CRISPR and crRNAs

The CRISPR-Cas system is a bacterial adaptive immunity mechanism that stores copies of foreign viral DNA and uses it to identify and destroy invading bacteriophages upon reinfection. Bacteria incorporate short segments of bacteriophage DNA into specific genomic regions called CRISPR, which serve as a molecular memory of past infections. When the same virus attacks again, the system rapidly recognizes and destroys the viral DNA.

Bacteria store viral DNA segments called spacer sequences in clustered regularly interspaced short palindromic repeats (CRISPR) regions of their genome. These spacer sequences are interspersed with bacterial repeat sequences and act as a molecular record of previous bacteriophage attacks. When a bacteriophage reinfects, bacteria use these stored spacer sequences to rapidly identify and target the specific viral DNA for destruction.

CRISPR RNA (crRNA) is produced from transcripts of the CRISPR genomic region and contains approximately 30 nucleotides, including the spacer sequence and nearby bacterial repeat sequence. The crRNA associates with Cas protein to form a ribonucleoprotein complex that recognizes viral DNA through sequence-specific base pairing with the spacer region, enabling targeted cleavage of invading bacteriophage DNA.

Cas proteins associate with CRISPR RNA to form a ribonucleoprotein complex that targets and cleaves viral DNA in a sequence-specific manner. Different CRISPR-Cas types employ different mechanisms: Type I systems use multiple Cas proteins including Cas3 to create double-stranded breaks, Type II systems use Cas9 nuclease alone, and Type III systems use Cas10 with multiple proteins and can target RNA as well.

The CRISPR-Cas system operates through three stages: acquisition, where viral protospacer DNA is cleaved and incorporated into the bacterial CRISPR locus; expression, where CRISPR and Cas genes are transcribed to produce crRNA and Cas protein; and interference, where the crRNA-Cas ribonucleoprotein complex targets and cleaves reinfecting viral DNA in a sequence-specific manner.

CRISPR-Cas9 is one of the most well-studied and widely used CRISPR system because it can be easily and effectively reprogrammed to target different genes using complementary guide RNA. The principles of the CRISPR-Cas system allow researchers to knockdown or modify any gene in an organism, making it simpler and more versatile than conventional genome editing techniques like restriction enzymes.

The CRISPR-Cas system is remarkably widespread, present in more than 45% of known bacteria and 90% of known archaea. Different types of CRISPR-Cas systems exist across these organisms, with Type I and Type III systems found in both bacteria and archaea, while Type II systems have been found only in bacteria, reflecting the diverse evolutionary strategies prokaryotes use for viral defense.