CRISPR tools found in thousands of viruses could boost gene editing

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

A systematic scan of viral genomes has revealed a number of potential CRISPR-based genome 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 released November 23rd at Cell finds CRISPR-Cas systems in 0.4% of publicly available genome sequences from viruses that can infect these microbes. Researchers think 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 were capable of editing plant and mammalian genomes and possess characteristics, such as a 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. “There are many new discoveries here.”

DNA shear defenses

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

Viruses sometimes pick up fragments of their hosts’ genomes, and researchers had previously found isolated examples of CRISPR-Cas in viral genomes. If those stolen DNA fragments give the virus a competitive edge, they could be retained and gradually modified to better serve the viral way of life. For example, a virus that infects bacteria Vibrio cholera uses CRISPR-Cas to cut and disable the DNA in the bacterium that encodes antiviral defenses2.

Molecular biologist Jennifer Doudna and microbiologist Jillian Banfield of the University of California, Berkeley and their colleagues set out 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 around 6,000, including representatives of every known type of CRISPR-Cas system. “The evidence would suggest that these are systems that are useful for phages,” Doudna says.

The team found a wide range of variations on the usual CRISPR-Cas structure, with some systems having no components and others being unusually compact. “Although phage-encoded CRISPR-Cas systems are rare, they are very diverse and widely distributed,” 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 efficient

Viral genomes tended to be compact and some of the viral Cas enzymes were remarkably small. This could offer a particular advantage for genome-editing applications, because smaller enzymes are easier to transport into cells. Doudna and his colleagues focused on a particular group of small Cas enzymes called Casλ and found that some of them could be used to modify the genomes of cells grown in the laboratory from thale cress (Arabidopsis thaliana), wheat, as well as human kidney cells.

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

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

“Every year we have thousands of new genomes becoming available, and some of them come from very distinct backgrounds,” he says. “So it’s going to be really interesting.”

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