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Genetic Sensor Boosts Biofuel Production

Designer microbes regulate their own pathways to optimize fuel production, boosting yields threefold.

Give bacteria a bit of self-awareness and they can be smarter about producing biofuel.  

Fuel boost: Jay Keasling (left) and Fuzhong Zhang, who is the lead author on a paper describing the new work, at Berkeley’s Joint BioEnergy Institute (JBEI).

That’s the conclusion from researchers at the University of California, Berkeley, who report a genetic sensor that enables bacteria to adjust their gene expression in response to varying levels of key intermediates for making biodiesel. As a result, the microbes produced three times as much fuel. Such a sensor-regulator system could eventually make advanced biofuels cheaper and bring them a step closer to being an economically viable replacement to petroleum-based products.

One issue that has limited the amount of biofuels that a microbe makes is an imbalance of the different biological ingredients, or precursors, used to make the final fuel product. In a study published this week in Nature Biotechnology, Jay Keasling, professor of chemical engineering and bioengineering at UC Berkeley, and colleagues describe a biological sensor system that lets bacteria regulate genes in its biofuel-production pathways according to the amount of certain precursors in the cell.

The researchers augmented a previously reported strain of engineered E. coli that creates biodiesel from two biological building blocks—fatty acids and ethanol. Over the life cycle of that strain, one precursor can be produced at a higher level than another, an inefficient and sometimes harmful situation.

“The pathways weren’t in balance,” says Keasling. “The cells were wasting resources producing one precursor at a higher level than another.” What’s more, he says, biofuel production would sometimes consume too many fatty acids, which the bacteria need at certain stages of their life cycle, making the strain unstable.

Keasling and coworkers designed a microbe, using a naturally occurring sensor, that responds to the amounts of internal fatty acids and related molecules and tunes the activity of its pathways accordingly. When limited amounts of fatty acid are in the cell, the sensor-regulator molecules puts the brakes on both the ethanol-producing pathway and the fatty acid-converting pathway. Conversely, when the bacteria contain higher levels of fatty acids, the brakes on these pathways are released.

The sensor-regulator system improves the engineered bacteria in two ways, says Keasling: the metabolic pathways are better balanced so that one precursor isn’t overproduced relative to the other, and the modified bacteria are more stable because the biofuel production isn’t robbing the cell of the ability to grow. This “self-awareness” increased the amount of biodiesel made by the bacteria to 28 percent of theoretical maximum, a threefold increase over the previously reported strain.  

Although the improvement is significant, biodiesel production is still too limited to bring the fuel into the mainstream. “There are many issues, including metabolic imbalances, that need to be solved to make biofuels a reality,” said Keasling in an e-mail. For instance, expanding these largely experimental cultures to commercial scale—on the order of a million liters—will be a challenge.

While the genetic regulator will not be the only key to opening up the nascent biofuels field, it is an elegant strategy for improving yields, says James Liao, a biomolecular engineer at the University of California, Los Angeles. “The sensor-regulator system will be a very useful tool in the toolbox we currently have.”

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