CRISPR tools found in thousands of viruses could boost gene editing

CRISPR tools found in thousands of viruses could boost gene editing

Colored transmission electron micrograph (TEM) of T2 bacteriophages attached to a bacterial cell wall fragment.

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 wealth 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 published on November 23 in Cell finds CRISPR-Cas systems in 0.4% of publicly available genomic sequences from viruses that can infect these microbes. Researchers believe viruses use CRISPR-Cas to compete with each other — and potentially also to manipulate gene activity in their host to their advantage.

Some of these viral systems were able to edit 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 uncovering 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 a lot of new discoveries here.”

Tusks cutting DNA

Although best known as a tool used to edit genomes in the lab, CRISPR-Cas may function in nature like a rudimentary immune system. About 40% of sampled bacteria and 85% of sampled archaea have CRISPR-Cas systems. Often these microbes can capture pieces of an invading virus’ genome and store the sequences in a region of their own genome called the CRISPR matrix. The CRISPR chips then serve as templates to generate RNAs that direct CRISPR-associated enzymes (Cas) to cut the corresponding DNA. This can allow network-carrying microbes to cut out the viral genome and potentially stop viral infections.

Viruses sometimes pick up snippets of their hosts’ genomes, and researchers had previously found isolated examples of CRISPR-Cas in viral genomes. If these stolen pieces of DNA give the virus a competitive edge, they could be kept and gradually modified to better serve the viral lifestyle. For example, a virus that infects bacteria Vibrio cholera uses CRISPR-Cas to cut and deactivate the bacteria’s DNA that codes for antiviral defenses2.

Molecular biologist Jennifer Doudna and microbiologist Jillian Banfield of the University of California at Berkeley and their colleagues decided to do a deeper search for CRISPR-Cas systems in viruses that infect bacteria and archaea, called 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 useful phage systems,” says Doudna.

The team found a wide range of variations on the usual CRISPR-Cas structure, with some systems lacking components and others unusually compact. “Even though phage-encoded CRISPR-Cas systems are rare, they are highly diverse and widely distributed,” says Anne Chevallereau, who studies phage ecology and evolution at the Center National de la Recherche Scientifique in Paris. “Nature is full of surprises.”

Small but effective

Viral genomes tend to be compact, and some of the viral Cas enzymes were remarkably small. This could offer a particular advantage for genome-editing applications, as 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 edit the genomes of cells cultured in the laboratory from Thale’s watercress (Arabidopsis thaliana), wheat, and human kidney cells.

The results suggest that viral Cas enzymes could join a growing collection of gene-editing tools discovered in microbes. Although researchers have discovered 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 search for microbes for potential improvements to known CRISPR-Cas systems. Makarova predicts that scientists will also be looking for CRISPR-Cas systems that have been picked up by plasmids – pieces of DNA that can be transferred from one microbe to another.

“Every year, thousands of new genomes become available, and some of them come from very distinct environments,” she says. “So it’s going to be really interesting.”

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