In developing alternatives to fossil fuels, one possibility lies in the polymer lignin, whose components can be engineered to develop fuel.
Most microorganisms cannot break down lignin, but in a study published earlier this month in the journal Nucleic Acids Research, Brown researchers described a possible mechanism for how the Streptomyces bacterium achieves this feat.
At present, the findings are mostly of academic interest, said Breann Brown GS, who worked on the research with Jennifer Davis GS under the guidance of Jason Sello, associate professor of chemistry, and Rebecca Page, associate professor of biology.
“What we’re contributing to the field is a better understanding of how the bacteria do what they do,” Brown said.
Streptomyces bacteria are able to metabolize lignin through enzymes that are only produced when a certain gene cluster is active, according to a University press release. But a protein called PcaV usually binds to the bacteria’s DNA, switching off the gene that signals the production of enzymes.
The researchers found that when bacteria are exposed to a specific enzyme, protocatechuate, PcaV loses its affinity for DNA, Page said. With the DNA now unblocked, “all the machinery that is needed to transcribe DNA to RNA can actually bind and work,” Page said.
To understand what was happening with the protein at a molecular level, the researchers used a technique called protein crystallography to compare what PcaV looks like with and without protocatechuate, Page said.
Results from the protein crystallography revealed that the amino acid arginine was involved in PcaV’s binding to DNA as well as PcaV’s binding to protocatechuate, according to the press release. This led the researchers to speculate that arginine might be the specific subunit responsible for the blocking and unblocking of DNA.
Sello called the crystallization “the most difficult part” of the research. None of the protein crystals that were bound to DNA diffracted enough to present a clear structure, and it would have been difficult to solve the structure of even fully formed crystals, Brown said. To understand the structures at a molecular level, the team had to test the bacteria in protein solutions in over 8,000 conditions, Sello said.
For Page, a highlight of the experiment was seeing the structure for the first time, “really seeing the beautiful density of the bound (protocatechuate),” she said.
The interdisciplinary nature of the paper makes it especially relevant to science today, which approaches experiments with a more holistic view, Sello said. “We have genetics, biochemistry, analytical chemistry, structural biology all put together in one paper,” he said. “One of (the) things we are particularly proud of is that the results contained in the paper usually would be found in three or four papers.”
“It’s good to see people with different expertise working on the same project, not only at the genetic level but also at the molecular level,” said Michael Thomas, an associate professor of bacteriology at the University of Wisconsin-Madison, who was not involved in the study. Though it is too soon to define the broader implications of the researchers’ findings, they are an important advancement toward alternative fuels, Thomas said.
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