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

Here we studied the molecular mechanisms that connect two of the most prominent prokaryotic immune systems: Restriction-Modification (RM) and Clustered, Regularly Interspaced Short Palindromic Repeats (CRISPR). While both systems employ enzymes that cleave a specific DNA sequence of the invader, CRISPR nucleases are programmed with small RNA guides (the CRISPR RNA or crRNA) to find their target site. CrRNAs are transcribed from short sequences of phage or plasmid origin, known as spacers, that are integrated into the CRISPR locus upon infection. We found that restriction endonucleases provide a short-term defense that is rapidly overcome through methylation of the phage genome, resulting in the death of the majority of the bacterial hosts. In a small fraction of the cells, however, restriction results in acquisition of spacer sequences from the cleaved site of the infecting phage, which mediate a robust type II-A CRISPR-Cas immune response and enable the survival of the population. This mechanism is reminiscent of eukaryotic immunity, where the innate response offers a first temporary line of defense, and also activates a second and more robust adaptive response.