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Chemical reaction

MnDRIVE award supports effort to build a predictive database of how chemicals can be degraded rapidly and safely by microorganisms.

banner image of Larry Wackett in laboratory

Chemicals are constantly entering the environment, ranging from the large-scale use of a pesticide in agriculture to something as seemingly insignificant as the soap used during hand washing. The fate of those chemicals once they are in the environment, however, is often unknown.

Larry Wackett and BioTechnology Institute colleagues Carrie Wilmot, Mikael Elias, Alptekin Aksan and Carl Rosen are planning to use an MnDRIVE Transdisciplinary Research Program award they received this summer to illuminate how chemicals degrade. Wilmot and Elias are experts in enzyme structure and evolution, Aksan encapsulates enzymes and bacteria for bioremediation, and Rosen is particularly interested in the formation and fate of acrylamide in foods. The principle aim of this transdisciplinary research is to create a predictive database of how all chemicals – including those already in use and those yet to be developed – can be degraded rapidly and safely by microorganisms.

“Every year, 1,000 new chemicals get registered at the EPA and they can’t do studies on how they’re all biodegraded,” Wackett says. “We need to develop better tools and use our knowledge to better understand how these many chemicals can get degraded.”

Bacteria have evolved to eat and degrade a range of chemicals including many that are toxic to humans or the environment. The Deepwater Horizon oil spill in 2010 or, more recently, the West Virginia coal cleaning chemical spill are both examples of harmful chemicals that were released into the environment and were largely cleaned up by bacteria that naturally occur in those waters. Ideally, the cleanup process can proceed more quickly by using encapsulated bacteria that degrade the chemical.

However, most lab biodegradation studies are designed to first isolate the bacteria that degrade the chemical and then work out the enzymatic pathways that complete the process. “By the time you do the research and publish the papers, the chemical is going to be long gone,” he says. “We want to streamline that process.”

Recent work from Wackett’s research group has shown that a bacterial enzyme that is used to degrade one toxic chemical, naphthalene, can in fact act on a large number of chemicals. Wackett and his colleagues will use the MnDRIVE award to begin building a database that starts with thousands of bacterial enzymes of known function and then computationally predicts which other chemicals the enzymes will modify.

“What we’d like to do is take any chemical any time there is a concern and find the enzyme and microbe that will eat it,” Wackett says. He hopes that by combining the predictive tool with experimental work, the biodegrader of a chemical can be identified in weeks or days instead of years. As part of the project, Aksan, a mechanical engineering professor, will package the correct bacteria in a materials that will allow them to function like a water filter: the contaminated water flows in, the bacteria convert it to a harmless product, and the cleaned water flows out.

Wackett said the goal is to eventually commercialize some of the products that are developed from this award, but that the scientists working on the research side of the project are often not the best people to determine if a product is marketable. On that end, Wackett and his team will also be working with Toby Nord, the director of the Ventures Enterprise in the Carlson School of Management, and students in his entrepreneurship course to evaluate the market for these bacterial cleaning systems given the various chemical environments they are expected to be able to decontaminate.

“It is a goal to go beyond developing this predictive  tool for lab use, and see these tools get used to clean up chemical spills in the real world,” Wackett says.

— Sarah Perdue


September, 2014