14. Bacterial adaptive immunity—Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)

Clustered regularly interspaced short palindromic repeats (CRISPR) are the bacterial loci that encode regulatory RNAs conferring sequence-directed immunity against phages. CRISPR is believed to be one of the most ancient bacterial adaptive mechanisms of protection against phages. This adaptive immunity involves an active process of integration of short fragments of foreign nucleic acids into clusters of CRISPRs, followed by expression of small RNAs from the loci. These RNAs target pathogen genomes for degradation.

Bacteria and Archaea lack bona fide sexual reproduction. Some of the mechanisms that they use instead for adaptation to stress and genome diversification include phage transduction, transformation, and conjugation, commonly known as mechanisms of horizontal gene transfer (HGT). Expression of these chromosomal or extrachromosomal genes acquired from without enable bacteria to thrive in the process of adaptive evolution. It would thus seem logical if bacteria would have special mechanisms allowing them to acquire and incorporate the external DNA quite efficiently. Indeed, some of the mechanisms, such as integrons, might assist bacteria to acquire antibiotic resistance. Integrons are genetic elements that, although being unable to move themselves, carry gene cassettes that can be mobilized either to other integrons or to alternate sites in the bacterial genome.