Seed, K. | Search bioRxiv

bioRxiv2018

Competition between mobile genetic elements drives optimization of a phage-encoded CRISPR-Cas system: Insights from a natural arms-race

CRISPR-Cas systems function as adaptive immune systems by acquiring nucleotide sequences called spacers that mediate sequence-specific defense against competitors. Uniquely, the phage ICP1 encodes a Type I-F CRISPR-Cas system that is deployed to target and overcome PLE, a mobile genetic element with anti-phage activity in Vibrio cholerae. Here, we exploit the arms race between ICP1 and PLE to examine spacer acquisition and interference under laboratory conditions to reconcile findings from wild populations. Natural ICP1 isolates encode multiple spacers directed against PLE, but we find that single spacers do not equally interfere with PLE mobilization. High-throughput sequencing to assay spacer acquisition reveals that ICP1 can also acquire spacers that target the V. cholerae chromosome. We find that targeting the V. cholerae chromosome proximal to PLE is sufficient to block PLE and propose a model in which indirect chromosomal spacers are able to circumvent PLE by Cas2-3-mediated processive degradation of the V. cholerae chromosome before PLE mobilization. Generally, laboratory acquired spacers are much more diverse than the subset of spacers maintained by ICP1 in nature, showing how evolutionary pressures can constrain CRISPR-Cas targeting in ways that are often not appreciated through in vitro analyses.

microbiology↗

bioRxiv2017

Anti-phage islands force their target phage to directly mediate island excision and spread

To defend against their adversaries, bacteria and phage engage in cycles of adaptation and counter-adaptation that shape their mutual evolution1-3. Vibrio cholerae, the causative agent of the diarrheal disease cholera, is antagonized by phages in the environment as well as in human hosts4,5. The lytic phage ICP1 has been recovered from cholera patient stool and water samples over at least 12 years in Bangladesh6-8 and is consequently considered a persistent predator of epidemic V. cholerae in this region. In previous work, we demonstrated that mobile genetic elements called phage-inducible chromosomal island-like elements (PLEs) protect V. cholerae from ICP1 infection7,9. PLEs initiate their anti-phage response by excising from the chromosome, however, the mechanism and molecular specificity underlying this response are not known. Here, we show that PLE 1 encodes a large serine recombinase, Int, that exploits an ICP1-specific protein, PexA, as a recombination directionality factor (RDF) to sense and excise in response to ICP1 infection. We validate the functionality and specificity of this unique recombination system, in which the recombinase and RDF are encoded in separate genomes. Additionally, we show that PexA is also hijacked to trigger excision in PLEs found in V. cholerae isolates recovered decades ago. Our results uncover an aspect of the molecular specificity underlying the longstanding conflict between a single predatory phage and V. cholerae PLE and contribute to our understanding of the molecular arms race that drives long-term evolution between combatting phage and their bacterial hosts in nature.

microbiology↗