Evolution of Modularity and Hierarchy in CRISPR-Cas Target Recognition

Clustered, regularly interspaced, short, palindromic repeats (CRISPR) constitute a genetic adaptive immune system unique to prokaryotic cells used to combat phage threats. The host cell incorporates DNA sequences from invading phages into its CRISPR locus as spacers. These spacers are expressed as guide RNAs that direct CRISPR-associated (Cas) proteins to protect against subsequent attack by the same phages. The guide RNA and Cas protein complex recognize three distinct sequence modules: (1) a protospacer associated motif (PAM), (2) a short seed region, and (3) the residual spacer basepairs. There is a hierarchical significance to these three elements, as mismatches between the CRISPR machinery and target sequence are most sensitive in the PAM region, followed by those in the seed. Here we show that the CRISPR-Cas machinery evolved with this selection for modularity and hierarchy in order to efficiently and effectively recognize invaders.