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

Abstract

Type IV-A CRISPR-Cas systems are primarily encoded on plasmids and form multi-subunit ribonucleoprotein complexes with unknown biological functions. In contrast to other CRISPR-Cas types, they lack the archetypical CRISPR acquisition module and encode a DinG helicase instead of a nuclease component. Type IV-A3 systems are carried by large conjugative plasmids that often harbor multiple antibiotic-resistance genes. Although their CRISPR array contents suggest a role in inter-plasmid conflicts, this function and the underlying mechanisms have remained unexplored. Here, we demonstrate that a plasmid-encoded type IV-A3 CRISPR-Cas system co-opts the type I-E adaptation machinery from its clinicalKlebsiella pneumoniaehost to update its CRISPR array. Furthermore, we demonstrate that robust interference of conjugative plasmids and phages is elicited through CRISPR RNA-dependent transcriptional repression. By targeting plasmid core functions, type IV-A3 can prevent the uptake of incoming plasmids, limit their horizontal transfer, and destabilize co-residing plasmids, altogether supporting type IV-A3's involvement in plasmid competition. Collectively, our findings shed light on the molecular mechanisms and ecological function of type IV-A3 systems and have broad implications for understanding and countering the spread of antibiotic resistance in clinically relevant strains.

An intron endonuclease facilitates interference competition between coinfecting viruses

“…In addition, regardless of sequence divergence, any conditions that physically separate two intracellular genomes but allow mixing of their encoded proteins present the potential to involve homing endonuclease–mediated interference competition if one of the genomes acquires a homing endonuclease. The relative fitness advantage we observed that is provided by a weaponized homing endonuclease could influence any intracellular genetic competition, including those arising between plasmids ( 50 ), viruses, and hosts.…”

A mobile intron facilitates interference competition between co-infecting viruses

“…This mechanism is especially important in the evolution of viruses due to their constant competition through co-infection 51,52 and rapid rates of viral replication where even small selective advantages are quickly amplified over time. More broadly, this new understanding of the fitness advantage provided by weaponized mobile introns could come into play under the right circumstances for any intracellular genetic competition, including between plasmids 62 , viruses, and hosts.…”

Bacteriophages suppress CRISPR–Cas immunity using RNA-based anti-CRISPRs

“…A growing body of work highlights the frequent co-option of CRISPR-Cas systems and their components by diverse MGEs 4 . Some specific CRISPR-Cas associations with MGEs have been characterized in detail, including crRNA-guided transposition 11,12 , transcriptional repression 13 and inter-viral 14 and inter-plasmid 15,16 conflicts, but others are poorly understood. An intriguing case is the bioinformatic identification in viral genomes of solitary repeat units (SRUs), which are often immediately downstream of a predicted promoter and not associated with cas genes 4 .…”