CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA

Science. 2008 Dec 19;322(5909):1843-5. doi: 10.1126/science.1165771.


Horizontal gene transfer (HGT) in bacteria and archaea occurs through phage transduction, transformation, or conjugation, and the latter is particularly important for the spread of antibiotic resistance. Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci confer sequence-directed immunity against phages. A clinical isolate of Staphylococcus epidermidis harbors a CRISPR spacer that matches the nickase gene present in nearly all staphylococcal conjugative plasmids. Here we show that CRISPR interference prevents conjugation and plasmid transformation in S. epidermidis. Insertion of a self-splicing intron into nickase blocks interference despite the reconstitution of the target sequence in the spliced mRNA, which indicates that the interference machinery targets DNA directly. We conclude that CRISPR loci counteract multiple routes of HGT and can limit the spread of antibiotic resistance in pathogenic bacteria.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Conjugation, Genetic*
  • DNA, Bacterial / genetics*
  • DNA, Bacterial / metabolism
  • Deoxyribonuclease I / genetics
  • Deoxyribonuclease I / metabolism
  • Gene Silencing*
  • Gene Transfer, Horizontal*
  • Plasmids / genetics
  • RNA Splicing
  • RNA, Bacterial / genetics*
  • RNA, Bacterial / metabolism
  • Repetitive Sequences, Nucleic Acid / genetics*
  • Staphylococcus Phages / genetics
  • Staphylococcus aureus / genetics
  • Staphylococcus epidermidis / genetics*
  • Transformation, Bacterial*


  • DNA, Bacterial
  • RNA, Bacterial
  • Deoxyribonuclease I