A Virus Arms its Bacterial Host with a Toxin, Helping Both to Thrive

While many viruses kill their hosts, not all viruses are harmful. In fact, some even benefit the cells they infect. For instance, temperate phages are viruses capable of replicating innocuously inside certain strains of bacteria. Microbiologists have long understood that these phages can help their primary hosts, emerging from the cells to infect and kill competitor strains.¹

But it turns out that some temperate phages can alter the bacterial battlefield without ever leaving the comfortable confines of their host cells. A recent study in Science Advances has shown that certain types of temperate phages called telomere phages have a previously unknown capability: They arm their hosts with the genetic blueprints for toxins, giving the bacteria a weapon with which to kill their competitors.²

Trevor Lithgow, a microbiologist at Monash University who led the study, had a general interest in bacteriophages, but he did not initially set out to discover a new one. Instead, he and his team were interested in the surface features that determine how a drug-resistant strain of Klebsiella pneumoniae bacteria interacts with its environment. K. pneumoniae are residents of the human gut microbiome that can cause problems when they gain a foothold in other parts of the body.

Lithgow’s team started by sequencing the strain’s genome. It’s fairly straightforward to get a good readout of a bacterium’s genetic code using short-read sequencing, which involves fragmenting the cell’s DNA, reading each fragment, and then reassembling the fragments into a single sequence. But perfect reassembly is not guaranteed with this method. Furthermore, it fails to distinguish pieces of DNA that are within the bacterium but separate from its genome. These extra pieces of DNA, called plasmids, do not contain the essential genes that keep a bacterium alive, but they can often confer unique advantages, such as antibiotic resistance or the ability to process a new nutrient.

Since Lithgow was planning a thorough investigation of this K. pneumoniae strain, his team also enlisted some outside help for long-read sequencing, which can distinguish those extra bits of DNA. “The person who did the sequencing and analyzed the data said, ‘Oh, I think there’s a telomere phage in there,’” said Lithgow. “And we, of course, all had to scurry off to PubMed to work out what is a telomere phage because no one had heard of them before.” Telomere phages, they learned, are DNA viruses capped with structures that look like telomeres, which are the ends of human chromosomes that famously shorten as a person ages.

Lithgow and his team checked to see if these viruses commonly infect K. pneumoniae. The scientists examined previously published genomes from other strains of the bacteria and found that more than 10 percent contained sequences which actually belonged to actively replicating telomere phages. Furthermore, many other bacterial strains contained a few remnant genes from a historical infection. Together, these results suggested that telomere phages are not only widely prevalent among K. pneumoniae strains today, but they also have been infecting the bacteria for much of the species’ evolutionary history.

And the viruses are demanding guests inside their bacterial hosts. Lithgow’s team found out that infected bacteria typically carried about 30 copies of the viral DNA. “That’s quite a load,” said Lithgow. So, he realized that the virus must confer some competitive advantage upon its host that would offset the cost of creating and maintaining so many copies of the virus’s DNA.

To figure out the exact nature of that advantage, Lithgow’s team harvested the proteins from the infected bacteria and used mass spectrometry to identify the proteins encoded by the viral genes. One of the viral proteins turned out to be a toxin that causes pores to form in a bacterium’s membrane, killing the cell. At the same time, another viral protein inhibited the toxin. Thus, the telomere phage equipped its host cell with a toxin to eliminate competitors and an antidote to ensure its host did not kill itself. Lithgow’s team grew infected and uninfected K. pneumoniae together and confirmed that the infected bacteria grew faster and took up more space and resources than their counterparts.

The virus earns its keep by granting its bacterial host a competitive advantage over other strains. Lithgow then became curious if every susceptible K. pneumoniae strain gained access to the same toxin-antidote pair after it had been infected by a telomere phage. So, his team looked back at the phage DNA they had identified in the previously published K. pneumoniae genomes. In fact, the viruses did not all contain the same pore-forming toxin and antidote, but most of them contained a bactericidal toxin and the corresponding antidote.

“That pair is always in exactly the same position in the genome,” said Lithgow. “It makes you think that early on this [toxin-immunity pair] was a feature of the telomere phage.” Over time, various strains of the virus have integrated new toxins, and some of these changes have turned out to be advantageous for the phages and their hosts.

Roberto Bastías, a microbiologist at the Pontifical Catholic University of Valparaíso who was not involved in the study, found the idea of a virus giving its bacterial host a weapon fascinating. He has been studying bacteriophages for some time, and he’s well acquainted with the idea of temperate phages that help their hosts by infecting and killing competitor strains. “But this was very new for me,” he said. “What’s interesting about this case is that the toxin is able to kill bacteria that [are] not susceptible to the phage.”

Because these viruses help their potentially pathogenic hosts thrive, they wouldn’t be ideal candidates for phage therapy. However, their genetic material contains the blueprints for new antibiotics that Bastías hopes someone will develop further.

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