Kristala L. J. Prather

Kristala L. J. Prather

Awarded in 2019

Biology the Chemist

Making Sense From Nature

Looking for an enzyme in a haystack

Dr. Kristala Prather describes the societal imperative prompting her research succinctly: “We have to stop digging up dead dinosaurs to make the world run. In other words, we have to get away from using fossil fuels and fossil inputs to produce the molecules we need for everyday life.” How, then, are we to synthesize molecules that have the right properties for their intended use? According to Dr. Prather, biology is a master chemist, capable of generating a diverse array of useful molecules. Her research proposes to refine and expand this capability by helping nature to evolve biosensors able to analyze a large amount of enzymes and identify the ones with the most relevant characteristics.

Finding just the right enzymes is a significant challenge, however. A method of altering enzyme traits known as directed evolution (for which Caltech’s Frances Arnold won the 2018 Nobel Prize in Chemistry) requires extremely large libraries of DNA sequences to be generated and screened—connecting the size of these libraries with sufficient throughput for screening is a major barrier. Two screening methods could be practical: one would utilize some kind of biosensor, the core element of which would be a transcription factor that responds favorably to the metabolite of interest and produces an easily detectable signal, such as fluorescence; the other would use the transcription factor to control expression of an essential gene, with best candidates identified from a standard enrichment culture. Dr. Prather’s novel approach to access such sensors is to expose half a dozen types of bacteria to half a dozen unique molecules, and through this exposure allow microbial cells to develop new sensors on their own; she will observe this action by measuring RNA levels and changes in gene expression.

I’m an engineer by training, so this research brings together different parts of my knowledge and skill set, and inspires me to explore new directions. I believe that the answers I seek may already be out there, waiting for me to discover.”


Speeding along evolution

“My central premise—that nature will both enhance and, if necessary, evolve metabolite-protein interactions through prolonged exposure—is a high-risk one,” says Dr. Prather. “After all, evolution occurs over very long time scales and there is no preliminary data to support my hypothesis. That’s why this work would almost certainly not be funded by traditional sources.” There are also technical challenges involved in this work, such as determining the right level of exposure and maintaining a sterile environment. In addition, a lot of inference is involved in deciding whether or not observed changes are actually connected to something useful. However, it has been proven that prolonged exposure of a microbial culture to a target molecule can result in the evolution of a relevant sensor (in Japan in 2016, a bacterium was discovered that had naturally evolved to consume plastic).


Uncommon sensors for the common good

The findings from this work could have broader impacts beyond those mentioned above. For example, the search for effective enzymes need not be limited to a goal of creating biological synthesis. Using these methods, microbial systems could be engineered to enhance the degradation of both toxic and non-toxic wastes (as in the Japan example above). Likewise, the approach for sensor development could be used for detecting small molecules in the environment or to be incorporated into microbial diagnostics. Sensors can further be utilized in the development of complex microbial systems that respond to varying environmental conditions by activating different cellular responses.


Pivotal pivoting

While Prather initially focused on engineering specialized proteins resembling natural sensors to broaden biosensor capabilities, the pandemic prompted a shift towards repurposing these sensors to address food waste challenges. This transition came from a Department of Defense directive concerning food waste management. “There are ways to generate biogas doing something basically like composting,” she says. Yet she envisioned a more sophisticated approach: harnessing these sensors to precisely target specific chemical compounds within food waste to produce more valuable molecules, thereby ensuring a consistent output regardless of the variability in input materials.

Using sensors inspired by nature to detect specific components in the waste, her team found that the presence of certain substances activates pathways that guide them into a desired outcome. The challenge is to have that outcome be steady even as the volume of those substances changes. Over the course of her research, her team observed a surprising phenomenon when separate pathways were combined into a single cell: one pathway started with high production levels when used alone but decreased when combined with the other, while another began with low levels alone and increased when in combination. Each pathway responded to its own sensor, making sure the conversion of two substances to one chemical happened the same way every time.

This success has led to further exploration of the sensors’ adaptability, with Prather envisioning their potential to detect multiple compounds within food waste. “It’s gotten us to think about new kinds of molecules and how to pull in all these different threads we’ve been working towards into one package—or one system—to increase the efficiency, productivity, and range of the kinds of products we’ll be able to make.” The scalability of this technology remains uncertain, but she is eager to explore its capacity to guide through diverse pathways and achieve consistent outcomes.