Salmonella are food-borne pathogens that infect millions of people a year. To do so, these bacteria depend on a complex network of genes and gene products that allow them to sense environmental conditions. In a new paper, researchers have investigated the role of small RNAs that help Salmonella express their virulence genes.

The bacteria infect humans by first invading the cells of the intestine using a needle-like structure, called a type 3 secretion system. This structure injects proteins directly into the cells, setting off a cascade of changes that cause inflammation, and ultimately cause diarrhea. The genes that encode this system, and other genes that are needed for invasion, are found on a region of DNA known as the Salmonella pathogenicity island 1.

“SPI-1 needs to be well controlled,” said Sabrina Abdulla, a graduate student in the Vanderpool lab, and the first author of the study. “If the type 3 secretion system needle apparatus is not made, Salmonella cannot cause an infection, and if too much of the needle apparatus is made, it makes Salmonella sick.”

SPI-1 is controlled by an extensive regulatory network. First, three transcription factors: HilD, HilC, and RtsA, all control their own and each other’s DNA expression. They also activate another transcription factor, HilA, which activates the rest of the SPI-1 genes. If this isn’t complicated enough, SPI-1 also needs to sense a variety of environmental cues and tune the expression of its genes in order to infect its host.

“We have known for a long time that there are a lot of environmental factors that feed into the gene regulation in Salmonella. However, we didn’t know how. That’s when researchers started looking at small RNAs,” Abdulla said.

Small RNAs play a crucial role in determining how genes function in bacterial cells. Typically, these molecules either interact with proteins, or the mRNA, which carries the instructions for making proteins. As a result, sRNAs affect a variety of bacterial functions, including virulence and responses to the environment.

In this paper, the researchers looked at the sRNAs that regulate the hilD mRNA, specifically a sequence on the mRNA called the 3’ untranslated region, a part of the mRNA not involved in making the HilD protein. In bacteria, the 3’ UTRs are usually 50-100 nucleotides long. However, the 3’ UTR of the hilD mRNA was 300 nucleotides long.

“The starting point for my work was the observation that when we deleted the 3’ UTR, the expression of the hilD gene went up 60-fold,” Abdulla said. “We then decided to look for sRNAs that might be interacting with this region.”

The researchers determined that although the sRNAs Spot 42 and SdsR can both target the 3’ UTR, they do so in different regions. “This result suggests that the entire 3’ UTR is important for regulation,” Abdulla said. “We showed that the sRNAs stabilize the hilD mRNA and protect it from being degraded.”

“Such long 3’ UTRs have not been well studied. With more genomic research, people are realizing more and more that these longer regions exist and that they are important for regulation,” Abdulla said.

Using mice, the researchers also looked at whether Spot 42 and SdsR can affect how Salmonella causes infections. They performed mouse competition assays, where they introduced mutant bacteria that lacked the sRNAs and bacteria that contained the sRNAs, to see which strains survive and cause infection. “We found that when the sRNAs are deleted, the bacteria cannot survive in the host. We also showed that the sRNAs play a role in helping SPI-1 invade the host cells,” Abdulla said.

“Now that we know that sRNAs play an important role in controlling SPI-1 through their regulatory effects on the hilD 3’ UTR, we want to extend our studies in two directions. We’d like to understand more about how, at a molecular level, the sRNAs influence hilD mRNA levels. We’d also like to better understand how sRNAs participate in regulating expression of other important SPI-1 genes,” said Cari Vanderpool (MME/IGOH), a professor of microbiology.

The study “Small RNAs activate Salmonella pathogenicity island 1 by modulating mRNA stability through the hilD mRNA 3′ UTR” was published in the Journal of Bacteriology and can be found at https://doi.org/10.1128/jb.00333-22.
 
The work was supported by the National Institutes of Health, the University of Illinois Department of Microbiology Marie Chow Teaching Scholarship, and the Francis M. and Harlie M. Clark Microbiology Fellowship.