Structural basis for CRISPR RNA-guided DNA recognition by Cascade

Nat Struct Mol Biol. 2011 May;18(5):529-36. doi: 10.1038/nsmb.2019. Epub 2011 Apr 3.

Abstract

The CRISPR (clustered regularly interspaced short palindromic repeats) immune system in prokaryotes uses small guide RNAs to neutralize invading viruses and plasmids. In Escherichia coli, immunity depends on a ribonucleoprotein complex called Cascade. Here we present the composition and low-resolution structure of Cascade and show how it recognizes double-stranded DNA (dsDNA) targets in a sequence-specific manner. Cascade is a 405-kDa complex comprising five functionally essential CRISPR-associated (Cas) proteins (CasA(1)B(2)C(6)D(1)E(1)) and a 61-nucleotide CRISPR RNA (crRNA) with 5'-hydroxyl and 2',3'-cyclic phosphate termini. The crRNA guides Cascade to dsDNA target sequences by forming base pairs with the complementary DNA strand while displacing the noncomplementary strand to form an R-loop. Cascade recognizes target DNA without consuming ATP, which suggests that continuous invader DNA surveillance takes place without energy investment. The structure of Cascade shows an unusual seahorse shape that undergoes conformational changes when it binds target DNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Binding Sites
  • DNA / chemistry*
  • Escherichia coli / immunology
  • Escherichia coli / metabolism
  • Escherichia coli / virology*
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / metabolism
  • Escherichia coli Proteins / physiology
  • Nucleic Acid Conformation
  • Protein Structure, Tertiary
  • RNA, Bacterial / chemistry
  • RNA, Bacterial / metabolism
  • RNA, Bacterial / physiology
  • RNA, Small Untranslated
  • Ribonucleoproteins / chemistry*
  • Ribonucleoproteins / metabolism
  • Ribonucleoproteins / physiology
  • Structure-Activity Relationship

Substances

  • Cse1 protein, E coli
  • Escherichia coli Proteins
  • RNA, Bacterial
  • Ribonucleoproteins
  • DNA
  • RNA, Small Untranslated