DiscoverScroll article

CRISPR (; acronym for clustered regularly interspaced short palindromic repeats) is a family of DNA sequences found in the genomes of prokaryotic organisms such as bacteria and archaea.

Each sequence within an individual prokaryotic CRISPR is derived from a DNA fragment of a bacteriophage that had previously infected the prokaryote or one of its ancestors. These sequences are used to detect and destroy DNA from similar bacteriophages during subsequent infections. Hence these sequences play a key role in the antiviral (i.e. anti-phage) defense system of prokaryotes and provide a form of heritable, acquired immunity. CRISPR is found in approximately 50% of sequenced bacterial genomes and nearly 90% of sequenced archaea. Cas9 (or "CRISPR-associated protein 9") is an enzyme that uses CRISPR sequences as a guide to recognize and open up specific strands of DNA that are complementary to the CRISPR sequence. Cas9 enzymes together with CRISPR sequences form the basis of a technology known as CRISPR-Cas9 that can be used to edit genes within living organisms. The development of the CRISPR-Cas9 genome editing technique was recognized by the Nobel Prize in Chemistry in 2020 awarded to Emmanuelle Charpentier and Jennifer Doudna.

The CRISPR/Cas system evolved in nature as a means for bacteria to protect themselves from invading viruses and bacteriophages by inserting pieces of their DNA into the host genome.

A CRISPR region in Streptococcus thermophilus acquired spacers from the DNA of an infecting bacteriophage. In 2008, Brouns and Van der Oost identified a complex of Cas proteins called Cascade, that in E. coli cut the CRISPR RNA precursor within the repeats into mature spacer-containing RNA molecules called CRISPR RNA (crRNA), which remained bound to the protein complex.

When a microbe is invaded by a bacteriophage, the first stage of the immune response is to capture phage DNA and insert it into a CRISPR locus in the form of a spacer.

Analysis of CRISPR-Cas systems showed PAMs to be important for type I and type II, but not type III systems during acquisition. In type I and type II systems, protospacers are excised at positions adjacent to a PAM sequence, with the other end of the spacer cut using a ruler mechanism, thus maintaining the regularity of the spacer size in the CRISPR array.

Analysis of Sulfolobus solfataricus CRISPRs revealed further complexities to the canonical model of spacer insertion, as one of its six CRISPR loci inserted new spacers randomly throughout its CRISPR array, as opposed to inserting closest to the leader sequence.

Type III systems were also found to target DNA in addition to RNA using a different Cas protein in the complex, Cas10.

To resist a phage infection, the sequence of the CRISPR spacer must correspond perfectly to the sequence of the target phage gene.

A study of 124 S. thermophilus strains showed that 26% of all spacers were unique and that different CRISPR loci showed different rates of spacer acquisition. However, this CRISPR added three spacers over 17 months, suggesting that even in an environment with significant CRISPR diversity some loci evolve slowly.

Degenerate repeat-specific primers can be used to amplify CRISPR spacers directly from environmental samples; amplicons containing two or three spacers can be then computationally assembled to reconstruct long CRISPR arrays. CRISPR identification in raw reads has been achieved using purely de novo identification or by using direct repeat sequences in partially assembled CRISPR arrays from contigs (overlapping DNA segments that together represent a consensus region of DNA) and direct repeat sequences from published genomes as a hook for identifying direct repeats in individual reads.

The system has 2 CRISPR loci and 9 Cas genes.

Overview of all the structural information available in the PDB for UniProt: Q46897 (CRISPR system Cascade subunit CasE) at the PDBe-KB.

Quick Facts

• Cas9 (or "CRISPR-associated protein 9") is an enzyme that uses CRISPR sequences as a guide to recognize and open up specific strands of DNA that are complementary to the CRISPR sequence.
• Cas9 enzymes together with CRISPR sequences form the basis of a technology known as CRISPR-Cas9 that can be used to edit genes within living organisms.
• The CRISPR/Cas system evolved in nature as a means for bacteria to protect themselves from invading viruses and bacteriophages by inserting pieces of their DNA into the host genome.
• CRISPR is found in approximately 50% of sequenced bacterial genomes and nearly 90% of sequenced archaea.
• Each sequence within an individual prokaryotic CRISPR is derived from a DNA fragment of a bacteriophage that had previously infected the prokaryote or one of its ancestors.

Source material: Wikipedia - "CRISPR". Adapted and summarized for DiscoverScroll. Original contributors are credited through the linked Wikipedia article. Read original on Wikipedia. CC BY-SA 4.0. Changes were made from the original.