A new study published in the Proceedings of the National Academy of Sciences has offered insight into how Staphylococcus aureus, a major human pathogen, fine-tunes its internal machinery to survive stress and potentially cause infection.
The research uncovers new details about the structure and function of a previously understudied nuclease, YhaM, revealing how it regulates cellular machinery and contributes to bacterial virulence, or severity.
“Our lab is interested in understanding how the ribosome — the machinery that makes all proteins — is regulated in Staph aureus,” said the study’s co-senior author M.-N. Frances Yap, PhD, associate professor of Microbiology-Immunology. “We were particularly interested in why the bacterium sometimes makes ribosomes that are not active in making protein, which we call hibernating ribosomes.”
Ribosomes are essential for producing proteins in all living cells, but bacteria can temporarily shut them down when under stress by forming so-called “hibernating” ribosomes. In S. aureus, this process is driven by the hibernation-promoting factor (Hpf), which stabilizes ribosomes and protects them from degradation.
“When ribosomes hibernate, they are more resistant to ribonuclease digestion,” Yap said. “The hibernation factor occupies the same binding site as RNase R, so the enzyme can no longer cleave the ribosome. It’s a protective mechanism that helps S. aureus preserve ribosome integrity under stress.”
In the current study, investigators combined a structural biology approach with functional experiments to better understand YhaM’s role. Using a wax moth larvae infection model, they found that bacteria lacking YhaM were less successful, suggesting the enzyme contributes to the pathogen’s ability to infect a host.
Next, scientists in the laboratory of the study’s co-senior author, Christine Dunham, PhD, a professor at Emory University, observed how YhaM interacts with RNA using high-resolution cryo-electron microscopy.
The team discovered that YhaM hexamer exists in two forms — a short and a long isoform — and that these are combined in different ways depending on the RNA it binds. This flexible assembly suggests that the enzyme can adapt its structure to its target, Yap said, a feature not previously described for similar enzymes.
“The arrangement of this hexameric ring and the combination of short and long isoforms are completely novel,” Yap said. “No bacterial ribonuclease is known to be composed this way. Until now, there have been very few biochemical or structural studies of this enzyme, even though it is broadly conserved in many bacteria.”
Together, the findings paint a clearer picture of how YhaM contributes to bacterial virulence.
“We wanted to understand the structure,” said Anna Liponska, PhD, a research associate in the Yap laboratory, who was co-first author of the study. “But in doing so, we uncovered something that connects to how the bacterium survives and causes disease.”
The findings also raise new questions about the enzyme’s broader role. Yap, Liponska and their collaborators are now exploring whether YhaM targets additional RNA molecules or even DNA.
“We are very interested in what other substrates YhaM cleaves in Staph aureus,” Yap said. “There is some evidence that, under laboratory conditions, it can degrade both RNA and DNA, which suggests additional biological functions we haven’t yet characterized.”
Future work will also examine how the bacteria regulate the production of YhaM’s short and long isoforms, and how this affects its catalytic activity.
“We plan to use genome-wide sequencing approaches to identify exactly what YhaM targets and under what conditions,” Yap said.
The study was supported by National Institutes of Health grants R01 GM121359, R01 AI150986, R01 GM093278, R35 GM156629, T32 GM008367 and an NSF GRFP fellowship (2021310209).
