An ancient viral system sheds light on the origins of CRISPR

The discovery of a new gene-targeting system used by viruses to fend off competitors gives a glimpse into the possible evolutionary origin of CRISPR, and may offer new opportunities for genome editing technologies.

Across two papers published in Science, researchers at the Innovative Genome Institute at UC Berkeley, California, report having identified a new strategy for viral adaptive immunity, termed the viral interference programmable repeat (VIPR) system. Using a combination of molecular biology and artificial intelligence (AI), the authors demonstrated how VIPR silences the DNA of other viruses, and how it may have contributed to the evolution of the CRISPR system used by bacteria to defend themselves against viral threats.

The research was led by Jennifer Doudna, professor of biochemistry, biophysics, and structural biology at UC Berkeley, who highlighted how this work, which could transform genome editing methods, is 'a great reminder of how complex biology is, and how little we still know … Fundamental concepts are still out there to be discovered. I think that's wonderful.'

Professor Doudna received the Nobel Prize in 2020 for her role in developing CRISPR/Cas9 genome editing technologies (see BioNews 1067). CRISPR systems are used by bacteria to fight against viruses. At a basic level, they work as a two-step system: tailored RNA molecules are an exact match for specific segments of target viral DNA, allowing dedicated proteins to then recognise and cut these sequences. Over the past decade or so, researchers have repurposed these systems for genome editing purposes.

VIPR systems also aim to deactivate target viral DNA sequences, yet through a distinct mechanism: rather than shredding the genome of a target virus, VIPR uses RNA to wrap around these sequences, making them inaccessible for transcription and effectively silencing them.

The researchers suggest that VIPR systems allow viruses to engage in a type of viral warfare: 'The viruses that are encoding these VIPR systems are targeting related viruses, often viruses that infect the same host, so it’s part of viral competition,' said Dr Peter Yoon, a co-first author on the studies who now works for Anthropic.

They also propose that VIPR systems, which appear to be over four billion years old, could represent an ancient viral system that contributed to the evolution of CRISPR systems.

To discover VIPR systems, the team focused on the proteins encoded by CRISPR genes, attempting to find older, related proteins outside of bacterial organisms. To do so, they used an AI method which would compare proteins based on their shape instead of their sequence, as the passing of time would offer more chances for the sequence to change, without affecting the shape and function of the protein.

The approach revealed the existence of a CRISPR-like protein in viruses, which was also paired with an RNA molecule. Confusingly, however, these RNA sequences did not match the viral DNA they were targeting, a significant departure from CRISPR systems. An AI language model was then developed to decipher how VIPR RNA could still target specific regions, revealing a unique pattern.

'I reasoned that if a genomic language model has been trained on enough of these sequences, it should have an idea of how to generate one of its own', said Kenneth Loi, a PhD student who contributed to both studies.

The language model showed that unlike CRISPR RNA, which requires a consecutive, exact match, VIPR RNA would match to DNA in sets of three, relying on exact matches for the first two bases whilst allowing the third to differ. This flexibility is important for targeting viral DNA, due to its tendency to mutate quickly.

'No known system does this, and this provides a very clear evolutionary rationale', says Dr Yoon. 'This is a mechanism that intentionally masks out the parts of the code that are likely to change. It's a de-noising algorithm. It makes it very difficult for the targeted virus to evolve out of danger.'

Understanding VIPR systems many offer advantages for gene silencing, including its smaller size, making it easier to deliver into cells, and its apparent ability to be programmed to target sites across the genome.

Additionally, given the long evolutionary trajectory of CRISPR systems, VIPR also points towards other systems in nature which may be used for genome editing.

Dr Rafael Pinilla-Redondo, a virologist at the University of Copenhagen who was not involved in the studies, commented to the New York Times: 'I would be very surprised if VIPR were the last unexpected targeting system we discover.'