Early career award funds study of messenger RNA stability

In an effort to improve microorganisms that can sustainably produce fuels and chemicals, a University of Wisconsin–Madison engineer is using a U.S. Department of Energy award to study what — if anything — gets lost in the translation of genetic information.

Brian Pfleger, an assistant professor of chemical and biological engineering, is drawing on powerful genetic sequencing tools to track the stability of messenger RNA — a fleeting molecule that conveys an organism’s genetic information to the protein factories within cells.

A five-year, $750,000 early-career award from the DOE Office of Biological and Environmental Research is funding his research. Pfleger is among 61 young faculty nationwide to receive the award.

Applying genetic engineering tools, Pfleger hopes to optimize the metabolism of a specific cyanobacterium that, when supplied with light, carbon dioxide and a few nutrients, can produce fuels and key chemical compounds.

The ability to control gene expression in those microorganisms is key to the endeavor’s success. Genetic information is stored in DNA and holds the instructions that dictate how all living organisms develop and function. Messenger RNA delivers the instructions and cells make proteins to carry out the instructions.

However, for a variety of reasons, messenger RNAs are rapidly degraded, and that turnover can affect the nature and quantity of proteins cells make. Currently, there are gaps in researchers’ understanding of messenger RNA stability — particularly outside model organisms such as E. coli.

Those unknowns affect Pfleger’s ability to engineer an effective microorganism. “In biology, you can’t just hope for the best,” he says. “You need to understand every aspect — otherwise, there’s a chance that something’s going to pop up and evolve in a way you didn’t expect it to.”

For the research, Pfleger and his students will leverage the U.S. Department of Energy Joint Genome Institute DNA and RNA sequencing capabilities, as well as pyrosequencing tools in the UW–Madison Biotechnology Center. “This RNA sequencing technology allows us to get base-pair resolution of the quantity of a messenger RNA,” he says.

Using the cyanobacterium genome, Pfleger and his students are studying whether certain genes decay rapidly and what messenger RNA sequence features affect that turnover. “We are studying the fundamental microbiology and biochemistry of RNA turnover in an organism that hasn’t been studied, and then using that information to build control structures to better design how to make a particular gene into a protein in these organisms,” he says. “Ultimately, this knowledge will enable us to design better cyanobacteria for producing fuels and chemicals.”