SAN FRANCISCO—For billions of years, viruses and bacteria have been embroiled in an arms race. In response to constant attacks by viruses known as bacteriophages—more commonly called "phages"—bacteria evolve new ways to defend themselves. And, in turn, phages evolve new strategies to overcome those defenses.
Now, in a study published in Molecular Cell, scientists at Gladstone Institutes and UC San Francisco (UCSF) have uncovered new details about this ongoing warfare related to an unexpected response among certain bacterial cells: self-destruction. The findings could be useful for developing novel antibiotics or treatments for drug-resistant infections.
The study deals with the most widespread antiviral defense in bacteria, a mechanism known as the "restriction modification" system. This defense system detects DNA from an invading phage and cuts it into pieces before the phage can take over the cell.
But some phages have developed counter-defenses that inhibit this system, allowing them to sneak in. The scientists observed that if bacterial cells sense this counter-defense, they trigger their own death using components of the very same systems that the phages were trying to inhibit.
"We think this is essentially the first and second lines of defense merged into one," says Gladstone Investigator Sukrit Silas, PhD, lead author of the study. "You could say it's the bacterial immune system deciding the infection has gone too far and altruistically initiating its own destruction or dormancy so the phage cannot replicate. This protects neighboring bacterial cells from becoming infected."
Overlooked Genes Hold Special Powers
Silas and his colleagues made their discovery while trying to better understand underexplored parts of phage genomes known as accessory regions. The genes in these regions aren't always essential for the phage's survival, but may be necessary in certain circumstances, such as helping them escape detection by bacterial immune systems.
Because accessory genes in phages are non-essential, they are often overlooked and most have yet to be identified; a big part of Silas' research at Gladstone is focused on filling this enormous knowledge gap.
"There are probably at least tens of thousands of these genes scattered all across phage genomes," says Silas, who's also an assistant professor in the Department of Microbiology and Immunology at UCSF. "Given that the few that have been previously explored often turn out to be counter-defense genes, I became very curious in finding more and learning what they do."
Traditional methods of studying accessory genes can only manage a handful of genes at a time. So, the researchers designed a new research platform with a more efficient algorithm that can study thousands of accessory genes at once for any phage genome family.
Using the new platform, Silas and his colleagues identified more than 10,000 novel accessory genes in more than 1,000 genomes of phages that infect bacteria in the Enterobacteria family, which includes E. coli. They took a closer look at 200 of these new genes by turning them on and off in different strains of E. coli to explore their effects.
Forcing Phages into a Trap
Some accessory genes neutralized bacterial restriction-modification systems, allowing phages to infect cells. However, some of the genes instead triggered bacterial cells in some strains of E. coli to self-destruct. In fact, the researchers found that multiple different phage accessory genes can trigger the same path to initiate cell death.
When they looked to see what defenses in the bacteria were responsible for this self-killing, they were surprised to find systems derived from the bacterial restriction-modification system itself.
"The bacteria's defense system can detect if the phage is trying to block it, and in response, the bacterial cell destroys itself from within," Silas says. "It's pretty remarkable that a system we've known about for so long can have this property we weren't aware of."
"Our study expands our understanding of the evolutionary arms race between bacteria and phages," says Joe Bondy-Denomy, PhD, of UCSF, who co-led the study with Silas. "These cell-killing responses seem to be evolutionary traps for phages; having these accessory genes may run the risk of triggering the death of the cells they're trying to infect. But losing the same genes could make phages vulnerable to the destruction of their own DNA."
New Opportunities for Discovery
The research platform developed for this study could accelerate the understanding of thousands of additional accessory genes in phages that infect a wide range of microbial species.
By illuminating specific tactics, vulnerabilities, and trends in the bacteria-phage arms race, this work could inform efforts to design novel antimicrobial treatments and fight drug-resistant bacteria.
"I'm an evolutionary biologist at heart, but the time that I've spent at Gladstone has been transformative in terms of how I think about my research," Silas says. "I'm not just asking what these genes do, but using that information to home in on what matters most to certain phages and bacteria, and what we would need to understand to design a novel treatment that could make it into a clinical trial."
