How Viruses Cooperate to Defeat CRISPR

Some weaken their hosts’ immune systems by sacrificing themselves in kamikaze fashion, paving the way for successful infections later.

Phages attached to a bacterial cell
Phages attached to a bacterial cell (Graham Beards / Wikimedia)

No single wolf can take down a bison on its own, but the pack has strength in numbers. A lone army ant is little threat, but an entire colony is a mighty destructive force. The natural world abounds with examples of predators that cooperate to take down their prey. And such teamwork also exists at a microscopic scale, among things that some scientists wouldn’t even classify as alive: viruses.

Most viruses don’t infect humans; instead, they target bacteria. These viruses, known as phages, are like miniature syringes. They commandeer bacteria by landing on them and injecting their genetic material inside. But bacteria can defend themselves from these incursions. They can store phage genes within their own DNA to build up a dossier of enemies past. They then use this cached information to guide destructive, scissor-like enzymes, which seek out any matching viruses and slice them up.

This defense system is known as CRISPR. It’s the basis of the gene-editing technique that is being used to treat human diseases, control invasive species, and inspire movie plots. But for billions of years before scientists realized that CRISPR could be used to alter DNA, bacteria were using it as part of their immune systems.

CRISPR doesn’t always work. In 2012, the microbiologist Joseph Bondy-Denomy pitted phages against CRISPR-wielding bacteria. Some of the viruses were destroyed, but others unexpectedly survived and infected the bacteria. Bondy-Denomy showed that those phages succeeded by relying on proteins that could shut down CRISPR inside the bacteria, by sticking to the scissor-like enzymes and blunting them.

So, bacteria and phages are locked in an arms race. The bacteria use CRISPR to defang the phages, and the phages use anti-CRISPRs to subvert the bacterial defenses. The only problem is that the anti-CRISPRs shouldn’t work.

It’s all a matter of timing. Once the phages inject their genes into their bacterial victims, some of those genes serve as blueprints for manufacturing anti-CRISPR proteins. That takes time. By contrast, the bacteria have their CRISPR defenses ready-made. These ought to immediately start destroying the phages before they can construct their anti-CRISPR countermeasures. Based on that, “we didn’t think the anti-CRISPRs would work,” says Bondy-Denomy, who now works at the University of California at San Francisco. “It seemed like a race against time.”

His colleague Adair Borges showed that the slower phages can still win this race—as long as there are enough of them. The first one attacks the bacterium, and is destroyed by CRISPR before it can make enough anti-CRISPR countermeasures. Still, whatever anti-CRISPRs it does manage to make will linger in the bacterium, partly suppressing its immune defenses. The next phages to invade might also be destroyed, but each one weakens the CRISPR defense even further, until finally, the viruses overwhelm their victim.

A second group of scientists, led by Stineke van Houte from the University of Exeter, independently found the same thing. They, too, showed that anti-CRISPRs are imperfect, and that their success depends entirely on how many phages there are. As long as there are enough phages to successively attack the same bacterium, the later ones will eventually succeed even if the first ones fail.

Indeed, it’s only because the first ones fail that any succeed at all. The first phages are like kamikaze bombers, throwing themselves at enemy forces. They sacrifice themselves, but they give the next wave a chance of breaking through. “Those next phages benefit from what the first phage leaves behind,” says van Houte. “That’s how they cooperate.”

There are very few microbes that can successfully infect a host from a single cell or particle, says Britt Koskella from UC Berkeley, who studies phages. Infections are almost always a numbers game. Still, the phages are unusual in that “previously unsuccessful infections can increase the success of future ones,” she says. “This is the opposite of what happens in most other systems, where previous exposure to pathogens typically primes the immune system and decreases the likelihood of future infection.”

To Bondy-Denomy, the phages’ behavior looks a lot like the altruism of, say, ants and bees, in which individuals make sacrifices to help others who share the same genes. Similarly, in sacrificing themselves, early phages help out later ones that are likely to be genetically identical. Bondy-Denomy admits that the term “altruism” is a loaded one, and seems like a stretch for viruses, which clearly don’t have any agency, and which straddle the boundaries between living and inanimate. “But it fits if you accept that altruism can be a non-neurological process, that doesn’t have to come from decisions by a member of a community,” he says.

These studies open more questions than they answer. When anti-CRISPR proteins suppress the immune systems of the bacteria, how long does that last? If one type of phage starts to weaken the bacteria, could another type cheat by exploiting the immunocompromised targets without making any anti-CRISPRs of its own? And how important is any of this in nature? It depends on “how many phages the average bacterial cell typically encounters,” Koskella says. “If it’s not very many, then the CRISPR system should be adequate in most environments. But if bacteria are constantly facing a barrage of phages, then this tipping point where phages override bacterial defenses could be commonly reached. The answer is probably somewhere in between.”

These battles are unlikely to affect the use of CRISPR in gene editing, but they “could have profound implications for phage therapy,” says Karen Maxwell from the University of Toronto. She’s talking about attempts at using phages to cure bacterial infections in humans. Phage therapy was long dismissed in the West as a kooky fringe idea, but it’s enjoying a resurgence after several recent successes at treating bacterial infections that resisted standard antibiotics.

But as Maxwell notes, numbers matter. “If too few phages are delivered, the therapy will fail, since the phages will be driven to extinction,” she says. By studying the battles between bacterial CRISPRs and phage anti-CRISPRs, researchers will be able to fine-tune the doses of virus that are needed to cure different infections.

“There are also implications for our understanding of viral infections in humans,” Maxwell adds. Our own cells can shut down viral genes in a way that’s analogous to CRISPR in bacteria, and several of the viruses that infect us get help from proteins that suppress these defenses. These arms races might help explain why some viruses are more infectious than others.