U of T researchers discover 9 genes used by bacteria to defend against viruses

University of Toronto researchers have discovered nine new genes used by bacteria to protect themselves against phages – viruses that infect them.

In a study published in Nature Microbiology, the researchers describe how they used a combination of bioinformatics and laboratory testing – on sediment samples obtained from tanks at Ripley’s Aquarium of Canada – to identify the previously unknown defence genes.

The findings could have profound implications for the development of strategies to treat bacterial infections, particularly those that are drug resistant.

“Phages are viruses that naturally predate bacteria,” explains the study’s first author Landon Getz, a post-doctoral researcher in the lab of Professor Karen Maxwell in the Temerty Faculty of Medicine’s department of biochemistry. “If we understand the defence mechanisms activated by the bacteria in response to phage infections, we can develop methods to bypass them.”

For the study, the researchers selected the bacterium Vibrio parahaemolyticus, which infects seafood and causes gastroenteritis in people when they consume raw or under-cooked seafood. Their experiments focused on a region of the bacterial genome, known as the integron, that stores foreign genes that bacteria pick up from other bacteria in the environment.

These genes are known to confer a survival advantage to bacteria – for example, making them immune to certain antibiotics – but their role in anti-phage defences is not well understood.

“We knew that genes associated with anti-phage defences cluster together in bacterial genomes,” says Getz, who holds a GSK EPIC Convergence Postdoctoral Fellowship in Antimicrobial Resistance. “When we identified a few known defence genes in the integron, we could hypothesize that we might find new anti-phage defence genes in that region.”

To test their hypothesis, Getz and co-authors first used bioinformatics to select 57 genes from the “Vibrio” integron. They also identified more than 70 phages to test whether the newly identified defence systems could protect the bacteria from phage infections.

The number of known phages that infect V. parahaemolyticus is small, so the researchers had to get creative and turn to an unusual place – sediments from tanks housing jellyfish and sea dragons in Toronto’s Ripley Aquarium.

Next, they used a technique called phage spotting to determine if the genes provided defence against viral infections.

“We cloned the 57 genes into different bacterial strains and grew them on agar plates,” says Sam Fairburn, co-author on the study and an undergraduate student at the University of Waterloo who worked as a co-op student in the Maxwell lab. “We then added a drop each of the different phage samples to the plates.”

Fairburn explains that in the absence of an active anti-phage defence, viral infections inhibit bacterial growth and cause a clear zone on the bacterial plate. Through these experiments, researchers identified the nine unique and previously unknown defence genes in the Vibrio integron.

While the genes help bacteria survive, turning them on consumes extra energy – so the bacteria activate the defences only in response to specific environmental cues.

The researchers discovered that in V. parahaemolyticus, four of the nine new defence systems were turned on in response to quorum sensing – which Getz explains is the ability of bacteria to listen to each other in crowded bacterial environments.

“Viral infections are a bigger problem for bacteria when they are present in large numbers, so it makes sense that these anti-phage defences are upregulated in response to quorum sensing,” says Getz, who is co-supervised by Mikko Taipale, an associate professor of molecular genetics at Temerty Medicine.

Moreover, Getz notes that integrons are found in virtually all Vibrio species and roughly 10 per cent of all bacterial genomes – so their widespread prevalence makes them a promising target for developing strategies to bolster the effectiveness of phage therapy.

“If we target phage defence systems present in bacteria to treat the infection, then we can get around some of the issues with antibiotic resistance and develop novel phage-based therapeutics with applications in shellfish fisheries, and potentially in humans.”