CRISPR tools found in thousands of viruses can boost gene editing

A systematic cleanup of viral genomes has revealed a wealth of potential CRISPR-based gene editing tools.

CRISPR-Cas systems are common in the microbial world of bacteria and archaea, where they often help cells fend off viruses. But an analysis¹ published on November 23 in Cell finds CRISPR-Cas systems in 0.4% of the publicly available genome sequences of viruses that can infect these microbes. Researchers think the viruses use CRISPR-Cas to compete with each other – and possibly also to manipulate gene activity in their host to their advantage.

Some of these viral systems were able to edit the genomes of plants and mammals and have features – such as compact structure and efficient editing – that could make them useful in the laboratory.

“This is an important step forward in the discovery of the enormous diversity of CRISPR-Cas systems,” said computational biologist Kira Makarova of the US National Center for Biotechnology Information in Bethesda, Maryland. “A lot of news has been discovered here.”

DNA-cutting defense

Although best known as a tool used to alter genomes in the lab, CRISPR–Cas can function in nature as a rudimentary immune system. About 40% of the sampled bacteria and 85% of the sampled archaea have CRISPR-Cas systems. Often these microbes can capture bits of the genome of an invading virus and store the sequences in a region of their own genome called a CRISPR array. CRISPR arrays then serve as templates to generate RNAs that direct CRISPR-associated (Cas) enzymes to cut the corresponding DNA. This allows microbes carrying the array to slice up the viral genome and potentially stop viral infections.

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Viruses sometimes pick up bits of their host’s genome, and researchers had previously found isolated examples of CRISPR-Cas in viral genomes. If those stolen bits of DNA give the virus a competitive advantage, they could be retained and gradually modified to better serve the viral lifestyle. For example, a virus that infects the bacteria Vibrio cholera uses CRISPR-Cas to cut up and knock out DNA in the bacteria that codes for antiviral defenses².

Molecular biologist Jennifer Doudna and microbiologist Jillian Banfield of the University of California, Berkeley, and their colleagues decided to look more extensively for CRISPR-Cas systems in viruses that infect bacteria and archaea, also known as phages. To their surprise, they found about 6,000, including representatives of every known type of CRISPR-Cas system. “There is some evidence that these are systems that are useful for phages,” says Doudna.

The team found a wide variety 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 widely distributed,” said Anne Chevallereau, who studies phage ecology and evolution at France’s National Center for Scientific Research in Paris. “Nature is full of surprises.”

Small but efficient

Viral genomes tend to be compact and some of the viral Cas enzymes were remarkably small. This could be particularly advantageous for genome editing applications, as smaller enzymes can be more easily transported 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 thale cress cells (Arabidopsis thaliana), wheat, as well as human kidney cells.

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

In the meantime, researchers will continue to search microbes for possible improvements to known CRISPR-Cas systems. Makarova expects scientists to also look for CRISPR-Cas systems picked up by plasmids — bits of DNA that can be transferred from microbe to microbe.

“Thousands of new genomes become available every year, and some come from very different environments,” she says. “So it gets really interesting.”