Production vs. Survival Problem

Joint BioEnergy Institute researchers make designer bugs even better
| June 17, 2011

What can common household cleaners like Pinesol tell us about wonder bugs and microbes used to produce advanced biofuels? Andrila Mukhopadhyay knows, and with help from her team at the University of California Berkeley’s Joint BioEnergy Institute, she has an entire library of data to tell us how. For the past two and a half years she has been studying the effects of antimicrobial-like compounds and their effect on biofuel-producing microbes that are, in most cases, hindered by the same compounds they produce. “There are two things that act as impediments when you are trying to make biofuels,” she says.

The first hurdle for the microbes stems from the compounds (which are actually used in both biojet fuel and Pinesol) and the level of toxicity in the compounds that can actually kill the microbes. The second, she says, is that even in the cases where a microbe produces nontoxic compounds suitable for advanced biofuels, those microbes are usually inhibited by the amount of compounds produced that cannot escape the microbial cells. “With these [two impediments] in mind, a lot of people have started to study and find tolerant bugs.” Instead of searching for the right bug, Mukhopadhyay decided to “cut to the chase” and simply search for the direct mechanism that makes a bug more tolerant and capable of reaching industrial-strength production levels. The answer, she found, was efflux pumps.

Efflux pumps are proteins in the cytoplasmic membrane whose main function is to transport, or pump, toxic substances out of the cell. “They are basically natural mechanisms that provide tolerance to antimicrobial compounds,” she says. To find the best available pumps, her team screened for a few good candidates and then searched for every similar sequenced species that might have similar qualities. “We put each pump against each other and created a culture competition to see which pump would win,” she says. Even though her team found the winning pumps they were looking for, she says they still were unsure of one thing: would a winning pump actually help to produce more molecules from the microbes?

“To our surprise,” she says, “our hypothesis was correct. Strains that can export these compounds actually make more.” So what does this mean for advanced biofuel production? Mukhopadhyay says it means a lot, but the work isn’t done yet. Although the team now has a library of pumps that will provide a microbe with more tolerance to both toxic compounds and help to stop product inhibition by exporting more of the compounds out the cell, she says they still need to find a way to turn the pumps on or off in an industrial setting. At this point, the team simply supplied an additive to the mix of sugar that would start the pumps, but this she says is unfeasible in an industrial setting.

Overall, however, she says the discovery of the winning pumps will play a huge role in future strain development of designer bugs. “Think about how industrial strength strains are tested,” she points out. The strains will be subjected to the rigors of the industrial setting over and over until the researchers know what the strain will do. If any of those conditions change, however, such as feedstock, temperature or anything else, the results can change. But by understanding the pump’s role, strain developers will have a better understanding of the microbe to begin with.  —Luke Geiver


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