Long before people became interested in killing bacteria, viruses were already 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 plates that would otherwise be covered in a lawn of bacteria. After playing a crucial role in the early development of molecular biology, a number of phages have been developed as potential therapeutics to be used when antibiotic resistance limits the effectiveness of traditional medicines.
But we are relative latecomers when it comes to turning phages into tools. Researchers have described a number of cases in which bacteria have retained parts of disabled viruses in their genomes and turned them into weapons that can be used to kill other bacteria that would otherwise compete for resources. I only just became aware of that weaponry, thanks to a new study showing that this process has helped maintain diverse bacterial populations for centuries.
Developing a killer
The new work began when researchers studied the population of bacteria associated with a wild-growing plant in Germany. The population included several members of the genus Pseudomonas, including plant pathogens. Normally, when bacteria infect a new victim, a single strain expands dramatically as it successfully exploits its host. In this case, however, the Pseudomonas The population contained a variety of different species that appeared to maintain stable competition.
To find out more, the researchers obtained more than 1,500 individual genomes from the bacterial population. More than 99 percent of those genomes contained pieces of virus, with the average strain of bacteria having two separate pieces of virus lurking in their genomes. These all had missing parts compared to a functional virus, indicating that they were the product of a virus that had been introduced in the past but had since suffered damage rendering them useless.
That in itself is not shocking. Many genomes (including ours) contain many disabled viruses. But bacteria tend to remove foreign DNA from their genomes quite quickly. In this case, one particular viral sequence appeared to trace back to the common ancestor of many of the strains, as the virus had been inserted into the same location in the genome in all of them and all copies of this particular virus had been eliminated by the loss of the same set genes. The researchers called this sequence VC2.
Many phages have a stereotypical structure: a large ‘head’ that contains their genetic material, atop a stalk that ends in a series of ‘legs’ that help latch onto their bacterial victims. Once the legs make contact, a stalk contracts, an action that helps transfer the virus’s genome into the bacterial cell. In the case of VC2, all copies of it lacked the genes for producing the main body, as well as any genes needed for processing the genome during infection.
This led the researchers to suspect that VC2 was something called a ‘tailocin’. These are former phages that have been domesticated by bacteria so that they can be used to harm the bacteria’s potential competition. Bacteria with a tailocin can produce partial phages consisting only of the legs and stem. These tailocins can still find and attach to other bacteria, but when the stem contracts there is no genome to inject. Instead, this merely 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 death.
An evolutionary free for all
To confirm that the VC2 sequence codes for a tailocin, the researchers grew some bacteria containing the sequence, purified proteins from them, and used electron microscopy to confirm that they contained headless phages. By exposing other bacteria to the tailocin, they found that although the strain that produced it was immune, it killed many other strains growing in the same environment. When the team deleted the genes that code for key parts of the tailocin, the killing disappeared.
The researchers hypothesize that the system is used to eliminate potential competition, but that many strains have developed resistance to the tailocin.
When the researchers conducted a genetic screen to identify resistant mutants, they found that resistance was caused by mutations that disrupted the production of complex sugar molecules found on 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 code for the legs and attach to these sugars.
So it appears that each bacterial strain is both an aggressor and a victim, and there is an evolutionary arms race that leads to a complex set of pairwise interactions between the strains – think of a rock-paper-scissors game with dozens of options. And the arms race has a history. Using ancient samples, the researchers show that many of the variations in these genes have existed for at least 200 years.
Evolutionary competitions are often thought of as a simple one-on-one battle, probably because it’s an easy way to think about it. But the reality is that most are more like a chaotic bar brawl, with it rare for either faction to gain a permanent advantage.
Science, 2024. DOI: 10.1126/science.ado0713 (About DOIs).