CRISPR tools found in thousands of viruses can enhance gene editing

Phages (shown here attacking a bacterial cell) might use CRISPR-Cas systems to compete with each other — or to manipulate genetic activity in their hosts.Credit: Biophoto Associates/SPL

Systematic scanning of viral genomes has revealed a suite of CRISPR-based genome editing tools.

CRISPR-Cas systems are common in the microbiome of bacteria and archaea, often helping cells fend off viruses. But analysis1 Posted on November 23 in cell discovered CRISPR-Cas systems in 0.4% of the publicly available genome sequences of viruses that can infect these microbes. Researchers believe that viruses use CRISPR-Cas technology to compete with each other — and possibly also to manipulate genetic activity in their host to their advantage.

Some of these viral systems have been able to edit plant and mammalian genomes, and possess features — such as compact structure and efficient editing — that can make them useful in the laboratory.

“This is an important step forward in discovering the huge diversity of CRISPR-Cas systems,” says computational biologist Kira Makarova at the US National Center for Biotechnology Information in Bethesda, Maryland. “A lot of new things have been discovered here.”

DNA cut defenses

Although CRISPR-Cas is best known as a tool used to alter genomes in the laboratory, in nature it can function as a primitive immune system. About 40% of bacteria samples and 85% of archaea taken from them have CRISPR-Cas systems. Often, these microbes can capture parts of the genome of an invading virus, and store the sequences in a region of their genome, called a CRISPR array. The CRISPR arrays then serve as templates to generate RNAs that direct CRISPR-binding (Cas) enzymes to cut the corresponding DNA. This could allow microbes carrying the array to slice into the viral genome and stop the viral infection.

Viruses sometimes capture snippets of their host’s genomes, and researchers have previously found isolated examples of CRISPR-Cas in viral genomes. If those stolen fragments of DNA give the virus a competitive edge, they can be preserved and gradually modified to better serve the viral lifestyle. For example, a virus that infects bacteria Vibrio cholera CRISPR-Cas is used to cut and disrupt DNA in bacteria that encodes antiviral defenses2.

Molecular biologist Jennifer Doudna, microbiologist Gillian Banfield at the University of California, Berkeley, and their colleagues decided to conduct a more thorough 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. “The evidence suggests that these are beneficial systems for phages,” Doudna says.

The team found a wide range of variations on the usual CRISPR-Cas architecture, with some systems missing components and others unusually compact. “Even if CRISPR-Cas systems encoded by phages are rare, they are very diverse and widely distributed,” says Anne Chevalereau, who studies the ecology and evolution of phages 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 viral Cas enzymes were remarkably small. This can provide a particular advantage for genome editing applications, because smaller enzymes are easier to transport into cells. Doudna and her colleagues focused on a specific group of small Cas enzymes called Casλ, and found that some of them could be used to modify the genomes of lab-grown cells of cress (Arabidopsis thaliana) and wheat as well as human kidney cells.

The results indicate that viral Cas enzymes could join a growing suite of gene-editing tools being discovered in microbes. Although researchers have discovered other small Cas enzymes in nature, so far many of them are relatively ineffective for genome-editing applications, Doudna says. By contrast, some Casλ viral enzymes combine small size with high efficiency.

In the meantime, the researchers will continue to search microbes for potential improvements to known CRISPR-Cas systems. Makarova expects scientists to also look for CRISPR-Cas systems captured by plasmids–parts of DNA that can be transferred from microbe to microbe.

“Every year we have thousands of new genomes available, some from very distinct environments,” she says. “So it’s going to be really fun.”

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