Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans

Plasmid-encoded type IV-A CRISPR-Cas systems lack an acquisition module,
feature a DinG helicase instead of a nuclease, and form ribonucleoprotein
complexes. Type IV-A3 systems are carried by conjugative plasmids that
often harbor antibiotic resistance genes. Their CRISPR array contents
suggest a role in inter-plasmid conflicts, but this function remains
unexplored. Here, we demonstrate that a plasmid-encoded type IV-A3 system
co-opts the type I-E adaptation machinery from its host, Klebsiella
pneumoniae, to update its CRISPR array. Furthermore, we reveal that robust
interference of conjugative plasmids and phages is elicited through CRISPR
RNA-dependent transcriptional repression. By silencing plasmid core
functions, type IV-A3 impacts the horizontal transfer and stability of
targeted plasmids, supporting its role in plasmid competition. Our
findings shed light on the mechanisms and ecological function of type
IV-A3 systems and demonstrate their practical efficacy for countering
antibiotic resistance in clinically relevant strains.