Mobile element warfare via CRISPR and anti-CRISPR in Pseudomonas aeruginosa

Bacteria deploy multiple defense mechanisms to prevent the invasion of mobile genetic elements (MGEs). CRISPR-Cas systems use RNA-guided nucleases to target MGEs, which in turn produce anti-CRISPR (Acr) proteins that inactivate Cas protein effectors. The minimal component Type I-C CRISPR-Cas subtype is highly prevalent in bacteria, and yet a lack of a tractable in vivo model system has slowed its study, the identification of cognate Acr proteins, and thus our understanding of its true role in nature. Here, we describe MGE-MGE conflict between a mobile Pseudomonas aeruginosa Type I-C CRISPR-Cas system always encoded on pKLC102-like conjugative elements, which are large mobile islands, and seven new Type I-C anti-CRISPRs (AcrIF2*, AcrIC3-IC8) encoded by phages, other mobile islands, and transposons. The P. aeruginosa Type I-C system possesses a total of 300 non-redundant spacers (from 980 spacers total) across the 42 genomes analyzed, predominantly targeting P. aeruginosa phages. Of the seven new Type I-C anti-CRISPRs, all but one are highly acidic, and four have surprisingly broad inhibition activity, blocking multiple distantly related P. aeruginosa Type I CRISPR system subtypes (e.g. I-C and I-F, or I-C and I-E), including AcrIF2 (now, AcrIF2*), a previously described DNA mimic. Anti-type I-C activity of AcrIF2* was far more sensitive to mutagenesis of acidic residues in AcrIF2* than anti-type I-F activity, suggesting distinct binding mechanisms for this highly negatively charged protein. Five of the seven Acr proteins block DNA-binding, while the other two act downstream of DNA-binding, likely by preventing Cas3 recruitment or activity. For one such Cas3 inhibitor (AcrIC3), we identify a novel anti-CRISPR evasion strategy: a cas3-cas8 gene fusion, which also occurs in nature. Collectively, the Type I-C CRISPR spacer diversity and corresponding anti-CRISPR response, all occurring on Pseudomonas MGEs, demonstrates an active co-evolutionary battle between parasitic elements.