Scientists have identified a previously unknown gene-editing system found in viruses that may represent the evolutionary precursor to the widely used CRISPR technology. This newly discovered system, named VIPR, is believed to be more than four billion years old and could offer distinct advantages over CRISPR in genetic engineering applications, according to recent research published in the journal Science.
CRISPR, a gene-editing tool that has revolutionized medicine, agriculture, and biotechnology over the past decade, was originally discovered in bacteria and other microbes as a natural defense mechanism against viruses. It consists of proteins and RNA molecules that locate and disable invading viral DNA sequences. However, the origins of this mechanism have remained unclear.
The VIPR system appears to predate CRISPR, based on its molecular structure and function, and it is found within viruses themselves rather than microbial hosts. Researchers say that VIPR’s smaller size makes it potentially easier to deliver into cells for therapeutic uses. Additionally, VIPR can target a broader range of genetic sequences, possibly enabling more extensive genome editing than CRISPR currently allows.
“The incredibly small size of VIPR makes these systems transformative tools for genome engineering,” said Philip Kranzusch, a microbiologist at Harvard University who was not involved in the study. Jennifer Doudna, a co-author of the research and a Nobel laureate recognized for her work on CRISPR, explained that the discovery sheds light on how natural gene-editing systems may have evolved. “It had to come from somewhere,” she said. “Maybe it was being used to do something else before, and maybe there’s still evidence of what it might have been doing.”
The breakthrough came when researchers shifted their focus from examining gene sequences to analyzing the shapes of proteins encoded by those genes. Proteins often retain their structural shape over vast evolutionary timeframes, even when their underlying genetic code undergoes mutations. By screening a database of approximately 2.3 million proteins, the team identified hundreds that resembled CRISPR-associated molecules but were not part of known gene-editing systems in microbes.
This approach allowed the scientists to trace the origins of gene-editing mechanisms back to ancient viral proteins, suggesting that VIPR-like systems could be the ancestral form of CRISPR. Understanding this evolutionary lineage could inform the development of new gene-editing technologies with improved capabilities for research and medical treatment.
The discovery opens new avenues for exploring viral biology and could enhance genome engineering tools by leveraging a naturally occurring system that is both compact and versatile. Further research will be needed to characterize VIPR’s mechanisms in detail and assess its potential applications in biotechnology.