The celebrated gene-editing tool CRISPR started out as a bacterial defense against invading viruses. But it turns out the intended targets have stolen CRISPR for their own arsenals. A new study reveals that thousands of the bacteria-attacking viruses known as bacteriophages (phages, for short) contain the CRISPR system’s genetic sequences, suggesting they may deploy them against rival phages. The finding is a testament to the molecular weapon’s power—and may make CRISPR even more valuable as a laboratory gene editor.
The discovery “opens doors for possible new applications of CRISPR systems,” says genomicist Mazhar Adli of Northwestern University’s Feinberg School of Medicine, who wasn’t connected to the research.
Like other viruses, phages cannot reproduce on their own. Instead, they hijack bacteria’s molecular machinery, often killing their hosts in the process. The CRISPR system enables bacteria to fight back. It includes repetitive stretches of DNA that match sequences of previously encountered phages. If these same phages attack a bacterium again, it uses this repetitive DNA to encode strands of RNA that can steer a partner enzyme, which acts like a pair of genetic scissors, to cut the phage’s genome at specific places. For about the past decade, scientists have been working to turn this immune defense into a gene-editing technique for myriad uses, including improving crop defenses, detecting pathogens, and fighting diseases such as cancer.
Characteristic DNA that encodes components of the CRISPR system had previously turned up in a handful of phages. But scientists regarded these finds as mere “curiosities,” says structural biologist Jennifer Doudna of the University of California (UC), Berkeley, who shared the 2020 Nobel Prize in Chemistry for showing how to tailor the CRISPR system to target particular sequences. “But they got us wondering if these systems were more common.”
To find out, Doudna, UC Berkeley geomicrobiologist Jillian Banfield, and their colleagues went looking for additional examples of CRISPR in the phage world. They probed DNA plucked from a variety of environments that are rich in bacterial hosts for the viruses, including soil and the human mouth. This trawl uncovered more than 6000 types of phages that contain CRISPR system DNA, the scientists report online today in Cell. They also examined phage genome sequences that had been posted to online databases and found even more instances of the CRISPR-carrying viruses. Although fewer than 1% of phages sport the sequences, the researchers did not expect “such a broad distribution of an anti-phage system in phages,” Doudna says.
Why would phages acquire a system that evolved to thwart them? The most likely reason, Doudna says, is to beat the competition. Multiple viruses can attack a bacterium at the same time, leading to “phage wars” inside an infected cell, she says. Bacteria are also vulnerable to rogue DNA strands known as plasmids that coerce the cells into copying them. By destroying these rivals with the CRISPR system, phages “can have the replication machinery all to themselves,” Doudna says.
The phages presumably swiped these CRISPR system sequences from their microbial victims, she says. Since then, the viruses have customized the systems for their own ends. For instance, some phages seem to have lost the capacity to generate certain molecules that can kill bacteria, possibly to preserve their hosts to produce more phages.
The phages’ gene-editing tricks may inspire new biotechnology. For instance, most CRISPR-based approaches now rely on the enzyme Cas9 to cut DNA. However, Cas9 is so large it cannot fit into some viruses used to genetically modify cells. A number of phages, however, boast a slimmed-down version known as Cas-lambda that is about 50% smaller, Doudna’s and Banfield’s team found. Adli says this smaller enzyme could allow new gene-editing applications for CRISPR, such as altering plant genomes, though researchers would first need to overcome several bioengineering hurdles.
Microbiologist Joseph Bondy-Denomy of UC San Francisco says Doudna and Banfield displayed a “[John] Lennon-[Paul] McCartney” level of synergy in ferreting out so many CRISPR-bearing phages that had eluded other scientists. Still, he wants to see evidence that phages actually put their CRISPR systems to use when they invade bacteria. Bondy-Denomy also suspects many more phages that wield CRISPR are waiting to be discovered. “The next step is more,” he says.