ATE1 enzyme plays role in cellular stress response, opening door to new therapeutic targets

A new paper in Nature communications illuminates how a previously poorly understood enzyme works in the cell. Many diseases are linked to chronic cellular stress, and Aaron T. Smith and colleagues at UMBC discovered that this enzyme plays an important role in the cellular stress response. A better understanding of how this enzyme functions and is controlled could lead to the discovery of new therapeutic targets for these diseases.

The enzyme is called ATE1 and it belongs to a family of enzymes called arginyl-tRNA transferases. These enzymes add arginine (an amino acid) to proteins, which often marks the proteins for destruction in the cell. Destruction of misfolded proteins, often as a result of cellular stress, is important to prevent these proteins from damaging cellular function. The accumulation of dysfunctional proteins can cause serious problems in the body, leading to diseases such as Alzheimer’s or cancer, so being able to effectively get rid of these proteins is key to long-term health.

Enticing effects

The new paper demonstrates that ATE1 binds to clusters of iron and sulfur ions, and that the enzyme’s activity increases two- to threefold when it binds to one of these iron-sulfur complexes. Furthermore, when the researchers blocked the cells’ ability to produce the complexes, ATE1 activity was dramatically reduced. They also found that ATE1 is highly sensitive to oxygen, which they believe is related to its role in moderating the cell’s stress response through a process known as oxidative stress.

“We were very excited about it, because it has a lot of very tantalizing implications,” especially related to the enzyme’s role in disease, says Smith, an associate professor of chemistry and biochemistry.

Smith’s lab initially works with the yeast protein, but has also shown that the mouse version of ATE1 behaves similarly. This is important, explains Smith. “Since the yeast protein and the mouse protein behave the same way,” he says, “there is reason to believe that because the human protein is quite similar to the mouse protein, it probably also behaves the same way.”

A new approach

Before making their discovery, Smith and then-grad student Verna Van, Ph.D. ’22, biochemistry and molecular biology, had been trying for some time to induce ATE1 to bind to heme, an iron-containing compound essential for binding oxygen in the blood, to confirm another group’s results. It wasn’t working and they were getting frustrated, Smith admits. But one day, as Smith was preparing a lecture on proteins that bind to clusters of metal and sulfur atoms, he realized that the proteins he was about to cover with his students resembled ATE1.

After this realization, Smith and Van took a new approach. In the lab, they added the raw materials for making iron-sulfur clusters to a solution with ATE1, and the results showed that ATE1 did bind the clusters. “That looks promising,” Smith remembers thinking. “We were very excited about it.”

The fact that the enzyme binds the clusters at all was interesting and novel, “but then we also asked if that affects the ability of the enzyme to do what it does,” says Smith. The answer, after more than a year of additional experimentation, was a resounding yes. In the process, Smith’s team also determined the structure of ATE1 in yeast (without the complex bound to it), which they published in Journal of Molecular Biology in November 2022.

Subtle but important

Around the same time, another group also published a slightly different ATE1 structure. The structure of the other group had a zinc ion (another metal) attached in place of the iron-sulfur complex. With zinc in place, a basic amino acid is rotated about 60 degrees. It may seem trivial, but Smith believes that rotation, which he hypothesizes is cluster-like, is key to the cluster’s role in ATE1 function.

The rotating amino acid is right next to where a protein would interact with ATE1 to modify it, ultimately marking it for degradation. Changing the angle of this amino acid changes the shape of the site where the protein would bind “very subtly,” but changes its activity “more than subtly,” Smith says.

Looking forward and looking back

Smith would also like to investigate how other metals, beyond zinc and the iron-sulfur complex, might affect the enzyme’s activity. Additionally, his lab is working to determine the structure of ATE1 in an organism other than yeast and to confirm the ATE1 structure with a bound iron-sulfur complex.

All these steps will create a clearer picture of how ATE1 functions and is regulated in the cell. Smith also says he thinks proteins that so far haven’t been shown to bind iron-sulfur clusters might actually rely on them.

This new document actually harkens back to Smith’s early days at UMBC. He has always been interested in protein modifications and the addition of arginine is more unusual. “It’s always something that I’ve put back in my head and thought, ‘Oh, it would be really interesting to get a better understanding of how this works,'” he says.

Several years later, his team is now on the cutting edge of discovering how arginine modifications affect cell function and disease.