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Nature. 2015 Nov 26;527(7579):535-8. doi: 10.1038/nature15760. Epub 2015 Oct 21.

Foreign DNA capture during CRISPR-Cas adaptive immunity.

Author information

1
Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA.
2
Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California 94720, USA.
3
Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.
4
Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA.
5
Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA.
6
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
7
Innovative Genomics Initiative, University of California, Berkeley, Berkeley, California 94720, USA.
8
Center for RNA Systems Biology, University of California, Berkeley, Berkeley, California 94720, USA.

Abstract

Bacteria and archaea generate adaptive immunity against phages and plasmids by integrating foreign DNA of specific 30-40-base-pair lengths into clustered regularly interspaced short palindromic repeat (CRISPR) loci as spacer segments. The universally conserved Cas1-Cas2 integrase complex catalyses spacer acquisition using a direct nucleophilic integration mechanism similar to retroviral integrases and transposases. How the Cas1-Cas2 complex selects foreign DNA substrates for integration remains unknown. Here we present X-ray crystal structures of the Escherichia coli Cas1-Cas2 complex bound to cognate 33-nucleotide protospacer DNA substrates. The protein complex creates a curved binding surface spanning the length of the DNA and splays the ends of the protospacer to allow each terminal nucleophilic 3'-OH to enter a channel leading into the Cas1 active sites. Phosphodiester backbone interactions between the protospacer and the proteins explain the sequence-nonspecific substrate selection observed in vivo. Our results uncover the structural basis for foreign DNA capture and the mechanism by which Cas1-Cas2 functions as a molecular ruler to dictate the sequence architecture of CRISPR loci.

PMID:
26503043
PMCID:
PMC4662619
DOI:
10.1038/nature15760
[Indexed for MEDLINE]
Free PMC Article

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