Skoltech researchers and their colleagues from the Pasteur Institute and the University of Lorraine, France, have uncovered some of the inner workings of a recently discovered bacterial immune system called PARIS, which can potentially make human pathogens resistant to phage therapy. A promising alternative to antibiotics, it refers to the use of viruses called phages to infect and destroy bacteria that cause disease in humans. Already used to some extent, the approach is expected to make advances when scientists have a better understanding of the interaction between bacteria and phages. That interaction is at the heart of the recent study published in the Philosophical Transactions of the Royal Society B and supported by the Russian Science Foundation.

The overuse and misuse of antimicrobial drugs in humans and farm animals leads to bacteria acquiring resistance to antibiotics. When common pathogens become resistant to previously effective drugs, relatively harmless infections can prove dangerous, particularly for elderly people and other risk groups. And new classes of antibiotics are notoriously difficult to discover.

One possible solution is to do to bacteria what they do to us: infect them. With viruses. This might sound bizarre but specialized viruses called phages, which target specific bacteria, are actually already used to treat some infections. This approach is known as phage therapy.

That said, bacteria are fairly quick to evolve sophisticated immune mechanisms to combat viruses that prey on them. Bacterial immunity has been studied since the 1960s, but so far scientists do not know enough about the interaction between bacteria and viruses to significantly advance phage therapy, for example by purposely “breeding” viruses that would overcome the microbes’ defenses.

Over the past five to seven years, 150 immune systems of bacteria have been identified. Among them is a system called PARIS, which the team had already studied before. The way it works is by causing the bacterial cell infected by a phage to self-destruct to arrest the spread of the virus. Specifically, the system operates by slashing transfer RNA molecules, which are a key player in protein synthesis. With the protein synthesis impaired, the cell cannot last.

In a devious feat of adaptation, a virus can encode tRNA molecules of its own in its genome and thus bring “replacement tRNA” along into the cell. These substitute molecules are functionally the same, restoring the cell’s ability to assemble proteins. Structurally, they are distinct from bacterial tRNA, rendering them untargetable by the PARIS immune system. Some phage strains do not carry any tRNA. Others encode a substitute molecule for just one bacterial tRNA, and others still can replace as many as 24 tRNAs — almost the entire set typically employed by the E. coli bacterium. Not long ago, scientists were scratching their heads wondering why a phage would ever carry the seemingly useless tRNA at all.

The study’s lead author Svetlana Belukhina, a research intern at Skoltech Bio and a PhD student of the Institute’s Life Sciences program, commented: “In this study, we have refined our understanding of the interaction between phages and the PARIS immune system in multiple ways. First, we have shown that PARIS attacks three tRNAs, not just one. This is consistent with the way certain toxins work. Second, it’s been confirmed that replacing the attacked tRNAs is sufficient for a virus to escape PARIS. Third, we have demonstrated that this protection is merely a matter of several mutations: Even closely related phage strains that are very much alike may or may not carry the necessary ‘replacement tRNAs’ to escape PARIS. You can’t tell in advance by looking at the viral genome.”

The team’s findings were obtained in an experiment that involved infecting Escherichia coli bacteria with two closely related phage strains — one of them carrying 24 tRNAs, the other 13 — as well as a third phage from another family, which encoded no tRNAs at all. The first phage is protected from PARIS, the second is not but gains protection with the addition of a single tRNA encoded by the first. The third, unrelated phage required the artificial replacement of all three of the PARIS targets to withstand the bacterial immunity.

A mystery for future research to resolve has to do with yet another strain, which also comes from the above family of tRNA-bearing phages and also carries 24 tRNA genes. While it is protected from PARIS, its variants of the three relevant tRNA molecules cannot artificially replace PARIS targets to help the other phages. This raises the question of why that phage is resistant to PARIS in the first place and how just a few mutations in tRNA genes can make such a difference in vulnerability to PARIS.