Research Article

Structures of the CRISPR genome integration complex

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Science  15 Sep 2017:
Vol. 357, Issue 6356, pp. 1113-1118
DOI: 10.1126/science.aao0679

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Host factor drives the big bend

Bacteria have a highly adaptable DNA-detecting and -editing machine called CRISPR-Cas to ward off virus attack. The Cas1-Cas2 integrase, with the help of an accessory protein called IHF (integration host factor), captures foreign DNA motifs into bacterial CRISPR loci. These motifs then act as sensors of any further invaders. By analyzing the integrase complex structure, Wright et al. show how Cas1-Cas2 recognizes the CRISPR array for site-specific integration (see the Perspective by Globus and Qimron). IHF sharply bends DNA, which allows DNA to access two active sites within the integrase complex to ensure sequence specificity for the integration reaction. The features of the CRISPR integrase complex may explain the natural divergence of CRISPR arrays in bacteria and can be exploited for genome-tagging applications.

Science, this issue p. 1113; see also p. 1096

Abstract

CRISPR-Cas systems depend on the Cas1-Cas2 integrase to capture and integrate short foreign DNA fragments into the CRISPR locus, enabling adaptation to new viruses. We present crystal structures of Cas1-Cas2 bound to both donor and target DNA in intermediate and product integration complexes, as well as a cryo–electron microscopy structure of the full CRISPR locus integration complex, including the accessory protein IHF (integration host factor). The structures show unexpectedly that indirect sequence recognition dictates integration site selection by favoring deformation of the repeat and the flanking sequences. IHF binding bends the DNA sharply, bringing an upstream recognition motif into contact with Cas1 to increase both the specificity and efficiency of integration. These results explain how the Cas1-Cas2 CRISPR integrase recognizes a sequence-dependent DNA structure to ensure site-selective CRISPR array expansion during the initial step of bacterial adaptive immunity.

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