CRISPR and crRNAs

Bacteria continuously face infections from bacteriophages, viruses that infect bacteria.

To deal with this threat, bacteria have evolved a sophisticated adaptive immunity system known as the CRISPR-Cas system to destroy bacteriophage DNA, in case of reinfection.  

This system involves three different processes – incorporation of the bacteriophage DNA segment into the bacterial genome, production of the CRISPR RNA and the Cas protein, and CRISPR RNA-Cas mediated cleavage of the bacteriophage DNA.

When a bacteriophage attacks, it attaches to the surface of the bacterial cell and inserts its DNA into the bacteria which is then cleaved by the bacterial system. 

A short segment of the bacteriophage DNA is then added into specific regions of the bacterial genome, called CRISPR, clustered regularly interspaced short palindromic repeats. These are genomic regions where bacterial sequence repeats are interspersed with the short varying spacer sequences from different bacteriophages.

These spacer sequences serve as a memory for the bacteria of all the bacteriophages that have previously attacked. Bacteria use spacer sequences to rapidly identify and destroy DNA from a particular type of bacteriophage if it attacks again.

The transcripts from the CRISPR region are processed to produce CRISPR RNA molecules, around 30 nucleotides long, that contain the spacer sequence and the nearby bacterial repeat sequence.

The CRISPR-associated or Cas systems encode the Cas protein. This Cas protein then associates with the CRISPR RNA molecule to form a ribonucleoprotein complex.

When the same type of bacteriophage attacks again, its DNA is recognized by its specific spacer sequence present in the CRISPR RNA.  Associated Cas protein then, either alone or with the help of multiple proteins, cuts both strands of the bacteriophage DNA.

The principles of the CRISPR-Cas system and its components can be used to knockdown or modify any gene in an organism using its complementary guide RNA. 

Different types of the CRISPR-Cas system are present in bacteria and archaea. Among them, the CRISPR-Cas9 system is one of the most well studied and widely used for different practical applications, as it can be easily and effectively reprogrammed to target different genes.