Earlham Biochemistry Faculty Member Earns $461,575 NSF Grant

Acknowledgment: Lexie Kuzmishin Nagy’s research is supported by the U.S. National Science Foundation through a Building Research Capacity in New Faculty in Biology (BRC-BIO) award, No. 2437568.

Disclaimer: Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Lexie Kuzmishin Nagy, assistant professor of biochemistry at Earlham, is a recent grantee of a $461,575 National Science Foundation grant in support of research that will deepen the world’s understanding of how bacteria sense and respond to their environment. The grant was funded by NSF’s BRC-BIO, or Building Research Capacity within the Biological Sciences Program. The funding mechanism was primarily to support the research of early-career tenure-track faculty at minority-serving institutions or smaller colleges like Earlham.

“The goal for this grant is to provide equipment, space and time for research,” Kuzmishin Nagy summarized. “We want to train students but also build research infrastructure. This is important for junior faculty, or those without tenure, because it gives us a firm stepping stone for future work and grants and gives us the ability to apply for those later on.”

More specifically, this grant has to do with L- and D-amino acids and tRNA-binding enzymes. Kuzmishin Nagy and her team study enzymes and amino acids, the building blocks of proteins in human cells, and this grant will enable them to deepen their research.

“At the lab we study how bacteria sense and respond to environment,” says Kuzmishin Nagy. “We’re working with amino acids, studying them to make sure the right protein gets to the right place at the right time.”

What the grant is about

The grant specifically studies the role ProXp-x plays in regulating aminoacyl-tRNAs, or tRNA molecules carrying an amino acid, in cells. When a protein is made in a cell, ribosomes stitch amino acids together to make the protein. aminoacyl-tRNAs come in and drop off their amino acids to make the protein. Ribosomes stich them together, and violá, new protein.

However, sometimes these functions go awry. There are twenty different amino acids in a cell, and each one needs to be loaded onto its “cognate” or particular tRNA. tRNAs act as barcodes for the ribosome; the ribosome interacts with the tRNA to learn which amino acid it carries rather than interacting with the amino acid directly. Therefore, it’s important that each tRNA molecule (of which there are over hundreds in a single cell!) is paired with its correct, single amino acid.

But, amino acids, despite being made of the same atoms, can be found in two different geometries, or atomical arrangements, called “L-” and “D-” amino acids. L-amino acids are the ones used to make proteins and D-amino acids for cell signaling. If D-amino acids are mistakenly dropped off to the ribosome, the ribosome will “jam” and stop making proteins or stitch this incorrect geometry into the protein it is building, which could prevent the protein from functioning correctly. That’s bad for a cell.

This is where ProXp-x comes in. ProXp-x acts as a double checker that makes sure that certain tRNA molecules are paired with the correct L-amino acid. When tRNAs deliver the wrong amino acid to the ribosome, the ribosome doesn’t know any better – it’ll use the incorrect amino acid when building a protein, which can change the structure and function of the protein it’s building. This can be stressful for cells if incorrectly built proteins accumulate; these incorrectly built proteins are generally nonfunctional or, worse, have negative effects on the cell.

Early evidence suggests ProXp-x swoops in and can remove some incorrect amino acids from tRNAs, which not only helps to correctly build the protein but also recycles amino acids as needed to help avoid mistakes within protein production in the cell. ProXp-x is one of many proteins that can do this job, but it’s one of the first that can recognize when D-amino acids have been loaded onto the tRNA.

That’s news to scientists like Kuzmishin Nagy.

“Evolutionarily speaking, this challenges a lot of pre-conceived notions we in the field had about how protein production works,” says Kuzmishin Nagy.

Up until now, scientists believed that enzymes have only one job, one function, on one cellular target, called a substrate. ProXp-x seems to recognize multiple different combinations of L- and D-amino acids on tRNA, meaning it has multiple, different substrates. ProXp-x’s job may also be more important to the cell at different points in its life. ProXp-x helps build correct proteins, but also has this additional response to cell stress, which fascinates Kuzmishin Nagy. She wants to understand why and how ProXp-x knows to come in and fix those possible mistakes in the cell. How does it know to respond to those potential stress responses? Additionally, from an evolution perspective, scientists are still trying to fully understand the chemistry of amino acids, so Kuzmishin Nagy also wants to have a better understanding of those L- and D-amino acids in general. What are the mechanisms that fuel protein production, and how does the cell know to choose L-amino acids over D-acids?

“We don’t really know what, evolutionarily, directed this, so this project addresses some of that and the mechanisms cells use to maintain that selection of L over D,” says Kuzmishin Nagy.

Research possibilities and applications

Overall, the applications of research on amino acids are far reaching.

“This grant has several extrapolations including antibiotics, bioterrorism and agriculture,” said Kuzmishin Nagy. “If someone is building a compound to breakdown bacteria, particularly infectious bacteria, this could have applications for antibiotics. Additionally, there are several pathogenic bacteria, so infectious bacteria, that have been classified as potential bioterror agents that do these same activities as these enzymes and amino acids. Now, they don’t all have ProXp-x, but they have to contend with this same issue. So what are defenses against those organisms to prevent them from being weaponized? Finally, the soil bacterium we study have implications for agriculture. Rhodopseudomonas palustris, for instance, helps farmers. They spread it on their crops and it helps to enrich the soil for better crop growth. Some cattle farmers also sprinkle it into their cattle feed, as the bacteria is beneficial for their livestock.”

Kuzmishin Nagy is using the medium of soil bacteria for her research. Earlham already has the ability to grow common lab strains, but a shaking incubator, part of the new equipment from the grant, will expand Earlham’s research capabilities and allow Kuzmishin Nagy to actually grow bacteria in the lab.

“This incubator will give us the ability to study bacteria under different light sources, different temperatures,” says Kuzmishin Nagy, “and different conditions. We’ll also be able to study the bacteria cells in their natural environment. My bacterium can be photosynthetic under the right conditions, so we can test some of those growth modes in our questions, and we can flood the instrument with different gaseous atmospheres, so we could simulate a micro-oxygen environment that a soil bacteria would inhabit. Organisms that photosynthesize also work with carbon dioxide, so we could also flood the instrument with carbon dioxide and really replicate that photosynthetic environment.”

Additionally, the grant allows four undergraduate students to conduct research over the course of three summers. These students will then be allowed to present their research at the annual Rustbelt RNA Meeting (RRM), a regional scientific conference. Being able to present scientific research is crucial for college students in their first few years in a STEM discipline. It allows them to gain the full experience of being a scientist and presenting research, and gives them a career discerning experience that they can use to hone in on their passion, whether that’s writing up scientific papers for conferences or studying cells in a lab.

But the benefits of this grant don’t stop there. “We are also planning for community outcomes with this grant with the Joseph Moore Museum,” explains Kuzmishin Nagy.

Visitors to the Joseph Moore Museum can look forward to escape rooms and refreshed exhibits that are in the works and based off of Kuzmishin Nagy’s research.

Written by Jay Kibble, writer/editor for Earlham College Office of Marketing and Communications

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