McGovern Fellows Jonathan Gootenberg (left), and Omar Abudayyeh (right) in their laboratory. Credit: Caitlin Curnningham
Researchers from MIT's McGovern Institute for Brain Research discovered a bacterial enzyme. This could allow scientists to expand their CRISPR toolkit. It would make it possible to edit RNA with precision that was previously only available for DNA editing. Cas7-11 modifies RNA targets and does not harm cells. This suggests that it is a useful research tool as well as a platform for therapeutic applications.
Omar Abudayyeh McGovern Fellow, says that the new enzyme is similar to the Cas9 enzyme of RNA. He refers to the DNA-cutting enzyme CRISPR, which has revolutionized biology by making DNA editing quick, cheap, and precise. He adds that it creates precise cuts and doesn’t damage the cell during the process, unlike other enzymes.
Cas13 is the only other family of RNA-targeting enzymes that has been extensively developed for RNA targeting purposes. Cas13 destroys all RNAs within the cell when it recognizes its target and causes the cell to die. Cas7-11, like Cas9 is part of a programmable program. It can be directed to specific RNA targets with a CRISPR guide. Through a deep examination of CRISPR systems in the microbial environment, Abudayyeh and Jonathan Gootenberg (McGovern Fellow), discovered Cas7-11. Recent research in Nature published their findings.
Exploring nature's diversity
Cas7-11, like other CRISPR proteins is used by bacteria to protect themselves against viruses. CRISPR-enabled bacteria keep track of any new viruses they encounter. This is done by keeping a small amount of the pathogen's genetic material. The CRISPR system activates if the virus returns. It is guided by a small amount of RNA and used to kill the virus's genome and eradicate the infection.
These ancient immune systems are diverse and widespread, with different bacteria using different proteins to combat viral invaders.
"Some target DNA, others target RNA. Some have some toxicities, while others are more efficient at cleaving the target. They can introduce different types and they can vary in specificity," Eugene Koonin (an evolutionary biologist at National Center for Biotechnology Information) says.
Abudayyeh and Gootenberg have been studying genome sequences in order to discover more about CRISPR systems' natural diversity. They also plan to use these sequences as tools. Abudayyeh explains that the idea is to use the evolutionary work in engineering protein machines.
Abudayyeh states, "We don’t know what we’ll find," but "let’s just explore and discover what’s out there."
While the team was looking through public databases for information on the components of various bacterial defense systems they discovered a protein that had been isolated in Tokyo Bay. The amino acid sequence of the protein indicated it belonged in a CRISPR system that uses large multiprotein machines to locate and cleave targets. This protein seemed to be able to do the job by itself. Koonin states that Cas7-11 is a single-protein Cas enzyme, which includes the Cas9 protein, widely used for DNA editing.
Cas7-11 was named by the team. Single proteins are easier to deliver and provide better tools than complex counterparts. Its composition also revealed an unexpected evolutionary history. The evidence showed that the components of a more complicated Cas machine had merged together to create the Cas7-11 protein. Gootenberg compares it to finding a bat after you assumed only birds could fly. This is a way of acknowledging that there are many evolutionary paths to flying. He says, "It completely changes the landscape of what these systems are considered functionally and evolutionaryarily."
Precision editing
Gootenberg, Abudayyeh and others created the Cas7-11 enzyme in their laboratory and began to experiment with it. They discovered that this unique enzyme was a powerful tool for manipulating and studying RNA. It was able to make precise cuts when they put it in cells with an RNA guide. While it snipped its targets, it left the rest of the RNA unaffected. Cas7-11 could be used to modify specific letters of the RNA code and correct genetic mutations. Cas7-11 could also be programmed to alter the levels of proteins encoded in RNA molecules within cells.
Abudayyeh, Gootenberg found that Cas7-11 could also cut RNA by using a protein that was likely to trigger programmed cell death. This suggests a link between CRISPR defenses and an extreme response to infection.
They demonstrated that cells can be delivered the entire Cas7-11 editing system via a gene therapy vector. This did not harm cells' health. The team hopes that the enzyme will be used in the future to remove disease-causing sequences from a patient's DNA and allow them to produce healthy proteins or reduce the amount of harmful genes.
Gootenberg states that Cas7-11 cuts in a unique way, which allows for many different applications. He also points out that no other CRISPR tool can cut RNA as precisely. He adds, "It's another great example of how basic-biology driven investigations can yield new tools to treat and diagnose." "And we are still only scratching the surface of all that's possible in natural diversity."
Learn more about the New CRISPR/Cas system that cuts virus RNA
Further information: Ahsen Zcan et. al., ProgrammableRNA targeting with single-protein CRISPR factor Cas7-11 Nature (2021). Information from Nature Ahsen Zcan et. al., ProgrammableRNA targeting with single-protein CRISPR factor Cas7-11. Journal (2021). DOI: 10.1038/s41586-021-03886-5
