Mechanism of CRISPR-RNA guided recognition of DNA targets in Escherichia coli

Paul B G Van Erp, Ryan N. Jackson, Joshua Carter, Sarah M. Golden, Scott Bailey, Blake Wiedenheft

Research output: Contribution to journalArticle

Abstract

In bacteria and archaea, short fragments of foreign DNA are integrated into Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) loci, providing a molecular memory of previous encounters with foreign genetic elements. In Escherichia coli, short CRISPR-derived RNAs are incorporated into a multi-subunit surveillance complex called Cascade (CRISPR-associated complex for antiviral defense). Recent structures of Cascade capture snapshots of this seahorse-shaped RNA-guided surveillance complex before and after binding to a DNA target. Here we determine a 3.2 Å x-ray crystal structure of Cascade in a new crystal form that provides insight into the mechanism of double-stranded DNA binding. Molecular dynamic simulations performed using available structures reveal functional roles for residues in the tail, backbone and belly subunits of Cascade that are critical for binding double-stranded DNA. Structural comparisons are used to make functional predictions and these predictions are tested in vivo and in vitro. Collectively, the results in this study reveal underlying mechanisms involved in target-induced conformational changes and highlight residues important in DNA binding and protospacer adjacent motif recognition.

Original languageEnglish (US)
Pages (from-to)8381-8391
Number of pages11
JournalNucleic Acids Research
Volume43
Issue number17
DOIs
StatePublished - Sep 30 2015

Fingerprint

Clustered Regularly Interspaced Short Palindromic Repeats
RNA
Escherichia coli
Antiviral Agents
DNA
Smegmamorpha
Archaea
Molecular Dynamics Simulation
Recognition (Psychology)
Tail
X-Rays
Bacteria

ASJC Scopus subject areas

  • Genetics

Cite this

Van Erp, P. B. G., Jackson, R. N., Carter, J., Golden, S. M., Bailey, S., & Wiedenheft, B. (2015). Mechanism of CRISPR-RNA guided recognition of DNA targets in Escherichia coli. Nucleic Acids Research, 43(17), 8381-8391. https://doi.org/10.1093/nar/gkv793

Mechanism of CRISPR-RNA guided recognition of DNA targets in Escherichia coli. / Van Erp, Paul B G; Jackson, Ryan N.; Carter, Joshua; Golden, Sarah M.; Bailey, Scott; Wiedenheft, Blake.

In: Nucleic Acids Research, Vol. 43, No. 17, 30.09.2015, p. 8381-8391.

Research output: Contribution to journalArticle

Van Erp, PBG, Jackson, RN, Carter, J, Golden, SM, Bailey, S & Wiedenheft, B 2015, 'Mechanism of CRISPR-RNA guided recognition of DNA targets in Escherichia coli', Nucleic Acids Research, vol. 43, no. 17, pp. 8381-8391. https://doi.org/10.1093/nar/gkv793
Van Erp, Paul B G ; Jackson, Ryan N. ; Carter, Joshua ; Golden, Sarah M. ; Bailey, Scott ; Wiedenheft, Blake. / Mechanism of CRISPR-RNA guided recognition of DNA targets in Escherichia coli. In: Nucleic Acids Research. 2015 ; Vol. 43, No. 17. pp. 8381-8391.
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