Spatiotemporal Control of Type III A CRISPR Cas Immunity: Coupling DNA Degradation with the Target RNA Recognition.
Streptococcus thermophilus (St) type III A CRISPR Cas system restricts MS2 RNA phage and cuts RNA in vitro. However, the CRISPR array spacers match DNA phages, raising the question: does the St CRISPR Cas system provide immunity by erasing phage mRNA or/and by eliminating invading DNA? We show that it does both. We find that (1) base pairing between crRNA and target RNA activates single stranded DNA (ssDNA) degradation by StCsm; (2) ssDNase activity is confined to the HD domain of Cas10; (3) target RNA cleavage by the Csm3 RNase suppresses Cas10 DNase activity, ensuring temporal control of DNA degradation; and (4) base pairing between crRNA 5' handle and target RNA 3' flanking sequence inhibits Cas10 ssDNase to prevent self targeting. We propose that upon phage infection, crRNA guided StCsm binding to the emerging transcript recruits Cas10 DNase to the actively transcribed phage DNA, resulting in degradation of both the transcript and phage DNA, but not the host DNA.
Molecular cell