Biofuels and the gene pool

The power of yeast genetics might make ethanol fuel much more cost-effective

Your kitchen is stocked with one of the mightiest tools of modern biology: yeast.

Common, everyday baker’s yeast, living in little packets in your fridge, and diffused throughout your bread, beer and wine.

Gregory Stephanopoulos, Hal Alper and Gerald Fink celebrate their success in creating yeast that shows higher tolerance for ethanol. Photo: Donna Coveney/MIT

This mundane single-cell organism not only allows researchers to beta-test countless genetic tools (many of which are eventually scaled up for human cells) but is employed to screen drugs and even to study certain diseases such as Parkinson’s. For any molecular biologist working today, it’s hard to overstate the contributions of yeast genetics.

Now, the benefits of so intimately knowing this microscopic life form are reaching beyond biomedicine into the realm of global warming.

Farming fuel

As politicians finally get serious about the need for the U.S. to decrease dependency on fossil fuels, there is one partial solution that they all like: ethanol.

But ethanol isn’t like crude oil. You can’t just drill down and then catch it as it gushes out. Instead, it takes a lot of energy to produce this colorless grain alcohol. The trick is to use the least energy possible to produce the most ethanol allowable.

So far, that’s been an elusive goal.

Last year, four billion gallons of ethanol were produced in the United States, while we consumed about 140 billion gallons of gasoline. Photo: Stockbyte Platinum

In the United States, ethanol is produced chiefly from corn, and working with corn demands a lot of energy. Everything from the growing process to producing fertilizers to harvesting the crop requires oil. Then the corn needs to be made into sugar, which is turned into ethanol—which still needs to be distilled prior to commercial use. On top of that, you need energy to ship the ethanol to regions of the country where corn isn’t plentiful.

It’s pretty easy for critics to start poking holes in this schematic. Because when it comes to ethanol as an alternative to oil, the energy return on the energy investment is much slimmer than desired.

This is precisely where yeast genetics can help.

Whitehead Member and yeast expert Gerald Fink has teamed up with chemical engineer Gregory Stephanopoulos of Massachusetts Institute of Technology to create a genetically altered strain of yeast that promises to make ethanol production far more efficient—50 percent more efficient.

Ethanol is produced through fermentation. After the corn has been made into sugar, baker’s yeast metabolizes the sugar, producing ethanol.

But there’s an unfortunate irony to this procedure. Yeast doesn’t tolerate ethanol very well. In fact, at certain levels, ethanol is toxic to it. And because yeast is indispensable to the process, there’s no way of getting around using it. The end result is inefficient production.

Many scientists have tried to engineer ethanol-tolerant strains of yeast, usually by tinkering with one or two key genes at a time. Hal Alper, a postdoctoral researcher in both the Fink and Stephanopoulos labs, decided to take a different approach.

Rather than homing in on a single gene, he thought, why not target a regulatory molecule that can affect many genes at once?

Power yeast

Transcription factors are nature’s equivalent to circuit breakers. Much as one circuit breaker activates the electricity in many rooms in your house, one transcription factor can control the activity of a whole network of genes in a cell. If the one-gene-at-a-time approach couldn’t make yeast more tolerant of ethanol, perhaps transcription factors could.

Alper decided to focus on two transcription factors. One of them, called the TATA-binding protein, yielded startling results in ethanol. When Alper altered this transcription factor, it over-expressed many genes, of which at least a dozen proved sufficient to elicit an improved ethanol tolerance. As a result, this altered strain of yeast could survive high ethanol concentrations. Over a 21-hour period, it produced 50 percent more ethanol than normal strains.

“What we have provided is an enabling technology,” says Stephanopoulos. “A key component of this is that when we think of a cell that makes a biofuel, the production of that biofuel is not a property of a single gene or a single enzyme. The production of ethanol is a property of a whole network of reactions, all of which need to work together so that the cell can make the molecule at efficient rates.”

The greatest significance of this research is that it opens up a new avenue for thinking about engineering other desirable properties in a cell, the researchers say.

“Before this, we had very few tools for improving a process that is controlled by many genes,” says Alper. “Now others can apply this approach for making ethanol production or other phenotypes of interest far more efficient.”

“This is a major contribution,” comments Michael Ladisch, a professor at Purdue University’s Laboratory of Renewable Resources Engineering. “This research demonstrates that ethanol tolerance is not a simple phenomenon. The fact that they’ve identified the genes involved and can efficiently track them is a major step forward.”

“Yeast has been key to advances in basic biology and medicine,” notes Fink. “I am very optimistic that this yeast will also contribute to improving our ability to make alternative fuels.”

Here's how ethanol fuel is created from corn. Yeast does all the heavy lifting in the fermentation process. Illustration: Tom Dicesare