CRISPR

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) are direct repeats found in the DNA of many bacteria and archaea. 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. Consequently, an active CRISPR repeat array may evolve 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 genes. 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. In the bacteria "E. coli" the CasA-E proteins form a functional complex, Cascade, that process CRISPR RNA transcripts into spacer-repeat units that are retained by Cascade. CRISPR-based phage inactivation in E. coli requires Cascade and Cas3, but not Cas1 and Cas2.

The understanding of the mechanism of action of CRISPR systems has progressed very quickly in the past few years; it may indeed represent a prokaryotic analog of eukaryotic RNA interference systems that provides bacteria with a form of acquired immunity.

References

#cite journal | author=Pourcel C, Salvignol G, Vergnaud G | title=CRISPR elements in "Yersinia pestis" acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies | journal=Microbiology | year=2005 | pages=653 | volume=151 | pmid=15758212 | doi=10.1099/mic.0.27437-0
#cite journal | author=Haft DH, Selengut J, Mongodin EF, Nelson KE | title=A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes | journal=PLoS Comput Biol. | year=2005 | pages=e60 | volume=1 | issue=6 | pmid=16292354 | doi=10.1371/journal.pcbi.0010060
#cite journal | author=Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV | title=A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action | journal=Biol Direct. | year=2006 | pages=7 | volume=1 | pmid=16545108 | doi=10.1186/1745-6150-1-7
#cite journal | author=Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P. | title=CRISPR provides acquired resistance against viruses in prokaryotes | journal=Science | year=2007 | pages=1709 | volume=315 | issue=5819 | pmid=17379808 | doi=10.1126/science.1138140
#cite journal | author=Sorek R, Kunin V, Hugenholtz P | title=CRISPR - a widespread system that provides acquired resistance against phages in bacteria and archaea | journal=Nat Rev Microbiol | year=2007 | pmid=18157154 | doi=10.1038/nrmicro1793 | volume=6 | pages=181
#cite journal | author=Brouns SJJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJH, Snijders APL, Dickman MJ, Makarova KS, Koonin EV, Van der Oost J | title=Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes | journal=Science | year=2008 | pmid=18703739 | doi=10.1126/science.1159689 | volume=321 | pages=960

External links

*http://crispr.u-psud.fr/Server/CRISPRfinder.php
*http://crispr.u-psud.fr/crispr/
*http://crispr.u-psud.fr/CRISPRcompar/