By analyzing microbial genomes, researchers have found what may be evolutionary ancestors of the Cas9 enzyme that snips out bits of DNA during CRISPR genome editing, according to a study published last week in Science.
According to Nature, the role of the microbial IscB protein family was unknown prior to the analysis, although IscB genes can be found in bacteria, archaea, and even inside algal chloroplasts. The researchers found that IscB genes sit near stretches of the genome coding for RNA molecules that guide the IscB protein to specific regions of DNA that it can cleave, similar to the guide RNA Cas9 uses to find its genetic target.
The bacteria-based CRISPR-Cas9 system was first proposed as a gene-editing tool by Jennifer Doudna and Emmanuelle Charpentier, who won the 2020 Nobel Prize in Chemistry for their work. Although scientists think it originated as a defense system against viral nucleic acids, the technology has exploded into multiple applications for research and human health, including diagnostics and possibly gene therapy.
Because algae are eukaryotic organisms, MIT molecular biologist and lead author Feng Zhang tells Nature that after being asked many times if he’s seen CRISPR activity in a eukaryotic cell, now he can finally say yes.
“We are super excited about the discovery of these widespread programmable enzymes, which have been hiding under our noses all along,” Zhang says in a press release by MIT’s McGovern Institute. “These results suggest the tantalizing possibility that there are many more programmable systems that await discovery and development as useful technologies.”
Zhang’s group also identified another protein family called TnpB that cuts specific regions of DNA when guided by RNA. They write in the paper that TnpB may be the genetic ancestor of the Cas12 enzyme.
The study authors classified TnpB, IscB, and an additional family called IsrB proteins as Obligate Mobile Element Guided Activity (OMEGAs), because the genes are found in “jumping gene” elements called transposons. The researchers dubbed RNA sequences that guide these proteins omega-RNA.
The team showed that IscB proteins can snip human DNA, and while this cutting was less effective than CRISPR-Cas9’s, Zhang says he thinks the process could be optimized. He says the protein’s diminutive size (30 percent smaller than Cas9, according to the McGovern Institute) may be useful in certain applications.
In total, the group’s genomic database searching returned more than one million genes that could code for TnpB-type proteins, coauthor Soumya Kannan tells Nature. “These programmable proteins are very useful, beyond basic biological interest,” Zhang tells the magazine. “And this mechanism of RNA-guided DNA recognition is likely something that nature has created independently multiple times.”
Australian National University in Canberra geneticist Gaetan Burgio, who was not among the paper’s authors, tells Nature that the discovery is “absolutely fascinating. It fills an important gap: we didn’t really know how these CRISPR systems became CRISPR.”