SELF VS. FOREIGN RECOGNITION DURING ACQUISITION IN TYPE I-E CRISPR-CAS SYSTEM

All immune systems must distinguish self from non-self to repel invaders without inducing autoimmunity. The CRISPR-Cas system, provides adaptive protection against foreign nucleic acids in a variety of bacteria and archaea strains via a 2-step process of sampling the invaders genome while integrating it inside the CRISPR array (acquisition) and targeting it for degradation (interference). However, the mechanism by which the sampled genomic parts termed "spacers" are preferentially acquired while the self genome is avoided remained a mystery. Using NGS methods we sequenced millions of spacers acquired by the E. coli type I-E CRISPR system and constructed a profile of genetic hotspots prone for sampling. These observations enabled us to construct and test a model for self-foreign recognition mediated by the recBCD complex activity. We found that while replication fork stall enhance acquisition of the surrounding DNA, Chi sites reduce it. These observations fit well with the rational that extensively replicating DNA elements such as phages and plasmids should be more prone for sampling while the self genome should be left unharmed.