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Virus-derived CRISPR systems may be added to the gene-editing toolbox

The CRISPR-Cas9 system revolutionised genome editing approaches. Recent work on the CRISPR gene editing technology won the 2020 Nobel Prize in Chemistry. Researchers, led by Professor Jennifer Doudna, who shared the Nobel Prize with Professor Emmanuelle Charpentier, have identified over 6000 CRISPR-encoding viruses. The study, published in Cell, highlighted the potential use of virus-derived CRISPR machinery in new gene-editing approaches.

Bacteriophages pull the UNO reverse card

The CRISPR-Cas9 system was first identified as a bacterial defence mechanism against invading viruses. Bacteria-invading viruses, called bacteriophages (or phages), insert their DNA into bacteria. As a defence mechanism, bacteria make two strands of RNA, one of which matches a part of the viral genome. The two RNA strands form a complex with Cas9, which is a nuclease enzyme that cuts DNA. The matching sequence, called the guide RNA, targets the viral DNA and directs the enzyme to ‘cut’ the genome. This disables the virus. The CRISPR-Cas9 system has been engineered to target any DNA sequence by changing the sequence of the guide RNA.

It is rare to find CRISPR-Cas systems in phage genomes. A few phages have previously been identified as encoding parts of the CRISPR system. However, they were just noted as “curiosities,” said Professor Doudna. “But they got us wondering if these systems were more common.”

Professor Doudna and colleagues at the University of California used a metagenomic approach to search for examples of virus-derived CRISPR systems.

The researchers first obtained microbial samples from bacteria-rich environments including the soil, water, humans and animals. Using genome-resolved metagenomic analysis, the samples were probed to identify phage-encoded CRISPR-Cas systems. The researchers identified around 6000 CRISPR-Cas system encoding phages. The systems belonged to every known CRISPR-Cas type that has been identified so far (in bacteria-encoded samples).

A new gene-editing tool

The researchers focused on a unique family of Cas enzymes called the Cas-lambda family. They investigated the utility of this enzyme as a new genome editing tool. The researchers found that Cas-lambda was around 50% smaller than Cas9, which current CRISPR approaches rely on. The enzyme was able to form an RNA-guided DNA recognition complex (figure 1).

Figure 1: Cryoelectron microscopy map of Cas-lambda complexed with the guide RNA and DNA. The target strand is shown in cyan and the non-target strand is shown in magenta. Source: Published in Cell.

The small size and high efficiency of this enzyme may open up new gene-editing applications for CRISPR. The researchers showed that Cas-lambda could be used to edit the genomes of plant (wheat) and mammalian (kidney) genomes.

The battle of the phages

The study also addressed why viruses encode anti-viral mechanisms. “Evidence would suggest that these are systems that are useful to phages,” said Professor Doudna.

The researchers speculated that this was because viruses compete against each other and bacterial plasmids for replication machinery within the host. The phages armed with a CRISPR-Cas system have the advantage of ‘slicing’ the genomes of their competitors.

Professor Doudna said, “By destroying these rivals with the CRISPR system, phages can have the replication machinery all to themselves.”