorporating a change that might make an enzyme more efficient, or boost production of a particular protein.

The DNA is mixed into a vial of bacteria, which is then put into a custom-made machine designed in Church’s lab. In the machine, the mixture is subjected to a precisely choreographed routine of temperature and chemical cycles that encourage the bacterial cells to take up the foreign DNA, swapping it into their genomes in place of the native piece it resembles. The single-stranded pieces of DNA are thought to “fake out the cell’s DNA replication machinery, sneaking in and filling a gap” during the replication process, says Church. Each generation of the rapidly reproducing bacteria takes up more of the foreign DNA, ultimately producing a population that has all the desired genetic changes.

As a test run of the device, Church and his team created bacteria that could more efficiently produce lycopene, an antioxidant abundant in tomatoes. They designed DNA strands targeting genes known to be involved in lycopene production, and then monitored multiple tubes of engineered bacteria for production of the bright-red compound. In just three days, they had generated a strain that could produce five times more lycopene, according to findings presented at a conference at Harvard this month. The best lycopene producer had 24 genetic changes–four that completed blocked production of the gene’s protein, and 20 that resulted in small or large changes in the expression of that gene.

Church and his collaborators, who ultimately plan on making a commercial version of the device, are now working on creating different types of chemicals, including biofuels and drug precursors.

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