Resurrected 2.6-billion-year-old CRISPR enzymes can still edit cells

Researchers in Spain have resurrected ancient CRISPR proteins from millions and even billions of years ago. Not only can they still edit human cells, but they’re more versatile than modern versions, paving the way for new and improved synthetic CRISPR gene-editing tools.

CRISPR systems evolved in bacteria as a self-defense mechanism. When a bacterium was infected by a virus, it would use CRISPR enzymes to snip off a fragment of the pathogen’s DNA and store it. If the bacterium later encountered that same type of virus, it would recognize it based on the DNA fragment and be able to fight it off more efficiently.

About a decade ago, scientists discovered that they could co-opt this mechanism of recognizing and cutting DNA, and use it to develop a powerful gene-editing tool. The resulting CRISPR-Cas9 system works like a pair of molecular scissors, snipping out sections of DNA from cells and replacing them with new ones. This is showing promise as a powerful tool for treating disease, improving crops and engineering bacteria for intriguing new purposes.

For the new study, researchers at CIC nanoGUNE in Spain set out to chart the evolution of CRISPR in microorganisms. To do so, they used a technique called ancestral sequence reconstruction, where specially designed algorithms are used to analyze and compare the genomes of living organisms, and determine what their common ancestors’ genomes would have looked like.

From this, the team identified and synthesized Cas enzymes that would likely have been used by ancient microorganisms, dating back between 37 million and 2.6 billion years ago. Tests in human cells confirmed that these ancestral enzymes were still functional in making gene edits.

Perhaps unsurprisingly, the ancient enzymes were far simpler than modern ones – a fingerprint of evolution in action. But intriguingly, that could allow them to be more versatile than their descendants, which have become more and more targeted to specific niches.

“Current systems are highly complex and are adapted to function within a bacterium,” said Raúl Pérez-Jiménez, lead researcher on the study. “When the system is used outside this environment, for example in human cells, it is rejected by the immune system and there are also certain molecular restrictions that limit its use. Oddly enough, in ancestral systems some of these restrictions disappear, which gives these systems greater versatility for new applications.”

The team says that this breakthrough could be used to produce new enzymes that target regions of the genome that current ones can’t edit, potentially opening new avenues for disease treatment and other gene-editing advances.

The research was published in the journal Nature Microbiology.

Source: CIC nanoGUNE

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