Fig. 5.

Model of primed adaptation in type I-E CRISPR–Cas systems. a Generation of spacer precursors involves coordination between interference and adaptation. Pathway on left depicts direct coordination between interference and adaptation in which Cas1–Cas2 associates with Cas3 as it moves along DNA^12,34. Pathway on right depicts indirect coordination between interference and adaptation in which Cas1–Cas2 captures products of Cas3-mediated DNA degradation^19,23. Both pathways generate spacer precursors containing a 3′-end overhang on the PAM-derived end and blunt PAM-distal end. Model depicts rapid degradation of DNA not selected as a spacer precursor by Cas3 and an unknown nuclease (brown). Binding of prespacers to Cas1–Cas2 prevents prespacer degradation. b Sequential integration of spacer precursors. First, binding of IHF to the leader stimulates integration of the blunt PAM-distal end between the leader and first repeat sequence³⁵. Second, the 3′-overhang present on the PAM-derived end is cleaved by Cas1³⁶ or DnaQ exonucleases^37,38 facilitating integration between the first repeat sequence and first spacer of the array. The order of events depicted results in integration of the spacer precursor in a direct orientation with respect to the PAM (see Fig. 3a)