CRISPR tools found in thousands of viruses can drive gene editing

A systematic study of viral genomes has revealed a range of potential tools for CRISPR-based genome editing.

CRISPR-Cas systems are common in the microbial world of bacteria and archaea, where they often help cells fend off viruses. But analysis¹ published on November 23 in cell found CRISPR-Cas systems in 0.4% of publicly available genome sequences from viruses that can infect these microbes. The researchers believe that viruses use CRISPR-Cas to compete with each other — and potentially also manipulate gene activity in their host to their advantage.

Some of these viral systems are capable of editing plant and mammalian genomes and possess characteristics — such as compact structure and efficient editing — that could make them useful in the laboratory.

“This is a significant step forward in discovering the enormous diversity of CRISPR-Cas systems,” says computational biologist Kira Makarova of the US National Center for Biotechnology Information in Bethesda, Maryland. “Many novelties have been discovered here.”

Protection against DNA cutting

Although it is best known as a tool used to alter genomes in the laboratory, CRISPR–Cas may function in nature as a rudimentary immune system. About 40% of the bacteria sampled and 85% of the archaea sampled have CRISPR-Cas systems. Often, these microbes can capture parts of the invading virus’s genome and store the sequences in a region of their own genome called a CRISPR array. The CRISPR arrays then serve as templates to generate RNA that directs CRISPR-associated (Cas) enzymes to cut the corresponding DNA. This could allow microbes carrying the array to cut the viral genome and potentially stop viral infections.

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Viruses sometimes pick up fragments of their hosts’ genomes, and researchers have previously found isolated examples of CRISPR-Cas in viral genomes. If these stolen pieces of DNA give the virus a competitive advantage, they can be preserved and gradually modified to better serve the viral lifestyle. For example, a virus that infects bacteria Vibrio cholerae used CRISPR-Cas to cut and disable the DNA in the bacterium that codes for the antiviral defense².

Molecular biologist Jennifer Doudna and microbiologist Gillian Banfield of the University of California, Berkeley, and their colleagues decided to do a more comprehensive search for CRISPR-Cas systems in viruses that infect bacteria and archaea known as phages. To their surprise, they found about 6,000 of them, including representatives of every known type of CRISPR-Cas system. “Evidence suggests that these are systems that are beneficial to phages,” says Doudna.

The team found a wide range of variations on the usual CRISPR-Cas structure, with some systems missing components and others being unusually compact. “Even if phage-encoded CRISPR-Cas systems are rare, they are very diverse and widespread,” says Anne Chevalero, who studies phage ecology and evolution at the French National Center for Scientific Research in Paris. “Nature is full of surprises.”

Small but effective

Viral genomes tend to be compact and some of the viral Cas enzymes are remarkably small. This may offer a particular advantage for genome editing applications, as smaller enzymes are easier to transport into cells. Doudna and her colleagues focused on a particular cluster of small Cas enzymes, called Casλ, and found that some of them could be used to edit the genomes of lab-grown watercress cells (Arabidopsis thaliana), wheat, as well as human kidney cells.

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The results suggest that viral Cas enzymes can join a growing collection of gene-editing tools found in microbes. Although researchers have revealed other small Cas enzymes in nature, many have so far been relatively ineffective for genome-editing applications, Doudna says. In contrast, some of the viral Casλ enzymes combine small size and high efficiency.

In the meantime, researchers will continue to look to microbes for potential improvements to known CRISPR-Cas systems. Makarova expects that scientists will also look for CRISPR-Cas systems that have been hijacked by plasmids — pieces of DNA that can be transferred from microbe to microbe.

“Every year we have thousands of new genomes becoming available, and some of them are from very different environments,” she says. “So it’s going to be really interesting.”