Long before people were interested in killing bacteria, viruses were at work. Viruses that attack bacteria, called “phages” (short for bacteriophage), were first identified by their ability to create bare spots on the surface of culture dishes that were otherwise covered in a lawn of bacteria. After playing a vital 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 relative latecomers when it comes to turning phages into tools. Scientists have described a number of cases where bacteria have retained pieces of affected viruses in their genomes, turning them into weapons that can be used to kill other bacteria that might otherwise compete for resources. I only now became aware of this weaponized technique, thanks to a new study showing that this process has helped maintain diverse bacterial populations for centuries.
Evolving killer
The new work began when researchers studied a population of bacteria associated with a plant growing wild in Germany. The population included various members of the genus Pseudomonas, which may include plant pathogens. Normally, when the bacteria infects a new victim, one strain expands dramatically as it successfully exploits its host. In this case though Pseudomonas the population contained a number of different strains that appeared to maintain stable competition.
To learn more, the scientists obtained more than 1,500 individual genomes from the bacterial population. More than 99 percent of these genomes contained pieces of virus, with the average bacterial strain having two separate pieces of virus in its genome. All of these had missing parts compared to a functional virus, suggesting that they were the product of a virus that had inserted itself in the past but had since acquired damage that rendered them inoperable.
This in itself is not shocking. Lots of genomes (including our own) have lots of affected viruses in them. But bacteria tend to eliminate foreign DNA from their genomes fairly quickly. In this case, one particular virus sequence appeared to come from a common ancestor of many strains, because they all had the virus inserted into the same place in the genome, and all instances of that particular virus were disabled 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 them attach to their bacterial victims. Once the legs make contact, the stalk retracts, an action that helps transfer the virus genome into the bacterial cell. In the case of VC2, all its copies lacked the genes for producing the head part, as well as all the genes needed to process its genome during infection.
This led researchers to suspect that VC2 was something called “tailocin.” These are former phages that have been domesticated by bacteria so they can be used to harm potential bacterial competition. Bacteria with tylocin can produce partial phages that consist only of legs and a stem. These tailocins can still find and attach to other bacteria, but when the stalk shrinks, there is no genome to inject. Instead, it just opens a hole in their victim’s membrane, partially removing 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 the proteins from it, and confirmed by electron microscopy 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 hypothesize that the system is used to kill potential competition, but that many strains have developed resistance to tylocin.
When scientists performed a genetic screen to identify resistant mutants, they found that resistance was conferred by mutations that disrupt the production of complex sugar molecules found on proteins that end up outside cells. At the same time, most of the genetic differences between the VC2 genes occur in the proteins that encode the legs that attach to these sugars.
Thus, each bacterial strain appears to be both aggressor and victim, and there is an evolutionary arms race that leads to a complex collection of pairwise interactions between strains—think a rock/paper/scissors game with dozens of possibilities. And the arms race has a history. Using ancient samples, the researchers show that many variations in these genes have existed for at least 200 years.
Evolutionary contests are often seen as simple one-on-one combat, probably because that’s an easy way to think about them. But the reality is that most of them are more akin to a chaotic bar brawl—one where it’s rare for either faction to gain a lasting advantage.
Science, 2024. DOI: 10.1126/science.ado0713 (About DOI).