High Frequency of Dynamic Rearrangements In Crispr loci

Abstract

CRISPR-Cas immunization of prokaryotes proceeds by the acquisition of short fragments of invading DNA and integrating them into specific positions within the host genome in a process called adaptation. Adaptation is thought to be polarised, which suggests that CRISPR array spacer order reflects the recentness of the infection. The detailed processes through which CRISPR loci arise, and how they evolve are not completely clear. In this study, we collected 12,461 prokaryotic genomes, and using a combination of four different approaches and a series of conservative filters, we identified CRISPR arrays in 82.7% of Archaea and 40.6% of Bacteria. To understand spacer evolution in these CRISPR loci we firstly tracked point mutations in CRISPR repeats, and secondly, we carried out a comparative analysis of arrays that share multiple similar spacers. Both results indicate that CRISPR arrays are frequently dynamically rearranged. These findings are at odds with a model that suggests that spacer order is likely to reflect the recentness of infection. We conclude that the order of spacers in a CRISPR array, as well as the spacer content of the array, is likely to arise from a combination of events, such as insertion in the middle of the array, recombination within or between arrays, or Horizontal transfer of all or part of an array. We suggest these rearrangements are favoured by natural selection in complex and dynamic environments.

EndogenousStaphylococcus aureusCRISPR-cassystem limits phage proliferation and efficiently excises from the genome as part of the SCCmeccassette

“…Inspection of the CRISPR arrays revealed conserved spacers at the 5' end of the array and curiously, CRISPR array 1 mainly differed at the center of the array. This supports recent findings that the order of spacers in CRISPR arrays may arise from a combination of events, including middle-array insertion, recombination within or between arrays and horizontal transfer of all or part of the array [37]. As spacer adaptation via Cas1 and Cas2 has been observed only with overexpression in an inducible setting [38], the type III-A system could rely on alternative mechanisms to adapt new spacers such as recombination between CRISPR spacers and their cognate protospacer [39] or from integration and excision of temperate phages [40].…”

An Endogenous Staphylococcus aureus CRISPR-Cas System Limits Phage Proliferation and Is Efficiently Excised from the Genome as Part of the SCC mec Cassette

“…Inspection of the ST630 CRISPR arrays revealed conserved spacers at the 5′ end of the array, and curiously, CRISPR array 1 mainly differed at the center of the array. This supports recent findings that the order of spacers in CRISPR arrays may arise from a combination of events, including middle-array insertion, recombination within or between arrays, and horizontal transfer of all or part of the array ( 39 ). As spacer adaptation via Cas1 and Cas2 in Staphylococcus has been observed only with overexpression in an inducible setting ( 40 ), the type III-A system could rely on alternative mechanisms to adapt new spacers, such as recombination between CRISPR spacers and their cognate protospacer ( 41 ) or integration and excision of temperate phages ( 42 ).…”

Analysis of CRISPR/Cas Genetic Structure, Spacer Content and Molecular Epidemiology in Brazilian Acinetobacter baumannii Clinical Isolates

“…This very nature of spacer acquisition in CRISPR loci makes it an interesting tool for molecular typing of strains [38]. Even though rearrangements can occur [39] and appear to be quite frequent in A. baumannii, as our results indicate, strains with similar sets of spacers are more likely to be genetically related, as we observed in the spacer-typing dendrogram and confirmed with the core-SNP tree. The CRISPR/Cas control strain A. baumannii AYE has a ST1 profile (CC1), and even though it is more distantly placed in the phylogenetic tree previously elaborated [23], the leader sequences from both CCs were identical, and two spacers were shared, suggesting some level of conservation between these CCs.…”