2013 Joukowsky Dissertation Prize

Davis: The mechanics of biofuel bacteria

May 16, 2013  |  Media Contact: David Orenstein |  401-863-1862
Jennifer R. Davis - “I’ve learned a variety of new techniques that are applicable in many 
different fields. That was one of the most rewarding things 
about my research.”
Jennifer R. Davis “I’ve learned a variety of new techniques that are applicable in many different fields. That was one of the most rewarding things about my research.” Credit: Mike Cohea/Brown University
Jennifer R. Davis’ Joukowsky Award-winning dissertation explaining how certain bacteria can turn plant matter into the precursors of biofuels was a novel project in Jason Sello’s chemistry lab. It is also a tour (de force) of genomics, bioinformatics, biochemistry, and structural biology that has made a promising scientist even more broadly skilled.

PROVIDENCE, R.I. [Brown University] — In essence, Jennifer R. Davis’s doctoral dissertation is a study of how microbes with a rare and precious aptitude could gain even greater potential. In some ways, that’s also the narrative of Davis herself. She arrived at Brown in 2008 as an uncommonly impressive go-getter. This week she graduates as a highly skilled scientist with the 2013 Joukowsky Outstanding Dissertation Award in the life sciences category.

“It was a great learning experience and I think that’s what a Ph.D. should be,” Davis said.

The subjects Davis studied are soil-dwelling bacteria with the uncommon ability to break down plant matter into the precursors of biofuels. If they could be engineered to do that to an industrial degree, rather than for their own natural purposes, the future of vehicle fuels could be changed forever. After five intense years of work, Davis’s exploration of their genes and the molecular processes that regulate their plant-processing prowess has made that new future considerably more plausible. Her research lays out where genetic engineers or synthetic biologists can look to make improvements.

This wasn’t a project Davis inherited or was assigned. The idea began with Davis and her adviser Jason K. Sello, associate professor of chemistry, brainstorming about new avenues of research she might pursue on a category of microbes called actinobacteria. Sello had been studying the Streptomyces genus, but mostly to learn about their ability to both produce and resist antibiotics. Biofuels emerged as an idea.

Davis searched the literature, journeying all the way back to 1981 when Don Crawford and Sylvester Antai at the University of Idaho published a paper in Applied and Environmental Microbiology about how some Streptomyces could break down lignin, a nearly indigestible plant material with a lot of energy-carrying carbon. Therein were the seeds of Davis’ award-winning dissertation topic, an NSF Graduate Research Fellowship, and a new area of research in the Sello lab.

“The work described in Jennifer’s thesis essentially put my research group on the map in the area of bioenergy,” Sello wrote in nominating Davis for the Joukowsky award.

All it required was for Davis and Sello to launch an entirely new endeavor. Their goal was to find out everything scientists might need to know to engineer these bacteria into lignin-digesting powerhouses.

“Starting something new is always challenging,” Davis said. “We were always figuring it out together. It was never, ‘Oh, this is the obvious next step.’”

As a finished product, the 200-plus page dissertation doesn’t make the work seem simple or easy, but for all its technical detail it makes each step that Davis undertook seem intuitive.

A sequence of sciences

First Davis wanted to find the genes that give these bacteria their lignin-busting ability. The first step was to sequence the genomes of two bacterial species, done with Department of Energy funding and through collaboration between Brown and the Joint Genome Institute. In turn, bioinformatics software enabled Davis, Sello, and their team to make predictions about which genes were responsible for lignin consumption. Davis fingered a cluster of genes that the bacteria require to metabolize protocatechuate, an intermediate in lignin breakdown.

Protocatechuate sounds like it could be the name of a New England city, but it’s mercifully abbreviated “PCA.” The prediction was that the genes she sought allowed the bacteria to convert PCA into “β-ketoadipate,” a compound that supports the growth and reproduction of the bacteria. Reflecting their role in catabolism of PCA, the team named the cluster of genes Davis found the “pca” genes.

But genes in and of themselves are just instructions. What matters in biology is how an organism controls — regulates — that information at the molecular level. The next task therefore was to study what regulates the expression of those genes. Davis discovered that the bacteria only turned on the pca genes when they are in the presence of PCA.

When Davis found the regulator gene, she dubbed it PcaV. The regulation story started to come together. She and her colleagues proposed that PcaV’s job is to repress the expression of pca genes and therefore only allow the production of enzymes when PCA is available to the bacteria. This keeps the bacterium from wasting energy when it is not.

Davis subsequently showed that PcaV is indeed able to repress gene expression and does so by binding DNA. To explain why the pca genes are only turned on in the presence of PCA, the group figured that PCA might interfere with the ability of PcaV to bind DNA.

So the next step was to investigate the physical interaction of PCA with the PcaV protein. Just how did the presence of PCA get PcaV to lay off suppressing the expression of the pca genes? That brought Davis into the realm of structural biology, a field she’d have to learn to continue her research. Working with Rebecca Page, associate professor of biology, and fellow student Breann Brown, she purified the protein and resolved its structure using X-ray crystallography. She showed where it binds PCA and how PcaV reshapes during that binding so that it can’t instead latch on to pca genes and suppress their expression.

All of this work in genomics, bioinformatics, biochemistry and structural biology gives engineers copious new insight into where they can tinker to make Streptomyces a more efficient biofuels refiner. Alternatively, it also tells synthetic biologists what they should extract from Streptomyces bacteria if they want to insert its lignin processing power into a more convenient organism (imagine yeast or E. coli with pca genes encoding enzymes of the β-ketoadipate pathway).

Davis’ work is notable for another reason. It turns out that PcaV is a member of the “MarR” family of gene transcription regulators, which have many important roles in biology. Although that family is about 12,000 members strong, PcaV is now the best characterized among them because Davis was able to capture it in the act of binding to its favorite target, or “ligand,” PCA. The ligand of most other MarR proteins simply isn’t known.

Her study could therefore help scientists better understand other MarR regulators.

“It enables us to make a comparative analysis to other MarR regulators for which the ligand is not known,” Davis said. “It enables us to make broader statements about how these transcription factors regulate gene transcription.”

But why end a dissertation there?

Davis also delved into how a different species of Streptomyces bacteria breaks down another plant material: cellulose. Again using genomic and molecular biological techniques, she discovered a gene and resulting protein, called CelR, that is a master regulator of the gene expression for multiple cellulose processing pathways. That line of research provides another potential way for biofuels engineers to extract even more energy from plants.

So many skills

Davis came to Brown primed for this kind of success. In 2008 she graduated summa cum laude from Clark University in Worcester, Mass., with a degree in biochemistry and molecular biology. A Connecticut resident at the time, she interned with pharmaceuticals giant Pfizer in Groton for three summers, studying comparative medicine, neuroscience, and pharmacology.

She won the American Institute of Chemists Award in biochemistry while at Clark and was elected to Phi Beta Kappa. A favorite mentor and adviser, Professor David Thurlow, got her particularly excited about molecular biology.

As many lab skills as she acquired at Clark and Pfizer, she gained many more in her Ph.D. work at Brown, including her proficiency in microbiology.

Davis is now looking for an industrial postdoctoral position in biotechnology and is doing it with a CV that includes a long and impressive list of distinct lab skills and numerous publications.

“I’ve learned a variety of new techniques that are applicable in many different fields,” she said. “That was one of the most rewarding things about my research.”

At Brown, her already uncommon potential became even greater.

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