Identification of the anti-permeable protection system of V. parahaemolyticus. A, V. Schematic diagram of a bioinformatic workflow for identification of anti-permeasure protection systems and determination of genomic contexts in parahaemolicatus. B, Histogram of the number of systems found in strains of V. parahaemolyticus by defensive finder. C, the number of systems identified by the defense finder according to each defense finder category. Only counts above 10 are displayed here. The complete graphs for all systems are shown in the extended data. Figure 1a. D, Quantification of five most common protein functions colocalized with anti-permeasure protection systems. E, Colocalization networks of various defense systems using DUF3265. The DUF3265 nodes are displayed in light blue and the defense system is displayed in dark blue. Credit: Natural Microbiology (2025). doi:10.1038/s41564-025-01927-7
Researchers at the University of Toronto have discovered nine new genes that bacteria are used to protect themselves from phages.
In a study published in Nature Microbiology, researchers explain how they used a combination of bioinformatics and clinical testing in sediment samples obtained from tanks at Ripley Aquarium, Canada, and identify previously unknown protective genes.
The findings could have a significant impact on the development of strategies to treat bacterial infections, particularly those that are drug resistant.
“Phages are naturally pre-bacterial viruses,” explains Landon Goetz, the first author of the study, as a postdoctoral researcher in the lab of Professor Karen Maxwell, of the Department of Biochemistry at Temarty School of Medicine. “If we understand the protective mechanisms activated by bacteria in response to phage infections, we can develop ways to bypass them.”
For this study, researchers selected the Vibrio bacteria, a bacteria that infects seafood and causes gastroenteritis when consumed raw or immature seafood. Their experiments focused on a region of the bacterial genome known as integrons, which store foreign genes that bacteria pick up from other bacteria in their environment.
These genes are known to confer survival benefits, for example, on bacteria that make immunity to certain antibiotics, but their role in anti-permeability protection is poorly understood.
“We knew that genes associated with anti-permeasure protection cluster together in the bacterial genome,” says Getz, who holds the GSK Epic Convergence Postdoctoral Fellowship in Antibiotic Resistance. “When we identified some known defense genes in Integron, we were able to assume that new anti-PHAGE defense genes could be found in that region.”
To test their hypothesis, Getz and co-authors first selected 57 genes from the “Vibrio” integron using bioinformatics. They also identified more than 70 phages to test whether newly identified defense systems could protect bacteria from phage infections.
The small number of known phages infecting V. parahaemolyticus meant that researchers had to become creative and head to an unusual location from the tanks housed jellyfish and sea dragons at the Ripley Aquarium in Toronto.
They then used a technique called phage spotting to determine whether the gene provided protection against viral infections.
“We cloned 57 genes into different bacterial strains and grew them on agar plates,” says study co-author Sam Fairburn, and Sam Fairburn, an undergraduate at the University of Waterloo who worked as a student at Maxwell Lab. “We then dropped various phage samples onto the plate.”
Fairburn explains that in the absence of active anti-permeability protection, viral infections inhibit bacteria growth and cause clear zones in the bacterial plate. Through these experiments, researchers identified nine unique and unknown defense genes for the Vibriointegron.
Genes help bacteria survive, but turning them on will consume extra energy. Therefore, bacteria activate defenses according to specific environmental cues.
The researcher is V. In parahaemolyticus, we discovered that four of the nine new defense systems are turned on in response to quorum sensing. This explains Getz has the ability to listen to each other in a crowded bacterial environment.
“Virus infections are a major problem for bacteria when there are many bacteria, so it makes sense that these anti-permeable protections are upregulated in response to quorum sensing,” says Getz, co-supervised by Miccotaipare, an associate professor of molecular genetics at Temathymedicine.
Furthermore, Getz points out that integrons are found in virtually all Vibrio species and around 10% of all bacterial genomes, and their widespread prevalence makes them a promising target for developing strategies to enhance the efficacy of phage therapy.
“Targeting the phage defense system present in bacteria to treat infections can avoid some of the problems with antibiotic resistance and develop novel phage-based therapeutics that are applied to shellfish fisheries and potentially humans.”
Details: Landon J. Getz et al, Integrons is the anti-permeable protection library of Vibrio Parahaemolyticus from Nature Microbiology (2025). doi:10.1038/s41564-025-01927-7
Provided by the University of Toronto
Citation: Announce Viral Defense of Bacteria: Nine Genes that Can Support Phage Therapy (March 19, 2025) was obtained on March 20, 2025 from https://phys.org/news/2025-03-unveiling-bacteria-viral-defense-genes.html
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