Updated Tue, November 14, 2023
The discovery started with an undergraduate class designed to teach students basic laboratory techniques, asking them to isolate phages from soil samples and study them using genetics.
In March 2020, Tagide deCarvalho saw something truly strange - something she thinks no other scientist has ever seen before: a virus with another, smaller virus latched onto its "neck." The backstory of this viral attachment is like a master class in how wild and weird biology can be.
The two microbes are both bacteriophages, viruses that infect bacteria, that were harvested from a clump of dirt in Poolesville, Md. Bacteriophages, also called simply phages, are among the most abundant organisms on Earth. There can be millions in a gram of dirt.
But with a special kind of microscope that uses a beam of electrons to capture images, deCarvalho witnessed a truly bizarre moment - kind of like a wildlife photographer who captures an animal behavior that no one had anticipated.
"I could see literally hundreds of them had this little guy attached at the neck, and it was clearly not random," said deCarvalho, who manages the Keith R. Porter Imaging Facility at University of Maryland at Baltimore County. "We know that viruses can do some amazing, interesting things. But this is just another new thing that no one could have predicted we would see."
In a recent study in the Journal of the International Society for Microbial Ecology, deCarvalho and colleagues explain how the viral odd couple likely came to be. The small virus, called MiniFlayer, lost the ability to make copies of itself inside cells, which is how viruses reproduce. So evolution devised a clever, parasitic workaround. MiniFlayer takes advantage of another virus, dubbed MindFlayer, by grabbing onto its neck, and when they enter cells together, MiniFlayer utilizes its companion's genetic machinery to proliferate.
Is it an embrace? A stranglehold? DeCarvalho compares the relationship to viral hitchhiking. Her collaborator, Ivan Erill, a computational biologist at UMBC, likens it to a vampire sinking its teeth into its prey. It's not a perfect analogy, but he notes that sometimes, when they find MindFlayer alone, they can find "bite marks" where MiniFlayer's tendrils were attached.
"Viruses will do anything. They are the most creative force of nature," Erill said. "If anything is possible, they will come up with a way to do it. But no one had anticipated that they would do something like this."
The strange universe of viruses
The discovery started with an undergraduate class designed to teach students basic laboratory techniques, asking them to isolate phages from soil samples and study them using genetics. DeCarvalho has been working with the program for seven years and says that for many of the students, seeing the phage is an exciting moment, like when expecting parents see the ultrasound of a fetus for the first time.
In this case, undergraduates Jenell Lewis and Hira Ahmed isolated and named their phage MindFlayer in 2019. But genome sequencing returned puzzling results, suggesting some kind of contamination. When deCarvalho looked at it with a microscope, she noticed not one phage, but two.
The "virosphere," as scientists call the strange universe of viruses, is known to include elements called "satellites" that have lost their ability to replicate inside cells. Usually, satellites overcome this deficiency by integrating into the genome of the cells that they infect. They lurk there until another virus, a "helper" that has the missing ingredients, happens to enter the cell. The satellites then seize the opportunity to make copies of themselves.
MiniFlayer is a satellite, but unlike the typical version, it doesn't have the ability to hide inside cells. That leaves it with a conundrum: How to make sure it ends up in the cell with its helper at the same time.
"What this virus has done is say, okay, I'm going to attach to my helper, attach to its neck - and travel with my helper until we find a new cell," Erill said.
This is par for the course in microbiology, where tactics like molecular piracy and hijacking have been honed over millions of years of evolution. Bacteria are wildly outnumbered by their viral predators, putting them in an ongoing evolutionary arms race. Bacteria develop defenses, and viral phages develop counter-defense strategies. Phages parasitize other phages.
Researchers are interested in using phages, the natural predators of bacteria, as medicine. Phage therapy can be used to target harmful infections, an approach that could become more important as antibiotic-resistant bacteria have become a growing threat.
Terje Dokland, a microbiology professor at the University of Alabama at Birmingham who was not involved in the study, said the observation of the two attached phages was "intriguing" but called for more images and research to draw firmer conclusions about the interaction, and to tease out whether the two viruses are really co-infecting cells.
The authors hope to collaborate with groups that use a different form of electron microscopy to understand what's happening more clearly. Unlike a vampire, deCarvalho points out, the MiniFlayer isn't sucking something out of MindFlayer.
"We don't know whether or not the satellite is injecting its DNA into the helper or if it's just hitchhiking along for a ride and then falling off, like a tick," deCarvalho said. "Hopefully someone else will pick up this work and figure out that really interesting question."
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