Mechanism of foreign DNA selection in a bacterial adaptive immune system

Mol Cell. 2012 Jun 8;46(5):606-15. doi: 10.1016/j.molcel.2012.03.020. Epub 2012 Apr 19.


In bacterial and archaeal CRISPR immune pathways, DNA sequences from invading bacteriophage or plasmids are integrated into CRISPR loci within the host genome, conferring immunity against subsequent infections. The ribonucleoprotein complex Cascade utilizes RNAs generated from these loci to target complementary "nonself" DNA sequences for destruction, while avoiding binding to "self" sequences within the CRISPR locus. Here we show that CasA, the largest protein subunit of Cascade, is required for nonself target recognition and binding. Combining a 2.3 Å crystal structure of CasA with cryo-EM structures of Cascade, we have identified a loop that is required for viral defense. This loop contacts a conserved three base pair motif that is required for nonself target selection. Our data suggest a model in which the CasA loop scans DNA for this short motif prior to target destabilization and binding, maximizing the efficiency of DNA surveillance by Cascade.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Binding Sites
  • DNA / chemistry
  • Escherichia coli / genetics
  • Escherichia coli / immunology*
  • Escherichia coli / virology
  • Escherichia coli Proteins / chemistry
  • Escherichia coli Proteins / immunology
  • Escherichia coli Proteins / physiology*
  • Models, Immunological
  • Models, Molecular
  • Nucleic Acid Conformation
  • Protein Subunits / metabolism
  • Protein Subunits / physiology*
  • RNA, Bacterial / chemistry
  • RNA, Bacterial / metabolism
  • RNA, Bacterial / physiology
  • Ribonucleoproteins / chemistry
  • Ribonucleoproteins / immunology
  • Ribonucleoproteins / physiology


  • Escherichia coli Proteins
  • Protein Subunits
  • RNA, Bacterial
  • Ribonucleoproteins
  • DNA

Associated data

  • PDB/4AN8