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Pulling the Plug on Viral Infections: CRISPR isn’t Just About Cutting

Thursday, April 27, 2023

Study shows how a Cas protein partners with a unique membrane protein to stop viral infection

CRISPR claimed scientific fame for its ability to quickly and accurately edit genes. But, at the core, CRISPR systems are immune systems that help bacteria protect themselves from viruses by targeting and destroying viral DNA and RNA. A new study published in Science reveals a previously unrecognized player in one such system – a membrane protein that enhances anti-viral defense – simultaneously broadening our understanding of and raising more questions related to the complexities of CRISPR.

Uncovering New Clues about CRISPR

CRISPR systems consist of two major components – a guide RNA that targets a specific viral DNA or RNA sequence and a Cas enzyme that cuts the targeted DNA or RNA, preventing a virus from replicating and spreading. A team at the University of Rochester Center for RNA Biology found that a specific Cas protein (Cas13b) not only cuts viral RNA, but communicates with another protein (Csx28) to augment its anti-viral defense.

In partnership with scientists at Cornell, the team discovered that the Csx28 protein forms a pore-like structure (i.e. it has a big hole in it). When they infected E. coli with a phage (virus that attacks bacteria) and deployed the CRISPR-Cas13 system to target and halt infection, they found that Cas13 signals to Csx28 to affect membrane permeability. Once this happens, Csx28 wreaks havoc in the infected cell, discombobulating membrane potential, crushing metabolism and hindering energy production. A virus can’t replicate under such unhospitable circumstances, leading to the team’s conclusion that Csx28 enhances CRISPR-Cas13b’s phage defense.

“This finding upends the idea that CRISPR systems mount their defense only by degrading RNA and DNA in cells and really broadens our view of how CRISPR systems may be working,” said corresponding author Mitchell O’Connell, PhD, assistant professor of Biochemistry and Biophysics at the University of Rochester Medical Center (URMC) and a member of the UR Center for RNA Biology. “When we think about CRISPR, we see Cas proteins such as Cas9 or Cas13 as the big hammer doing all the damage, but that might not be the case; we found that Cas13 and Csx28 are working together to effectively extinguish a virus.”

“When you read this paper you think to yourself…‘what?’ This is such a weird mechanism and not the way I would have predicted that bacteria would work,” added John Lueck, PhD, assistant professor of Pharmacology and Physiology at URMC. “It is really impressive that the team identified this pore-like protein that doesn’t resemble anything else we’ve seen before, and now that we know that this mechanism exists people will start to look for it in other systems. This is exciting because in science, when you scratch the surface, you often find that there is an entirely new world behind it.”