Walter lab: RNA molecule senses a small metal ion to ramp up bacterium’s detox machine

Bacterial cells use riboswitches--intricate RNA structures that sense the environment of a bacterial cell--for survival by keeping needed trace metals below toxic levels.  Certain riboswitches can selectively sense trace metals, such as manganese. Up until this point, researchers had only a vague understanding of how manganese triggers the riboswitch to ramp up the cell’s detox machinery to keep manganese at a safe level.

Now, researchers an international collaboration of researchers have published a thorough visualization of the manganese riboswitch mechanism of action in a study in Nature Communications. They showed that the RNA structure changed when it was bound to manganese, compared to a magnesium atom of similar size and charge. This shift in binding results in a change in the number of proteins that are synthesized in the cell.

This work has important implications due to the prevalence of bacteria in everyday life, explained Chemistry professor Nils Walter, a corresponding author on the publication.  One way that bacteria survive is by using riboswitches, which require trace metals. “Like any living organism, bacteria need trace metal elements, which are like the ones we take in vitamin tablets. Bacteria often regulate their metal uptake using riboswitches,” Walter said.

Examples of commonly studied biological metals are iron and zinc, but RNA researchers have been especially interested in manganese (Mn). Another element, magnesium (Mg), is a similarly sized metal, and both Mn and Mg in the cell typically have a doubly positive charge (2+). The chemical similarity of these two elements and their effects on RNA structure is central to the recent Nature Communications study. Mg²⁺ is required for a range of cellular functions, but is less toxic than Mn²⁺ and accumulates to higher levels in the cell, so how the RNA senses Mn²⁺ in this excess of Mg²⁺ is something that researchers have not understood thus far. “How can an RNA find the Mn²⁺ in a sea of Mg²⁺? There were hints in a previous crystal structure that there were tiny chemical differences between Mn²⁺ and Mg²⁺ that could be exploited,” Dr. Walter explained.

However, visualizing these chemical differences has been a challenge due to the size difference between the small Mn²⁺ or Mg²⁺ ions and the large, complex RNA structure. “Mn²⁺ is extremely small—it’s just one atom,” Walter said. “An RNA, by comparison, has thousands of atoms. So how does this little tiny metal ion connect to the machinery that reads out this RNA and ultimately produces a protein? It is a David versus Goliath story.”This work has important implications due to the prevalence of bacteria in everyday life, explained Chemistry professor Nils Walter, a corresponding author on the publication.  One way that bacteria survive is by using riboswitches, which require trace metals. “Like any living organism, bacteria need trace metal elements, which are like the ones we take in vitamin tablets; bacteria often regulate their metal uptake using riboswitches,” Walter said.

Their work required catching RNA riboswitches in different binding states and identifying their structures. “We were able to show that the RNA can sense whether the site is occupied by Mn²⁺ or the competing Mg²⁺ ion because the RNA gets ‘locked down’, and the Mn²⁺ holds the folded RNA together like a linchpin,” Walter explained.Essentially, RNA can fold and unfold to allow ions to try out that specific site. Mg²⁺ ions will occupy the site at times due to their sheer number in the cell, but RNA will not be in a stable “locked position” until a Mn²⁺ occupies the site. Further downstream in the protein-making process, the RNA cannot express the protein unless it is in the “locked position”, meaning the RNA must have a Mn²⁺ ion bound for protein production.

“What our story is about is learning that the tiny Mn²⁺ is being caught by the large RNA structure in hair-trigger fashion… Which induces the downstream expression of proteins that appear in the cell,” Walter said. “Such an increase in concentration of a key export protein has serious consequences on the survival of the bacterium by detoxifying excess Mn²⁺.”

“This work could have applications in the medical field,” Dr. Walter explained. “Bacteria live in our soil, in our bodies, and they are a single cell, which means they alone have to gate or guard what’s coming in and what’s going out.” One way to disrupt certain bacteria that cause diseases in humans or animals is changing their manganese levels. “Could we trick them into thinking they don’t have enough Mn²⁺, so they import more and die? This idea is a potential path to a new antibiotic.”

This research study was a collaboration across universities and nations, born of a collegial relationship between professors over several years and projects. “Science, nowadays, is a very collaborative effort,” Walter pointed out. “On some level, it’s because we are becoming more specialized, which allows us to dig much deeper into the science, which then is countered by joining forces as we were able to achieve here,” he said.