CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids

Area of Science:

• Microbiology
• Genetics
• Molecular Biology

Background:

• Prokaryotes utilize CRISPR-Cas systems for adaptive immunity against mobile genetic elements (MGEs).
• CRISPR-Cas loci are also found on MGEs, but their distribution, diversity, and function on plasmids remain largely uncharacterized.
• Understanding these elements is crucial for comprehending microbial evolution and inter-organismal interactions.

Purpose of the Study:

• To systematically analyze CRISPR-Cas loci in a large collection of natural bacterial and archaeal plasmids.
• To determine the distribution, prevalence, diversity, and potential function of plasmid-encoded CRISPR-Cas systems.
• To compare plasmid CRISPR-Cas characteristics with those found on host chromosomes.

Main Methods:

• Curated a comprehensive collection of natural bacterial and archaeal plasmids.
• Performed systematic investigation and analysis of CRISPR-Cas loci across the plasmid collection.
• Analyzed spacer content to infer targeting preferences of plasmid and chromosomal CRISPR-Cas systems.

Main Results:

• CRISPR-Cas loci are widely, though unevenly, distributed across plasmids, with higher prevalence per Mbp compared to chromosomes.
• Plasmid CRISPR arrays show a distinct targeting bias towards other plasmids, unlike chromosomal arrays which target viruses.
• CRISPR-Cas systems are frequent accessory components of plasmids, a previously underestimated phenomenon.

Conclusions:

• CRISPR-Cas systems are integral and common features of many plasmids, not just chromosomal elements.
• The targeting specificity suggests a significant role in mediating plasmid-plasmid conflicts and maintaining plasmid independence.
• The presence of CRISPR-Cas on plasmids may contribute to their dissemination and evolution within microbiomes.