CRISPR (Clustered regularly interspaced short palindromic repeats) are direct repeats found in the DNA of many bacteria and archaea. The name is an acronym for clustered regularly interspaced short palindromic repeats. These repeats range in size from 24 to 48 base pairs. They usually show some dyad symmetry but are not truly palindromic. The repeats are separated by spacers of similar length. Spacers are usually unique in a genome. Some spacer sequences match sequences in phage genomes; it was proposed, and more recently demonstrated, that these spacers can be derived from phage and subsequently help protect the cell from infection. The CRISPR repeat array evolves rapidly. Different strains of the same species of bacterium often can be differentiated according to differences in the spacers in their CRISPR arrays, a technique called spoligotyping.
Sets of genes have been described recently that are found only in genomes that contain CRISPR repeats, and almost always near the repeats themselves. Such CRISPR-associated genes are called cas. More than forty different Cas protein families have been described. The most important of these is Cas1, which is present in almost every CRISPR/Cas system. Particular combinations of cas genes are found together regularly, along with characteristic subclasses of CRISPR repeat and corresponding subfamilies of the Cas1 family. These combinations appear to represent distinct CRISPR/Cas subtypes; several different subtypes may occur in a single genome. The sporadic distribution of each CRISPR/cas subtype suggests that these elements undergo numerous horizontal gene transfer events during microbial evolution.
The mechanism of action of CRISPR systems is unknown, but may represent a prokaryotic analog of eukaryotic RNA interference systems.
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