Anti-CRISPR Proteins from Prophages Discovered in Proteobacterial Genomes

Researchers from the University of Toronto and the University of Otago have discovered five new proteins that block the bacterial CRISPR/Cas immune system. The anti-CRISPR proteins are encoded in genes belonging to bacteriophage sequences inserted in the bacterial genome. The new findings, published in the journal Nature Microbiology, enlarge the list of known anti-CRISPR systems.

CRISPR/Cas is a bacterial immune system that has been recently adapted as genomic editing tool. CRISPR cuts fragments of alien DNA and incorporates them in CRISPR loci. CRISPR transcripts (crRNA) bind and guide Cas endonucleases to cut genomic DNA complementary to crRNA. Researchers Doudna and Charpentier co-opted the system by altering the guide RNA sequence at will, matching it to the desired genomic target.

Previous studies by Davidson’s team found that nine proteins encoded in prophage DNA sequences integrated in Pseudomonas aeruginosa’s genome had anti-CRISPR activity. For the next study, the researchers decided to look for regions encoding anti-CRISPR proteins in the Proteobacteria phylum.

A way to modulate CRISPR-based genome editing?

Davidson and his collaborators analyzed several Proteobacteria species, looking for regions homologous to a transcriptional regulator always present upstream the anti-CRISPR genes they had discovered. Next, they cloned the putative anti-CRISPR genes in plasmids that were introduced in Proteobacteria, and tested their capacity to support phage replication in the presence of CRISPR systems targeting the phage. With this experiment, the researchers found five anti-CRISPR proteins: four worked against CRISPR type I-F, and one against both I-F and I-E types.

The seemingly vast amount of anti-CRISPR proteins indicates that these are very important for phage survival and replication, and that CRISPR is a very effective immune system. The emergence of these proteins can be easily explained in the context of the arms race that always happens in host-parasite interactions. The discovery will probably have practical consequences in genome editing: anti-CRISPR proteins could be adapted as CRISPR-mediated editing modulators.