Researchers in the University of Wisconsin–Madison Department of Biochemistry and Great Lakes Bioenergy Research Center (GLBRC) will utilize a $2.1 million grant from the United States Department of Energy to elucidate the properties of a potentially useful and understudied class of genes and enzymes in important bioenergy crops, such as poplar, sorghum, and switchgrass. The project is led by professors Brian Fox and John Ralph.
The two kinds of enzymes — called acyl-CoA ligases and BAHD acyltransferases — together create a large variety of potentially useful molecules. In a breakthrough application of their methods, the group found that very similar genes — predicted to have similar functions — acted very differently.
“Now, we hope to identify the role of a bunch of unknown genes and their corresponding enzymes that are in a class that appears to be important for many reasons,” explains Ralph, whose lab is part of the Wisconsin Energy Institute, which houses GLBRC. “We don’t know much about what they do but the few we have studied have been interesting and useful, so we are excited to explore the rest.”
Professor John Ralph and research scientist Steven Karlen. Photo by
The potential exists to engineer plants with modified capabilities that can help them produce useful compounds or make them more readily useable for biofuel production. However, without knowing anything about these classes of enzymes — similar to a mechanic not knowing anything about the parts of a car engine — it is difficult if not impossible to understand the breadth of possibilities ahead.
For example, their work in these and related enzymes has already given some exciting results. They’ve been able to create “zip lignin” — lignin being a compound that makes plants woody — to make it easier to convert plant material in precursors for biofuel production. They later found that the gene for zip lignin was already naturally present in poplar trees, the plant they studied, which simulated their interest in carrying out the current study.
Recently, they also found a way synthesize acetaminophen, the active ingredient in Tylenol, from a natural compound derived from plant material. While the application of this process is far from reality with more research needed, it opens up the possibility of a more natural way to make the compound, rather than relying on fossil fuels.
It’s exciting possibilities like these, coupled with the opportunity to create a database or “toolbox” containing these genes and information about what they do for other scientists to also use, that motivates the work. The researchers have no way of knowing what many of the enzymes could do but are eager to find out.
Assistant scientist Rebecca Smith. Photo by Matt
“We’ll hopefully ultimately have functions for all of these enzymes beyond biofuel production, which is of interest to us,” says Rebecca Smith, an assistant scientist in the Ralph Lab. “Once we know what they do we can start designing plants that are better for this or better for that. We’ll also have the structural information to generate good models for other plants and related enzymes in a library or toolkit for other researchers to use.”
Craig Bingman and a Fox Lab member Kirk Vander Meulen are working to get a list of about 700 genes to study. The chosen sequences will be sent to the Department of Energy Joint Genome Institute for processing and then back to the Fox Lab, where they can synthesize proteins from the genes using a cell-free protein translation method that is quick and efficient. Smith and associate scientist Steven Karlen in the Ralph Lab will then test for the activity of the enzymes to find out their function. As an additional step, Bingman, who leads the Department of Biochemistry’s Crystallography Core will work to solve the 3-dimensional structures of those enzymes that are most interesting.
Their approach allows them to systematically go through the entire poplar genome, and that of other important bioenergy crops like sorghum and switchgrass, to test all of the possible functions.
“It’s a bit of a mind shift in how we think about what we can do since we now have well-defined starting points and so many rapid ways of doing things,” Fox says. “Now we are able to bring all of these pieces together to address the contributions of these uncharacterized enzymes, which will bring useful new properties to aid plant engineering.”
Read more about this area of research in the UW–Madison Department of Biochemistry: