Take One for the Team: Bacteria Self-CRISPR to Defeat Phages

Altruism, the most elevated of behaviors, may seem alien to lowly bacteria. But in fact, individual bacteria have been known to sacrifice themselves for the sake of the bacterial colonies to which they belong. Bacteria may share nutrients. Bacteria may absorb more than their share of antibiotics. And, according to a new study, bacteria may turn their anti-phage weaponry on themselves, preventing infectious phages from propagating through the bacterial collective.

When under viral attack, a bacterium may use Cas13, an element of its CRISPR immune system, to put itself into a dormant state. Ordinarily, Cas13 is used to cleave foreign RNA. Yet it may also be used to cleave the bacterium’s own RNA, inducing dormancy.

When Cas13 is used in this way, it may fight not only RNA phages, but DNA phages, which are far more common. That is, Cas13, which ordinarily works directly, by cutting apart RNA from RNA phages, may also work indirectly, by denying DNA phages a fully functioning host.

The ability of bacteria to fall on their own Cas13 swords was discovered by scientists based at Rockefeller University. These scientists, led by Luciano Marraffini, PhD, professor at Rockefeller University, also found that Cas13 kills viruses more thoroughly than other Cas enzymes. Standard CRISPR-Cas systems are highly specific, cutting up bits of DNA that match a precise genetic sequence. And while this specificity can be an asset, it also comes with a big drawback: If a virus mutates, CRISPR cannot recognize the invader, and the phage escapes scot-free.

“If a phage has a single point mutation in its target sequence, then usually the virus is invisible to Cas and the infection will succeed,” said Marraffini. “But with Cas13 we didn’t see any escaper mutants.”

The Rockefeller scientists presented their findings in a paper (“Cas13-induced cellular dormancy prevents the rise of CRISPR-resistant bacteriophage”) that appeared May 29 in the journal Nature.

“Although it has been hypothesized that Cas13 naturally defends against RNA phages8, type VI spacer sequences have exclusively been found to match the genomes of double-stranded DNA phages, suggesting that Cas13 can provide immunity against these invaders,” the paper indicated. “We show that trans-cleavage of transcripts halts the growth of the host cell and is sufficient to abort the infectious cycle. This depletes the phage population and provides herd immunity to uninfected bacteria.”

Bacteria have at their disposal many different CRISPR-Cas systems, one of which caught the attention of Marraffini due to its unique strategy for fending off intruders. Whereas most Cas enzymes destroy viral DNA, Cas13 works by cleaving RNA.

“Since Cas13 targets RNA, it was initially thought to have evolved to impede phages with RNA genomes. The problem is, RNA phages exceedingly rare,” he explained. “So, we wanted to see whether it might have evolved to serve a different function.”

Working with Alexander Meeske, PhD, Helen Hay Whitney postdoctoral associate, Marraffini showed that activation of Cas13 actually protects bacteria from phages with DNA genomes, which are far more common.

By acting on the host rather than directly targeting the virus, Cas13 not only provides robust defense against DNA phages, but also prevent outbreaks of CRISPR-resistant phage.

The researchers attribute this superb virus-fighting power to the fact that cell dormancy does not target one particular virus, but rather makes it impossible for any phage—including mutants—to propagate. And while an indefinite nap may not seem like much of a life for a microbe, Meeske notes that the real benefit of Cas13 lies not at the level of the individual, but of the bacterial community as a whole.

“The phage has one shot to deliver its genetic payload and replicate,” said Meeske. “So, if they inject their genome into a host that turns out to be inhospitable, the infection stops there. The phage loses, and the bacterial colony wins.”

Although bacteria that turn Cas13 on themselves cease to grow, they do not die. This observation prompted the scientists to speculate about mechanisms that would allow bacteria to clear phage genomes after Cas13a activation, permitting the cell to recover from dormancy. “If such a mechanism exists,” they indicated, “the infected cell itself would benefit from the presence of the type VI CRISPR system and immunity would not be an exclusively altruistic event.”