Disassembling CRISPR piece by piece

A team of researchers led by Alan Davidson at the University of Toronto have discovered a small protein that can disassemble a stable bacterial CRISPR-Cas7 complex without using adenosine triphosphateor another apparent energy source (Nature 2024, DOI: 10.1038/s41586-024-07642-3). The protein, dubbed AcrIF25, comes from a bacteriophage, and the CRISPR-Cas7 complex it attacks comes from the bacterium Pseudomonas aeruginosa. A team led by Yanli Wang of the Chinese Academy of Sciences solved the structure of the protein.

Anti-CRISPR proteins were first characterized by Joseph Bondy-Denomy in a paper published in 2012, when he was a doctoral student in Davidson’s lab (Nature, 2012 DOI:10.1038/nature11723). Bondy-Denomy, who now leads his own lab at the University of California, San Francisco, says that just as bacteria evolved CRISPR as a way to combat bacteriophages, so phages developed ways to thwart CRISPR.

This “arms race” for survival plays out very quickly, because bacteria and phages change at a much faster clip than most eukaryotes do. “If you wanted to figure out new ways that have evolved in nature for one thing to inhibit another thing, looking at the CRISPR and anti-CRISPR arms race is a great place to look for that sort of mechanistic novelty, and that’s exactly what they’ve uncovered here,” Bondy-Denomy says.

The mechanistic novelty lies in how this anti-CRISPR protein functions. Rather than interfere directly with the CRISPR complex as it binds or cuts DNA. AcrIF25 takes advantage of the structure of the CRISPR complex, which is partially composed of six identical Cas7 monomers connected in a curved row. First, AcrIF25 binds to a vulnerable region on one of these monomers. It then peels that monomer away from the complex, making the next one exposed to another AcrIF25 peeling it away, continuing—until the complex is fully disassembled, all without a discernible external energy source powering the process.

Davidson says it’s like someone trying to destroy a conga line by jumping on a dancer’s back: Those in the middle are initially protected from being attacked, but the last person’s back isn’t covered. The disruptor could jump on that dancer’s back, separate them from the line, and continue jumping on people until no one’s left.

While anti-CRISPRs have shown potential in curbing rogue gene editing, Davidson and Bondy-Denomy say that this finding has broader implications because it could be a new, nonenzymatic mechanism to unravel big biological complexes. “When you have a stable complex and you’re pulling a protein out of it, you would think you have to have some mechanism to do it, some energy or something,” Davidson says. But AcrIF25 shows that a protein may not need enzymatic activity to do the job, it may simply take joining the conga line at the right time.