Pruning and Tending Immune Memories: Spacer Dynamics in the CRISPR Array

Abstract

CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated genes) is a type of prokaryotic immune system that is unique in its ability to provide sequence-specific adaptive protection, which can be updated in response to new threats. CRISPR-Cas does this by storing fragments of DNA from invading genetic elements in an array interspersed with short repeats. The CRISPR array can be continuously updated through integration of new DNA fragments (termed spacers) at one end, but over time existing spacers become obsolete. To optimize immunity, spacer uptake, residency, and loss must be regulated. This mini-review summarizes what is known about how spacers are organized, maintained, and lost from CRISPR arrays.

Keywords: CRISPR; adaptation; array; repeat; spacer acquisition; spacer deletion.

FIGURE 1

Cartoon diagram of CRISPR array organization and key processes. (A) CRISPR arrays from related strains or isolates were compared; differences in spacer composition illustrated three key characteristics: highest spacer diversity is found at the leader-adjacent end of the array (highlighted in green), missing spacers in the array suggest spacer deletion events, and repeated blocks or repeated individual spacers suggests duplication events. (B) Sequencing showed that the downstream repeat is maintained after an upstream spacer-repeat unit deletion. (C) Example internal repeat (R) and terminal repeat (TR) for a type II-A CRISPR array from Streptococcus thermophilus. The 3′ end (leader distal) has two nucleotide substitutions, which disrupt dyad symmetry at the ends.

FIGURE 2

Cartoon diagram of spacer-repeat duplication and deletion events created by misalignment of the nascent strand during replication. L, leader; TR, terminal repeat, all other repeats depicted in black, spacers depicted in color (orange, yellow, green, aqua).