Unveiling Bacterial Immune Mechanisms Against Temperate Phages

Like humans, bacteria can be attacked by viruses. In the case of bacteria, these viral attackers are referred to as bacteriophages, a term derived from the Greek word for bacteria-eaters, or simply “phages.”

Researchers have been investigating how these single-celled organisms withstand phage infections to gain insights into human immunity and to develop strategies for disease treatment.

Scientists from Johns Hopkins Medicine have provided new insights into how bacteria defend themselves against specific phage invaders by acquiring genetic material from weakened, dormant phages and utilizing it to “vaccinate” themselves, thereby triggering an immune response.

In their studies, the researchers found that Streptococcus pyogenes bacteria (the causative agent of strep throat) exploit a category of phages known as temperate phages, which can either kill host cells or enter a dormant state.

During this dormant phase, the bacteria capture genetic material from the temperate phages, creating a biological “memory” of the invader that is passed on to their progeny as the bacteria reproduce. Armed with these memories, the new bacterial generation can recognize and combat these viruses.

A report detailing the experiments, partially funded by the National Institutes of Health, was published in the journal Cell Host & Microbe.

The findings enhance the understanding of how bacterial cells responsible for severe diseases, such as Staph and E. coli infections and cholera, become harmful to humans, a process that involves the expression of toxic genes from otherwise dormant phages residing within the bacterial cell, according to Corresponding Author Joshua Modell, Ph.D., an 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 do not 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?”

Joshua Modell, Corresponding Author and Associate Professor, Molecular Biology and Genetics, Johns Hopkins University

The Johns Hopkins researchers note that bacteria have long been recognized for utilizing CRISPR-Cas systems to cleave phage DNA, degrade it, and eliminate it. Importantly, CRISPR systems can only target and destroy DNA that corresponds to a “memory” acquired from a previous infection and stored within the bacteria’s genome, the researchers state.

Thus, the CRISPR system functions as a recording mechanism that logs the extensive list of foreign invaders encountered by a specific bacterial strain.

To carry out their research, the scientists infected bacterial populations with naturally occurring phages that enter dormancy or genetically modified non-dormant phages in separate flasks containing 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. When we tested phages that could not go dormant, the CRISPR system did not work nearly as well.”

Joshua Modell, Corresponding Author and Associate Professor, Molecular Biology and Genetics, Johns Hopkins University

After isolating the surviving bacteria and allowing them to repopulate the flask, the scientists employed genome sequencing to catalog hundreds of thousands of new DNA memories generated by the CRISPR Cas9 system from the test phages, focusing on those that enhance cellular immunity.

They also found that the bacteria formed these memories during the temperate phage’s dormancy period when it posed no threat to the population.

This is conceptually similar to a vaccine with an attenuated virus. 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.”

Nicholas Keith, Graduate Student and Study First Author, Johns Hopkins University

In future studies, the scientists plan to investigate how CRISPR systems protect bacterial cells from viruses that do not enter dormancy, according to Modell.

Modell stated, “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. 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.”