CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA.
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.
Marraffini
Luciano A
LA
Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA.
Sontheimer
Erik J
EJ
D001483:Base Sequence; D003227:Conjugation, Genetic; D004269:DNA, Bacterial / Q000235:genetics* / Q000378:metabolism; D003850:Deoxyribonuclease I / Q000235:genetics / Q000378:metabolism; D020868:Gene Silencing; D022761:Gene Transfer, Horizontal; D010957:Plasmids / Q000235:genetics; D012326:RNA Splicing; D012329:RNA, Bacterial / Q000235:genetics* / Q000378:metabolism; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D013204:Staphylococcus Phages / Q000235:genetics; D013211:Staphylococcus aureus / Q000235:genetics; D013212:Staphylococcus epidermidis / Q000235:genetics*; D014169:Transformation, Bacterial
D004269:DNA, Bacterial; D012329:RNA, Bacterial; D003850:Deoxyribonuclease I