We’re a medicated society — and because many pharmaceuticals can pass through our bodies without being degraded, we have medicated wastewater as well. Scientists have found scores of different drugs in water flowing into wastewater treatment plants. And, with these facilities not designed to break down many of these compounds, an unsettling number are found in water flowing out of them, too — with largely unknown consequences for people and wildlife who ingest them.
Now University of Minnesota scientists led by research associate Kelly Aukema and professor Larry Wackett of the Department of Biochemistry, Molecular Biology and Biophysics and the BioTechnology Institute have come up with a promising new strategy for dealing with this dilemma. Using a mixture of computation and experimentation, they have developed a process that can be used to identify enzymes — molecules found in nature that break down other molecules — most likely to be able to degrade a given compound.
The conventional approach to enlisting organisms to break down pollutants, known as bioremediation, is to expose a wide variety of microbes containing a wide variety of enzymes to the compound of concern in hopes that one will emerge victorious. But this approach can be expensive, tedious and slow — too slow to keep pace with the plethora of new compounds humans are creating.
“You shouldn’t have to take every single chemical you’re interested in and every enzyme possible and test all of those,” Aukema says. “That would be a huge experiment. It’s just not possible.”
To find a better way, Aukema teamed up with Diego Escalante, a Ph.D. student advised by Department of Mechanical Engineering professor Alptekin Aksan, in a strategic search for an enzyme that could degrade one particularly challenging compound, carbamazepine.
Used to treat epilepsy, bipolar disease, ADHD and related disorders, carbamazepine is both common and notoriously hard to break down in wastewater treatment plants. In fact, the researchers chose it as a subject for study after they learned it was being found in individuals who ate crops irrigated with treated wastewater.
To figure out a way to break carbamazepine down into harmless components, Aukema and Escalante used a process known as rational design that’s based on the fact that enzymes operate in a lock-and-key fashion, with each enzyme containing a pocket-like space into which the molecule to be degraded fits and in which it’s broken down. Using their knowledge of the shape of the carbamazepine molecule and the shape of pockets of various enzymes, the researchers were able to select a few that might be a good fit for carbamazepine. They then tested these selected enzymes and found one, made by the bacterium Paraburkholderia xenovorans, that readily degraded the drug into innocuous molecules.
Aukema hopes civil engineers will be able to use this information to introduce a carbamazepine-destroying functionality into wastewater treatments plants. On a broader scale, she notes the successful use of the process bodes well for breakdown not only of carbamazepine but of other pharmaceuticals as well. It turns out that P. xenovorans, which was first found at a waste site in New York where it was degrading PCBs, makes a number of enzymes that look promising for breaking down other substances, too. In fact, in further tests, the researchers found the bacterium was able to at least partly break down 12 of 22 persistent contaminants tested.
“We were surprised to see how many different compounds … actually could be removed by this strain,” she says.
The research team is now in the process of developing an internet-based tool known as RAPID (for Reaction Activity Prediction IDentification) that others can use to perform similar searches for other compounds. The RAPID system is a collaboration between the research groups of Wackett and Aksan, with the help of Lynda Ellis, emerita professor of health informatics.
“This was definitely a test case,” Aukema says. “We could imagine someone might say, ‘I have this kind of compound that is a problem. How are we going to be able to remediate this? What sorts of enzymes might work on it?’ Then we’re hoping people might be able to come to the website put it in and get a prediction.” —Mary Hoff