TU Delft: New CRISPR-Cas system with on-off switch cuts proteins

Researchers from TU Delft in the group of Stan Brouns have discovered a CRISPR-Cas system that cuts proteins instead of DNA. The discovery opens the door to the development of a range of biotechnological and medical applications, for example for sensing RNA molecules in pathogens. Their research was published in Science yesterday.

Researchers have been using CRISPR-Cas to precisely modify DNA for some years now, but bacteria have been using it for billions of years as an immune system against invading viruses. CRISPR-Cas proteins can cut the DNA of viruses and thereby render it harmless. But CRISPR-Cas now appears to go even further than cutting DNA.

“When we discovered CRISPR-Cas, we observed that it cuts viral DNA in precise locations,” explains Brouns. “But the protein had more surprises in store: we later discovered that some variants of CRISPR-Cas can also cut viral RNA. Now CRISPR-Cas goes one step further cutting proteins with high precision.”

Dormancy
Proteins are the organs of a bacterium and perform all kinds of functions to keep the bacterium alive. If important proteins are destroyed when the CRISPR-Cas system cuts them, this can cause the bacterium to go dormant. Dormancy is a kind of hibernation during which viruses can no longer multiply in the bacteria. As no new viruses are created, this is also beneficial to the surrounding bacteria.

“Dormancy is an important defence strategy of bacteria,” explains PhD student Sam van Beljouw, lead author on the article. “But unnecessary dormancy, for example when no virus is present, can be very harmful. We have now discovered that the cutting protein is only activated if it recognises the RNA of the virus. Bacteria therefore only activate the immune system if the virus is present in the cell. We are now trying to find out exactly how the cut proteins cause dormancy.”

Electron microscopy
To obtain a detailed picture of the mechanism in the cutting protein, the researchers studied the process under an electron microscope in collaboration with the American research team of Professor Ailong Ke from Cornell University. “An electron microscope emits a beam of electrons which we can use to very precisely observe the three-dimensional folding of a protein,” explains Van Beljouw. “We were able to observe details smaller than a nanometre in the cutting protein and discovered an ingenious switch that can activate the cutting protein after RNA binding.”

CRISPR sensor for pathogens
Although the research is still in its infancy, this CRISPR-Cas protein could play a future role as a sensor for RNA molecules coming from Covid-19 or other pathogens. The researchers also think they may be able to modify the cutting protein to cut other proteins. “It currently only cuts a very specific bacterial protein, but we expect that we can modify the cutting protein in the lab so that it cuts other proteins,” says Brouns. “We see a promising future for this new CRISPR tool with on-off switch.”