Dynamics of the CRISPR array

The CRISPR pathway creates an array of stored sequences in the genome called the CRISPR array. The CRISPR array is comprised of contiguous DNA sequences, called spacers, separated by a common repeat sequence. These spacers enable microbes to degrade targeted DNA sequences that match a given spacer sequence. CRISPR arrays identified in sequenced bacterial genomes range in length from tens to hundreds of spacer sequences. Although prior studies have noted changes in the array length, the detailed dynamics of the CRISPR array have not been examined. We used a combination of experiments and theory to understand how the Cas proteins, the genomic content of a cell, and other aspects of the cellular context interact to set the size and sequence of the CRISPR array. This work focused on Type 1E CRISPR/Cas system expressed from synthetic constructs in Escherichia coli. Specifically, we measured the expansion of the CRISPR array over time for a range of biological contexts, establishing how the evolution of the array is modulated by biological parameters. The relationship between the array expansion rate and fitness were quantified in the context of phage infection. A quantitative model of CRISPR array content and dynamics will aid the development of many future applications that utilize the CRISPR arrays for genome editing and may elucidate how CRISPR shapes genome evolution.