CRISPR tools found in thousands of viruses could boost gene editing

CRISPR tools found in thousands of viruses could boost gene editing

CRISPR tools found in thousands of viruses could boost gene editing

Phages (seen here attacking a bacterial cell) can use CRISPR-Cas systems to compete with each other – or to manipulate gene activity in their hosts.Credit: Biophoto Associates/SPL

A systematic review of viral genomes has revealed a wealth 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 fight off viruses. But the analysis1 published on November 23 Cell finds CRISPR-Cas systems in 0.4% of publicly available genome sequences of viruses that can infect these microbes. Researchers think viruses use CRISPR-Cas to compete with each other — and potentially to manipulate gene activity in their host to their advantage.

Some of these viral systems have been able to edit the genomes of plants and mammals, 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 revealing the enormous diversity of the CRISPR-Cas system,” says computational biologist Kira Makarova of the US National Center for Biotechnology Information in Bethesda, Maryland. “Many novelties have been discovered here.”

DNA cutting defense

Although 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 sampled bacteria and 85% of the sampled archaea have the CRISPR-Cas system. Often, these microbes can capture parts of the genome of an attacking 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-associated enzymes (Cas) to cut the corresponding DNA. This may allow microbes carrying the sequence to disassemble the viral genome and potentially stop viral infections.

Viruses sometimes pick up bits 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 could be retained and gradually modified to better serve the viral lifestyle. For example, a virus that infects a bacterium Vibrio cholera uses CRISPR-Cas to cut and disable the DNA in 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 perform a more comprehensive search for the CRISPR-Cas system in viruses that infect bacteria and archaea, known as phages. To their surprise, they found about 6,000 of them, including representatives of all known types of CRISPR-Cas systems. “Evidence suggests that these are systems that are beneficial to phages,” says Doudna.

The team found a wide range of variations on the common 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 Chevallereau, 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 were extremely small. This could offer a particular advantage for genome editing applications, as smaller enzymes are 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 laboratory-grown thale cress cells (Arabidopsis thaliana), wheat, as well as human kidney cells.

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

In the meantime, researchers will continue to look to microbes for potential improvements to known CRISPR-Cas systems. Makarova predicts that scientists will also look for CRISPR-Cas systems picked up 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.”

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