New study sheds light on how bacteria ‘vaccinate’ themselves with genetic material from dormant viruses

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Key Takeaways:

Bacteria get invaded by viruses called phages. Scientists are studying how bacteria use CRISPR to defend themselves from phages, which will inform new phage-based treatments for bacterial infections that are resistant to antibiotics. Bacteria seize genetic material from weakened, dormant phages and use it to form a biological “memory” of the invader that their offspring inherit and use for anti-phage defense. Like people, bacteria get invaded by viruses. In bacteria, the viral invaders are called bacteriophages, derived from the Greek word for bacteria-eaters, or in shortened form, “phages.” Scientists have sought to learn how the single-cell organisms survive phage infection in a bid to further understand human immunity and develop ways to combat diseases.

Now, Johns Hopkins Medicine scientists say they have shed new light on how bacteria protect themselves from certain phage invaders — by seizing genetic material from weakened, dormant phages and using it to “vaccinate” themselves to elicit an immune response.

In their experiments, the scientists say Streptococcus pyogenes bacteria (which cause strep throat) take advantage of a class of phages known as temperate phages, which can either kill cells or become dormant. The bacteria steal genetic material from temperate phages during this dormant period and form a biological “memory” of the invader that their offspring inherit as the bacteria multiply. Equipped with these memories, the new population can recognize these viruses and fight them off.

A report on the experiments, supported in part by the National Institutes of Health, was published March 12 in the journal Cell Host & Microbe. The findings help scientists better understand how bacterial cells that cause serious diseases, including Staph and E. coli infections and cholera, become toxic to humans — a process that involves toxic genes expressed by otherwise dormant phages that reside within the bacterial cell, says corresponding author Joshua Modell, Ph.D., associate professor of molecular biology and genetics at the Johns Hopkins University School of Medicine.

“We essentially wanted to answer the question: If bacterial cells don’t have any memory, or survival skills, to combat a new temperate phage that shows up, how do they buy themselves enough time to establish a new memory, before they succumb to that initial infection?” says Modell.

The Johns Hopkins investigators say bacteria have long been known to use CRISPR-Cas systems to chop up phage DNA, break it down and get rid of it. Crucially, CRISPR systems can only destroy DNA that matches a “memory” captured from a prior infection and stored within the bacteria’s own genome, say the researchers. In this way, the CRISPR system acts as a recording device that documents the long list of foreign invaders encountered by a particular bacterial strain.

To conduct their research, the scientists say they infected populations of bacteria with naturally occurring phages that go dormant or genetically engineered non-dormant phages in separate flasks that contained millions of bacterial cells.

“Our results indicate that the bacteria’s CRISPR system was more effective at using the naturally dormant phage to pull parts of the viral genetic code into their genome,” says Modell. “When we tested phages that could not go dormant, the CRISPR system did not work nearly as well.”

After isolating the bacteria that survived, and letting the survivors repopulate the flask, the scientists used genome sequencing to catalog hundreds of thousands of new DNA memories that the CRISPR Cas9 system had created from the test phages, honing in on those that contribute to cell immunity. The scientists also determined that bacteria created those memories during the temperate phage’s dormancy period, when it did not pose a threat to the population.

“This is conceptually similar to a vaccine with an attenuated virus,” says Nicholas Keith, a graduate student and first author of the paper. “We believe this is the reason why the CRISPR Cas9 system has a unique relationship with this specific class of temperate phage.”

“We can use these types of experiments to find what elements of the phage, the bacterial host and its CRISPR system are important for all stages of bacterial immunity,” Keith says.

In future experiments, the scientists aim to learn more about how CRISPR systems protect bacteria cells from viruses that don’t go dormant, Modell says.

“We know CRISPR systems are one of the first lines of defense against the transfer of hazardous genes from phages that turn bacterial cells toxic,” says Modell. “Furthermore, our studies will inform the design of ‘phage therapies’ which could be used in clinical cases where a bacterial infection is resistant to all available antibiotics.”

In addition to Keith and Modell, study contributors are Rhett Snyder from Johns Hopkins and Chad Euler from Hunter College.

The research was funded by the Johns Hopkins University School of Medicine, the National Institutes of Health National Institute of General Medical Sciences (R35GM142731), the Rita Allen Foundation and the National Science Foundation.

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