Old dog, new tricks: Prehistoric viruses can be used to defend bacterial cells

UNIVERSITY PARK, Pa. — For billions of years, bacteria have waged an ongoing arms race against viruses, evolving many defense mechanisms against the infectious invaders. Now, these evolutions may offer innovative ways for humans to fight viruses, according to Thomas Wood, professor of chemical engineering at Penn State. 

Wood and his team recently observed a previously overlooked defense mechanism in bacteria containing extremely old, dormant viruses. They investigated this mechanism in the cells containing these sleeping defenders, finding it could successfully help bacteria defend against viruses. The researchers published their work, which the team said could potentially be employed to create stronger antivirus systems for the medical and food industries, in Nucleic Acids Research. 

“There’s been a flurry of discoveries in the past few years related to antivirus systems in bacteria,” said Wood, who led the project. “Antibiotics are failing, and the most likely substitute is viruses themselves. Before using viruses as antibiotic replacements to treat human infections, however, we must understand how the bacterium defends itself from viral attack.” 

According to Wood, researchers have long known that ancient dormant viruses, known as cryptic prophages, infuse their genetic information into the bacterial cell’s DNA, which can then use specific enzymes and proteins to stop new viruses — or phages — from infecting the host cell. In this study, the team investigated this process and identified that recombinase — a type of protein called an enzyme that cuts and joins strands of DNA — can reactively adjust cell DNA to defend against viruses if a prophage is integrated into the bacteria’s DNA.  

The specific recombinase behind this defense is known as PinQ. Upon identifying the presence of a virus on the cell, the enzyme facilitates a genetic mutation known as inversion, which flips the genetic information found in the bacteria. This inversion creates two new “chimeric proteins,” or proteins consisting of the inverted DNA from the prophage found within, in a specific location of the cell’s chromosome. Adjusting these proteins — known collectively as Stf — counteracts the virus's ability to land on and inject the bacteria, protecting it from viral infection. 

“It’s remarkable that this process actually produces new chimeric proteins, specifically from the inverted DNA — most of the time when you change DNA, you just get genetic mutations leading to inactive proteins,” Wood said. “These inversions and adaptations are clear evidence that this is a fine-tuned antivirus system that has evolved over millions of years.” 

One of several factors behind the increasing prevalence of antibiotic-resistant diseases is the overprescription of antibiotics, Wood explained. Viruses offer hope as a possible replacement for antibiotics due to their ability to specifically target and neutralize the antibiotic-resistant bacterial strains that make humans sick, all while multiplying and evolving alongside their host. By understanding and adapting this defense mechanism facilitated by the recombinase, doctors will have more options to fight infections, while prescribing fewer antibiotics. 

Although recombinase had been previously identified near the areas of bacteria responsible for defense, Wood said, this is the first time researchers have realized that recombinase is involved in virus defense. 

“It’s not that researchers missed these enzymes, it’s that they saw them and overlooked them as mere markers of virus genes,” Wood explained. “To defend against viruses, bacteria must have many different defense systems, and this is just yet another example of one of those systems.” 

The team tested the system by overproducing Stf proteins in a sample of E. coli bacteria, to which they then added viruses. They let the mixture sit overnight and then measured its turbidity, or cloudiness, to determine if the viruses had infected the bacteria — the cloudier the mixture, the less phages are present. The team also used computer modeling to simulate viruses latching onto the surface of bacterial cells, a process known as adsorption, verifying the accuracy of the simulations and their measurements by observing the experiments. 

“When we overproduce the protein, we initially stop the virus from landing on the cell surface,” Wood said. “After eight experimental iterations, however, the virus changes its landing proteins — how it identifies and attaches to the bacteria — and can get by this defense.” 

This research has improved the team’s understanding of how antivirus systems operate, Wood said, which can help them more effectively cultivate the bacteria used to ferment foods like cheese and yogurt, as well as improve how bacterial infections are managed in health care settings. Looking forward, Wood said the team plans to continue researching the antivirus applications of eight additional prophages currently in their lab. 

“This is a story about how a fossil protects its host from the outsider, and we have 10 other fossil-related stories that could offer their own defenses waiting to be tested,” Wood said. “Having a greater understanding of how these viruses interact with bacteria will give us incredible insight on how to effectively and safely harness bacteria in bioengineering.” 

Other co-authors include Joy Kirigo, who recently received her doctorate in chemical engineering from Penn State; Daniel Huelgas-Méndez, a chemical engineering doctoral candidate from the National Autonomous University of Mexico (UNAM) who conducted a research stay at Penn State; Rodolfo García‐Contreras, a professor of microbiology at UNAM and adviser to Huelgas-Méndez; María Tomás, coordinator of the Genomic Diagnosis Unit at the  University Hospital of A Coruña; and Michael J Benedik, Regents Professor of Biology at Texas A&M University. 

This research was supported by the Biotechnology Endowment, the National Autonomous University of Mexico and the Secretariat of Science, Humanities, Technology and Innovation.