Cleavage of viral DNA by restriction endonucleases stimulates the type II CRISPR-Cas immune response

Mol Cell. 2022 Mar 3;82(5):907-919.e7. doi: 10.1016/j.molcel.2022.01.012. Epub 2022 Feb 7.


Prokaryotic organisms have developed multiple defense systems against phages; however, little is known about whether and how these interact with each other. Here, we studied the connection between two of the most prominent prokaryotic immune systems: restriction-modification and CRISPR. While both systems employ enzymes that cleave a specific DNA sequence of the invader, CRISPR nucleases are programmed with phage-derived spacer sequences, which are integrated into the CRISPR locus upon infection. We found that restriction endonucleases provide a short-term defense, which is rapidly overcome through methylation of the phage genome. In a small fraction of the cells, however, restriction results in the acquisition of spacer sequences from the cleavage site, which mediates a robust type II-A CRISPR-Cas immune response against the methylated phage. This mechanism is reminiscent of eukaryotic immunity in which the innate response offers a first temporary line of defense and also activates a second and more robust adaptive response.

Keywords: CRISPR; Cas9; bacteriophage; restriction-modification; spacer acquisition; staphylococcus.

Publication types

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

MeSH terms

  • Bacteriophages* / metabolism
  • CRISPR-Cas Systems
  • DNA Restriction Enzymes / genetics
  • DNA, Viral* / genetics
  • Endonucleases / genetics
  • Immunity


  • DNA, Viral
  • Endonucleases
  • DNA Restriction Enzymes