Long before people became interested in killing bacteria, viruses were at work. Bacteria-attacking viruses called “phages” (short for bacteriophage) were first identified by their ability to create bare spots on the surface of culture plates that were otherwise covered by a lawn of bacteria. Having played a critical role in the early development of molecular biology, a number of phages have been developed as potential therapies to be used when antibiotic resistance limits the effectiveness of traditional drugs.
But we are relatively latecomers in turning phages into tools. Researchers have described a number of cases where bacteria have kept parts of damaged viruses in their genomes and turned them into weapons that can be used to kill other bacteria that might otherwise compete for resources. I just found out about this weaponization, thanks to a new study showing that this process has helped sustain diverse bacterial populations for centuries.
Evolving killer
The new work began when the researchers studied the population of bacteria associated with a plant growing wild in Germany. The population includes various members of the genus Pseudomonas, which may include plant pathogens. Typically, when bacteria infect a new victim, one strain expands dramatically as it successfully exploits its host. In this case, however, Pseudomonas the population contains a variety of different strains that appear to maintain stable competition.
To learn more, the researchers obtained over 1,500 individual genomes from the bacterial population. Over 99 percent of these genomes contain parts of a virus, with the average bacterial strain having two separate parts of a virus lurking in their genomes. They all had pieces missing compared to a functional virus, suggesting they were the product of a virus that had been inserted in the past but then caused damage that disabled them.
In itself, this is not shocking. Many genomes (including our own) have many deactivated viruses in them. But bacteria tend to eliminate foreign DNA from their genomes quite quickly. In this case, one particular viral sequence appears to date back to the common ancestor of many of the strains, because in all of them the virus was inserted at the same place in the genome, and all instances of that particular virus were inactivated by losing the same set of genes. The researchers named this sequence VC2.
Many phages have a stereotypical structure: a large “head” that contains their genetic material perched atop a stalk that ends in a set of “legs” that help grip their bacterial victims. Once the legs make contact, the stalk contracts, an action that helps transfer the virus genome into the bacterial cell. In the case of VC2, all its copies lack the genes for head production, as well as all the genes needed to process its genome during infection.
This leads researchers to suspect that VC2 is something called “tylocin.” These are former phages that have been domesticated by bacteria so they can be used to harm potential competition from the bacteria. Bacteria with tylocin can produce partial phages that consist only of a leg and a stalk. These tylocins can still find and latch on to other bacteria, but when the stalk shrinks, there is no genome to inject. Instead, it simply opens a hole in their victim’s membrane, partially eliminating the cell’s boundary and allowing some of its contents to leak out, leading to its death.
An evolutionary free for all
To confirm that the VC2 sequence encodes tylocin, the researchers grew some bacteria that contained the sequence, purified proteins from it, and used electron microscopy to confirm that they contained headless phages. By exposing other bacteria to tylocin, they found that while the strain that produced it was immune, many other strains growing in the same environment were killed by it. When the team deleted the genes that code for key parts of tylocin, the killing disappeared.
The researchers suggest that the system is used to kill off potential competition, but that many strains have developed resistance to tylocin.
When the researchers did a genetic screen to identify resistant mutants, they found that the resistance is provided by mutations that interfere with the production of complex sugar molecules that are found in proteins that end up on the outside of cells. At the same time, most of the genetic differences between the VC2 genes occur in the proteins that encode the legs that latch onto these sugars.
So each bacterial strain appears to be both aggressor and victim, and there is an evolutionary arms race that results in a complex collection of pairwise interactions between strains—think of a rock/scissors/paper game with dozens of options. And the arms race has a history. Using old samples, the researchers show that many of the variations in these genes have existed for at least 200 years.
Evolutionary races are often seen as a simple one-on-one battle, probably because that’s an easy way to think about them. But the reality is that most are closer to a chaotic bar brawl – one where it’s rare for either faction to gain a consistent advantage.
Science, 2024. DOI: 10.1126/science.ado0713 (About DOI).
