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CRISPR tools found in thousands of viruses could boost gene editing

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Phages (seen here attacking a bacterial cell) can use the CRISPR-Cas system to compete with each other or manipulate host gene activity.Credit: Biophoto Associates/SPL

A systematic sweep of the viral genome has revealed a mountain of potential CRISPR-based genome-editing tools.

The CRISPR-Cas system is common in the bacterial and archaeal microbial kingdoms and often helps cells fend off viruses.Analysis1 Published on November 23rd at cell From viruses that can infect these organisms, we found the CRISPR-Cas system in 0.4% of the published genome sequences. Researchers believe that viruses may use CRISPR–Cas to compete with each other and further manipulate the host’s genetic activity to their advantage.

Some of these viral systems are capable of editing plant and mammalian genomes and possess useful features in the laboratory, such as compact structures and efficient editing.

“This is an important step in discovering the vast diversity of CRISPR-Cas systems,” says Kira Makarova, a computational biologist at the National Center for Biotechnology Information in Bethesda, Maryland. “There are many new discoveries here.”

DNA break protection

Although best known as a tool used to modify genomes in the laboratory, CRISPR–Cas can function as a rudimentary immune system in natureApproximately 40% of sampled bacteria and 85% of sampled archaea have CRISPR–Cas systems. These microbes can often capture parts of the genome of an invading virus and store the sequences in regions of their genome called CRISPR arrays. The CRISPR array acts as a template to generate RNA that allows CRISPR-associated (Cas) enzymes to cleave the corresponding DNA. This could allow array-carrying microbes to slice the viral genome and stop viral infection.

Viruses can pick up fragments of the host’s genome, and researchers had previously found isolated instances of CRISPR–Cas in viral genomes. If these stolen pieces of DNA give the virus a competitive advantage, they can be retained and gradually modified to better suit the virus’ lifestyle.For example, viruses that infect bacteria Vibrio cholerae Uses CRISPR–Cas to slice and disable bacterial DNA that encodes antiviral defenses2.

Molecular biologist Jennifer Doudna and microbiologist Gillian Banfield (University of California, Berkeley) decided to search more comprehensively for the CRISPR-Cas systems of viruses known as phages and those that infect bacteria and archaea. did. To our surprise, we found about 6,000 of them, including representatives of her CRISPR–Cas system of all known types. “Evidence suggests that these are useful systems for phage,” he says Doudna.

The team found many variations on the normal CRISPR–Cas structure. Some systems are missing components, others are very compact. Anne Chevallereau, who studies phage ecology and evolution at the French National Center for Scientific Research in Paris, said: “Nature is full of surprises.”

small but efficient

Viral genomes tend to be compact and some viral Cas enzymes were very small. This can be particularly advantageous for genome editing applications, as small enzymes are more mobile inside cells. Doudna and her colleagues focused on a specific cluster of her Cas enzymes, called Casλ, and discovered that some of them could be used to edit the genomes of cells grown in Tare’s lab. discovered(Arabidopsis thaliana), wheat, and human kidney cells.

This result suggests that the viral Cas enzyme may bind Growing Collection of Gene-Editing Tools Discovered in MicrobesAlthough the researchers found Other small Cas enzymes Essentially, many of them have so far been relatively inefficient for genome-editing applications, says Doudna. In contrast, some of the viral Casλ enzymes combine small size with high efficiency.

In the meantime, researchers will continue to search microbes for potential improvements to known CRISPR-Cas systems. Makarova anticipates that scientists will also be looking for plasmid-detected CRISPR–Cas systems (segments of DNA that can be transferred from microbe to microbe).

“Every year, thousands of new genomes become available, some of which are from very different environments,” she says. “So it will be really interesting.”

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