Joseph Bondy-Denomy knew he could find viruses that would be hard to kill. But he wasn’t expecting to discover one that was quite so invincible.
The viruses that Bondy-Denomy studies at the University of California at San Francisco don’t bother humans. Known as phages, they infect and kill bacteria instead. Bacteria can defend themselves against these assaults. They can recognize the genes of the phages that threaten them, and deploy scissorlike enzymes to slice up those genes and disable the viruses. This defense system is known as CRISPR. Billions of years before humans discovered it and used it as a tool for editing DNA, bacteria were using CRISPR to fight off phages.
But phages have their own countermeasures. In 2012, Bondy-Denomy discovered that some of these viruses are resistant to CRISPR, because they have proteins that stick to those scissorlike enzymes and blunt them. A bacterium can mount its CRISPR defense, but ultimately the virus can still force itself in and triumph. This suggested that bacteria and phages are likely locked in an arms race. The former evolve new kinds of scissor enzymes, and the latter evolve new ways of disabling them. Intrigued, Bondy-Denomy started searching for more CRISPR-resistant phages.
He soon found one that was resistant, and then some. It’s called phi-kappa-zeta (or phiKZ)—a name that it coincidentally shares with a sorority. Unusually large for a virus, phiKZ typically infects a bacterium called Pseudomonas aeruginosa. Unsurprisingly, it could resist the version of CRISPR used by its host. Unexpectedly, it also resisted every other version of CRISPR that the team tried, including those from bacteria that it would never have naturally encountered. Its armor seemed to work against every possible weapon. No anti-CRISPR protein should work in such a universal way. “It didn’t make any sense,” Bondy-Denomy says.
He slowly realized what was happening after chatting with David Agard, who works in the same building. In 2017, Agard, along with Joe Pogliano and other colleagues, discovered that another phage does something that viruses are not meant to do. It encapsulates its DNA inside a shell of protein, which it suspends inside itself with thin filaments. That’s exceptionally odd. The cells of animals and plants also house their DNA within a special compartment—the nucleus. But such compartments aren’t meant to exist in simpler cells, like those of bacteria. And they’re certainly not meant to exist in viruses, which some scientists don’t even regard as alive. And yet, here was a phage, packaging its DNA in something akin to a nucleus. Why?
Agard told Bondy-Denomy about the phage that surrounds its DNA in a shell. Bondy-Denomy told Agard about the phage that’s resistant to all forms of CRISPR. It slowly dawned on the duo that the viruses they were studying were closely related, and that the weird phenomena they had found were linked. CRISPR can’t destroy what it can’t reach, and the shell stops it from getting at the phage’s DNA. The phiKZ phage and its relatives don’t need to evolve countermeasures against each and every form of CRISPR when they have ways of excluding them all. “Proving it was the hard part,” Bondy-Denomy says. “That took a couple of years.”
His student Eliza Nieweglowska confirmed, using a microscope, that the CRISPR scissors really are blocked by the shell. Meanwhile, another student, Senén Mendoza, showed that once the phage’s DNA was removed from the shell, the CRISPR scissors were perfectly capable of cutting it up. Mendoza also managed to smuggle the scissors into the shell by fusing them with proteins that are normally allowed to pass. When that happened, the phages were destroyed. “This work definitively shows that the structure protects against CRISPR,” says Benjamin Chan, who studies phages at Yale University. The similarity to a nucleus “is fascinating,” he adds.
Finding new forms of CRISPR, or new defenses against it, could lead to ways of controlling gene-editing technologies more carefully or efficiently. But on a more basic level, Bondy-Denomy’s discovery might hint at a bit of evolutionary history, of our own cells. If viruses can protect their DNA from bacterial enemies using a nucleus-like structure, perhaps the nucleus itself evolved as a way for cells to protect their DNA from viruses? To explore that idea, Bondy-Denomy and his team are trying to understand more about how the mysterious shell functions. It’s incredibly selective, blocking everything except the proteins that the virus uses to copy its DNA and switch on its genes. “It’s not clear how it works,” Bondy-Denomy says. “But we’re really in love with it now.”
“It’s yet another example of the ingenuity of phages,” says Karen Maxwell of the University of Toronto. But why, she wonders, haven’t all phages evolved a nucleus-like structure, if it provides such wide-ranging benefits? Is there some downside to that defense that isn’t yet clear? Such questions matter, especially because scientists are turning to phages as ways of treating drug-resistant infections. A phage with a protective nucleus “provides a new prototype that could prove useful for these purposes,” Maxwell adds.
Phages are often discussed in aggregate, as if they were all roughly the same. But as Bondy-Denomy’s work shows, “there’s a staggering amount of diversity,” he says. “I tell everyone who joins my lab that they can find something cool and new, because every phage does something different.”
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