Scientists Study Makeup of Oil-Eating Bacteria


In research that could pave the way for new chemical systems to treat toxic wastes in the environment, MIT scientists are working to understand how certain bacteria digest oil, PCBs and other carbon-based compounds, especially methane (natural gas).

Specifically, the scientists are working to determine the molecular structure of the protein system that allows such a diet. They also hope to work out a kind of "motion picture" of how the reactions involved proceed.

"Once we learn the fundamentals of how nature does it, we can attempt to design simpler chemical molecules that could treat [carbon-based] wastes in contaminated water, chemical dumps, or other places where living organisms couldn't survive," said Stephen Lippard, professor of chemistry and principal researcher in the work.

Although scientists have known about methane-eating bacteria for some time-three years ago related organisms were used to clean up oil from stretches of beaches in Alaska after the Exxon Valdez spill-they don't know exactly how the bacteria use oxygen and iron to convert such surprising food into alcohol (methanol), water, and carbon dioxide, the principal byproducts.

Professor Lippard and colleagues are working with a strain of methane-eating bacteria from the hot springs in Bath, England, to find out.

Central to the study, which has been supported by the National Institutes of Health for several years, is the methane monooxygenase (MMO) system responsible for this digestive phenomenon. (There are actually two MMO systems in each organism; which one is used depends on environmental conditions.)

The MMO system the MIT chemists are studying is made up of three proteins. The largest of these-called the hydroxylase-is of special interest because it is the one that contains iron and binds carbon-based compounds. As a result, the Lippard group is focusing first on finding the three-dimensional structure of this protein.

Last year the scientists had a breakthrough when Amy Rosenzweig, a graduate student in chemistry, succeeded in growing crystals of the hydroxylase. "That's a very important first step in getting the three-dimensional structure of the protein," Professor Lippard said. "Many other groups were trying to do it."

Earlier the MIT scientists had come up with a model of what the iron core of the hydroxylase looks like. But although that work "gave us a fair amount of information, it didn't give the complete story," Professor Lippard said. Ms. Rosenzweig's crystals should allow the scientists to confirm the model of the core and work out the protein's three-dimensional structure.

"If we're lucky, we could have a preliminary structure within a year," Professor Lippard said. (He notes that "for small molecules, once you have crystals you can often work out their structure overnight." For large molecules, however, "it's thousands of times more complex." And the hydroxylase, with a molecular weight of 250,000, "is roughly ten times as large as the average protein.")

Once the scientists determine the hydroxylase structure, they hope to take the work a step further by crystallizing a hydroxylase that's attached to a substrate molecule like methane.

Recently Ms. Rosenzweig, former graduate student Xudong Feng, and Professor Lippard published a summary of their work with the hydroxylase and model compounds as a chapter in the book Applications of Enzyme Biotechnology.

In addition to the hydroxylase studies, the scientists are also investigating the overall MMO system. Their ultimate goal is to develop a kind of "motion picture" of how the system works-how bonds break and form as methane is converted to methanol.

Professor Lippard notes that this is a long-term project. To put the work in perspective, he compares the crystal structure of the hydroxylase to "a still picture, a shot of the landscape" in the overall "movie".

So far the scientists' work on this "movie" has focused on the relationships between the hydroxylase and two smaller proteins in the MMO system, which Professor Lippard calls "a wonderful example of bioengineering." Why? "Because the bacteria have arranged [the MMO] proteins in such a way as to avoid self-destruction."

Recently, he explained, chemistry graduate student Kathy Liu, another member of the research group, showed that the two smaller proteins in the MMO system control the transfer of electrons, or energy, into the hydroxylase. They only let electrons in when methane or a similar substrate molecule is present.

"If there were no methane around and electrons got into the iron center of the hydroxylase," Professor Lippard said, "activated forms of oxygen might attack the hydroxylase itself."

The scientists still have some way to go before they completely understand the MMO system, an understanding that could result in new ways to treat hazardous wastes. But the research is also an end in itself because, said Professor Lippard, "it's intrinsically interesting."

A version of this
article appeared in the
April 1, 1992

issue of MIT Tech Talk (Volume
36, Number
25).


Topics: Biology

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