Making living matter programmable

synbercpanel350
Thirty years ago, the future lay in programming computers. Today, it’s programming cells.

That was the message of panelists at an afternoon session yesterday (March 25) in Stanley Hall auditorium titled “Programming Life: the revolutionary potential of synthetic biology.” Co-presented by UC Berkeley’s Synthetic Biology Engineering Research Center (SynBERC) and Discover magazine, the panels brought together a dozen of synthetic biology’s pioneers from academia and industry, in addition to ethicists focused on the societal impact of the technology.

Keynote speaker Juan Enriquez, a self-described “curiosity expert” and co-founder of the company Synthetic Genomics, compared the digital revolution spawned by thinking of information as a string of ones and zeros to the coming synthetic biology revolution, premised on thinking about life as a mix of interchangeable parts – genes and gene networks – that can be learned and manipulated like any language.

At the moment, this genetic manipulation, a natural outgrowth of genetic engineering, focuses on altering bacteria and yeast to produce products they wouldn’t normally make, such as fuels or drugs. “To do with biology what you would do if you were designing a piece of software,” according to moderator Corey Powell, editor at large of Discover, which plans to publish a story about the conference and post the video online.

UC Berkeley chemical engineer Jay Keasling has been a key player in developing the field of synthetic biology over the last decade. Enriquez introduced Keasling as someone “who in his spare time goes out and tries to build stuff that will cure malaria, and biofuels and the next generation of clean tech, all while mentoring students at this university and at the national labs and creating whole new fields of science.”

Keasling, director of SynBERC, a UC Berkeley-led multi-institution collaboration that is laying the foundations for the field, expressed excitement about the newest development: the release next month by the pharmaceutical company sanofi aventis of a synthetic version of artemsinin, “the world’s best antimalarial drug,” he said. Sparked by discoveries in Keasling’s lab more than a decade ago, the drug is produced by engineered yeast and will be the first product from synthetic biology to reach the market.

“There are roughly 300 to 500 million cases of malaria each year,” he said. “Sanofi will initially produce about 100 million treatments, which will cover one-third to one-quarter of the need.”

Biofuels from yeast

As CEO of the Joint BioEnergy Institute, Keasling is now focused on engineering microbes to turn “a billion tons of biomass that go unutilized in the U.S. on an annual basis … into fuel, producing roughly a third of the need in the U.S.”

But other advances are on the horizon, he said, such as engineering new materials and engineering “green” replacements for all the products now made from petroleum. “Some of these have the potential to significantly reduce our carbon footprint, by say, 80 percent,” he said.

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via UC Berkeley
 

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Researchers Develop a New Candidate for a Cleaner, Greener and Renewable Diesel Fuel

Fragrant New Biofuel

A class of chemical compounds best known today for fragrance and flavor may one day provide the clean, green and renewable fuel with which truck and auto drivers fill their tanks. Researchers at the U.S. Department of Energy’s Joint BioEnergy Institute (JBEI) have engineered Escherichia coli (E. coli) bacteria to generate significant quantities of methyl ketone compounds from glucose. In subsequent tests, these methyl ketones yielded high cetane numbers — a diesel fuel rating comparable to the octane number for gasoline — making them strong candidates for the production of advanced biofuels.

“Our findings add to the list of naturally occurring chemical compounds that could serve as biofuels, which means more flexibility and options for the biofuels industry,” says Harry Beller, a JBEI microbiologist who led this study. “We’re especially encouraged by our finding that it is possible to increase the methyl ketone titer production of E. coli more than 4,000-fold with a relatively small number of genetic modifications.”

Beller directs the Biofuels Pathways department for JBEI’s Fuels Synthesis Division, and also is a senior scientist with the Earth Sciences Division of Lawrence Berkeley National Laboratory (Berkeley Lab). He is the corresponding author of a paper describing this work titled “Engineering of Bacterial Methyl Ketone Synthesis for Biofuels,” which was published in the journal Applied and Environmental Microbiology. Co-authoring this paper were Ee-Been Goh, who is the first author on the paper, plus Edward Baidoo and Jay Keasling.

Advanced biofuels — liquid transportation fuels derived from the cellulosic biomass of perennial grasses and other non-food plants, as well as from agricultural waste — are highly touted as potential replacements for gasoline, diesel and jet fuels. Equally touted is the synthesis of these fuels through microbes that digest the biomass and convert its sugars into fuel molecules. At JBEI, researchers are focusing on developing advanced biofuels that can be used in today’s engines and distribution infrastructures. In previous research, Beller and his colleagues engineered E. coli with special enzymes to synthesize from fatty acids long-chain alkene hydrocarbons that can be turned into diesel fuel. Fatty acids are the energy-rich molecules in bacterial and plant cells that have been dubbed nature’s petroleum.

“In those studies, we noticed that bacteria engineered to produce unnaturally high levels of fatty acids also produced some methyl ketones,” Beller says. “When we tested the cetane numbers of these ketones and saw that they were quite favorable, we were prompted to look more closely at developing methyl ketones as biofuels.”

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Bacteria Transformed into Biofuel Refineries

Escherichia coli: Gram negative rod off a cult...
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Synthetic biology has allowed scientists to tweak E. coli to produce fuels from sugar and, more sustainably, cellulose

The bacteria responsible for most cases of food poisoning in the U.S. has been turned into an efficient biological factory to make chemicals, medicines and, now, fuels. Chemical engineer Jay Keasling of the University of California, Berkeley, and his colleagues have manipulated the genetic code of Escherichia coli, a common gut bacteria, so that it can chew up plant-derived sugar to produce diesel and other hydrocarbons, according to results published in the January 28 issue of Nature. (Scientific American is part of Nature Publishing Group.)

“We incorporated genes that enabled production of biodiesel—esters [organic compounds] of fatty acids and ethanol—directly,” Keasling explains. “The fuel that is produced by our E. coli can be used directly as biodiesel. In contrast, fats or oils from plants must be chemically esterified before they can be used.”

Perhaps more importantly, the researchers have also imported genes that allow E. coli to secrete enzymes that break down the tough material that makes up the bulk of plants—cellulose, specifically hemicellulose—and produce the sugar needed to fuel this process. “The organism can produce the fuel from a very inexpensive sugar supply, namely cellulosic biomass,” Keasling adds.

The E. coli directly secretes the resulting biodiesel, which then floats to the top of a fermentation vat, so there is neither the necessity for distillation or other purification processes nor the need, as in biodiesel from algae, to break the cell to get the oil out.

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