Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

CRISPR — a widespread system that provides acquired resistance against phages in bacteria and archaea

Abstract

Arrays of clustered, regularly interspaced short palindromic repeats (CRISPRs) are widespread in the genomes of many bacteria and almost all archaea. These arrays are composed of direct repeats that are separated by similarly sized non-repetitive spacers. CRISPR arrays, together with a group of associated proteins, confer resistance to phages, possibly by an RNA-interference-like mechanism. This Progress discusses the structure and function of this newly recognized antiviral mechanism.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: CRISPR structure and function.
Figure 2: Applications of CRISPRs.

References

  1. 1

    Breitbart, M. & Rohwer, F. Here a virus, there a virus, everywhere the same virus? Trends Microbiol. 13, 278–284 (2005).

    CAS  Article  Google Scholar 

  2. 2

    Wommack, K. E. & Colwell, R. R. Virioplankton: viruses in aquatic ecosystems. Microbiol. Mol. Biol. Rev. 64, 69–114 (2000).

    CAS  Article  Google Scholar 

  3. 3

    Sturino, J. M. & Klaenhammer, T. R. Engineered bacteriophage-defence systems in bioprocessing. Nature Rev. Microbiol. 4, 395–404 (2006).

    CAS  Article  Google Scholar 

  4. 4

    Ishino, Y., Shinagawa, H., Makino, K., Amemura, M. & Nakata, A. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J. Bacteriol. 169, 5429–5433 (1987).

    CAS  Article  Google Scholar 

  5. 5

    Nakata, A., Amemura, M. & Makino, K. Unusual nucleotide arrangement with repeated sequences in the Escherichia coli K-12 chromosome. J. Bacteriol. 171, 3553–3556 (1989).

    CAS  Article  Google Scholar 

  6. 6

    Hermans, P. W. et al. Insertion element IS987 from Mycobacterium bovis BCG is located in a hot-spot integration region for insertion elements in Mycobacterium tuberculosis complex strains. Infect. Immun. 59, 2695–2705 (1991).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. 7

    Mojica, F. J., Ferrer, C., Juez, G. & Rodriguez-Valera, F. Long stretches of short tandem repeats are present in the largest replicons of the Archaea Haloferax mediterranei and Haloferax volcanii and could be involved in replicon partitioning. Mol. Microbiol. 17, 85–93 (1995).

    CAS  Article  Google Scholar 

  8. 8

    Bult, C. J. et al. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273, 1058–1073 (1996).

    CAS  Article  Google Scholar 

  9. 9

    Nelson, K. E. et al. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399, 323–329 (1999).

    CAS  Article  Google Scholar 

  10. 10

    Mojica, F. J., Diez-Villasenor, C., Soria, E. & Juez, G. Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria. Mol. Microbiol. 36, 244–246 (2000).

    CAS  Article  Google Scholar 

  11. 11

    Kunin, V., Sorek, R. & Hugenholtz, P. Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biol. 8, R61 (2007).

    Article  Google Scholar 

  12. 12

    Grissa, I., Vergnaud, G. & Pourcel, C. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics 8, 172 (2007).

    Article  Google Scholar 

  13. 13

    Jansen, R., van Embden, J. D., Gaastra, W. & Schouls, L. M. Identification of a novel family of sequence repeats among prokaryotes. OMICS 6, 23–33 (2002).

    CAS  Article  Google Scholar 

  14. 14

    Jansen, R., Embden, J. D., Gaastra, W. & Schouls, L. M. Identification of genes that are associated with DNA repeats in prokaryotes. Mol. Microbiol. 43, 1565–1575 (2002).

    CAS  Article  Google Scholar 

  15. 15

    Makarova, K. S., Aravind, L., Grishin, N. V., Rogozin, I. B. & Koonin, E. V. A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res. 30, 482–496 (2002).

    CAS  Article  Google Scholar 

  16. 16

    Makarova, K. S., Grishin, N. V., Shabalina, S. A., Wolf, Y. I. & Koonin, E. V. 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. Biol. Direct 1, 7 (2006).

    Article  Google Scholar 

  17. 17

    Haft, D. H., Selengut, J., Mongodin, E. F. & Nelson, K. E. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput. Biol. 1, e60 (2005).

    Article  Google Scholar 

  18. 18

    Mojica, F. J., Diez-Villasenor, C., Garcia-Martinez, J. & Soria, E. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J. Mol. Evol. 60, 174–182 (2005).

    CAS  Article  Google Scholar 

  19. 19

    Pourcel, C., Salvignol, G. & Vergnaud, G. CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology 151, 653–663 (2005).

    CAS  Article  Google Scholar 

  20. 20

    Bolotin, A., Quinquis, B., Sorokin, A. & Ehrlich, S. D. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology 151, 2551–2561 (2005).

    CAS  Article  Google Scholar 

  21. 21

    Barrangou, R. et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315, 1709–1712 (2007).

    CAS  Article  Google Scholar 

  22. 22

    Deveau, H. et al. Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. J. Bacteriol. 7 Dec 2007 (doi:10.1128/JB.01412-07).

  23. 23

    Horvath, P. et al. Diversity, activity and evolution of CRISPR loci in Streptococcus thermophilus. J. Bacteriol. 7 Dec 2007 (doi:10.1128/JB.01415-07).

  24. 24

    Godde, J. S. & Bickerton, A. The repetitive DNA elements called CRISPRs and their associated genes: evidence of horizontal transfer among prokaryotes. J. Mol. Evol. 62, 718–729 (2006).

    CAS  Article  Google Scholar 

  25. 25

    Tang, T. H. et al. Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus. Proc. Natl Acad. Sci. USA 99, 7536–7541 (2002).

    CAS  Article  Google Scholar 

  26. 26

    Tang, T. H. et al. Identification of novel non-coding RNAs as potential antisense regulators in the archaeon Sulfolobus solfataricus. Mol. Microbiol. 55, 469–481 (2005).

    CAS  Article  Google Scholar 

  27. 27

    Lillestøl, R. K., Redder, P., Garrett, R. A. & Brügger, K. A putative viral defence mechanism in archaeal cells. Archaea 2, 59–72 (2006).

    Article  Google Scholar 

  28. 28

    Edwards, R. A. & Rohwer, F. Viral metagenomics. Nature Rev. Microbiol. 3, 504–510 (2005).

    CAS  Article  Google Scholar 

  29. 29

    Klenk, H. P. et al. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390, 364–370 (1997).

    CAS  Article  Google Scholar 

  30. 30

    Smith, D. R. et al. Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics. J. Bacteriol. 179, 7135–7155 (1997).

    CAS  Article  Google Scholar 

  31. 31

    Ebihara, A. et al. Crystal structure of hypothetical protein TTHB192 from Thermus thermophilus HB8 reveals a new protein family with an RNA recognition motif-like domain. Protein Sci. 15, 1494–1499 (2006).

    CAS  Article  Google Scholar 

  32. 32

    Hannon, G. J. RNA interference. Nature 418, 244–251 (2002).

    CAS  Article  Google Scholar 

  33. 33

    Sontheimer, E. J. Assembly and function of RNA silencing complexes. Nature Rev. Mol. Cell Biol. 6, 127–138 (2005).

    CAS  Article  Google Scholar 

  34. 34

    Tyson, G. W. & Banfield, J. F. Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environ. Microbiol. 26 Sep 2007 (doi: 10.1111/j.1462-2920.2007.01444.x).

  35. 35

    Greve, B., Jensen, S., Brügger, K., Zillig, W. & Garrett, R. A. Genomic comparison of archaeal conjugative plasmids from Sulfolobus. Archaea 1, 231–239 (2004).

    CAS  Article  Google Scholar 

  36. 36

    Sebaihia, M. et al. The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nature Genet. 38, 779–786 (2006).

    Article  Google Scholar 

  37. 37

    Groenen, P. M., Bunschoten, A. E., van Soolingen, D. & van Embden, J. D. Nature of DNA polymorphism in the direct repeat cluster of Mycobacterium tuberculosis; application for strain differentiation by a novel typing method. Mol. Microbiol. 10, 1057–1065 (1993).

    CAS  Article  Google Scholar 

  38. 38

    Kamerbeek, J. et al. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J. Clin. Microbiol. 35, 907–914 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  39. 39

    Crawford, J. T. Genotyping in contact investigations: a CDC perspective. Int. J. Tuberc. Lung Dis. 7, S453–S457 (2003).

    CAS  PubMed  Google Scholar 

  40. 40

    Brudey, K. et al. Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology. BMC Microbiol. 6, 23 (2006).

    Article  Google Scholar 

  41. 41

    Mokrousov, I., Limeschenko, E., Vyazovaya, A. & Narvskaya, O. Corynebacterium diphtheriae spoligotyping based on combined use of two CRISPR loci. Biotechnol. J. 2, 901–906 (2007).

    CAS  Article  Google Scholar 

  42. 42

    Schouls, L. M. et al. Comparative genotyping of Campylobacter jejuni by amplified fragment length polymorphism, multilocus sequence typing, and short repeat sequencing: strain diversity, host range, and recombination. J. Clin. Microbiol. 41, 15–26 (2003).

    CAS  Article  Google Scholar 

  43. 43

    DeBoy, R. T., Mongodin, E. F., Emerson, J. B. & Nelson, K. E. Chromosome evolution in the Thermotogales: large-scale inversions and strain diversification of CRISPR sequences. J. Bacteriol. 188, 2364–2374 (2006).

    CAS  Article  Google Scholar 

  44. 44

    Russell, W. M., Barrangou, R. & Horvath, P. Detection and typing of bacterial strains. US Patent Application 20060199190 (2006).

  45. 45

    Horvath, P., Barrangou, R., Fremaux, C., Boyaval, P. & Romero, D. International Patent Application 2007025097 (2007).

  46. 46

    Suttle, C. A. Viruses in the sea. Nature 437, 356–361 (2005).

    CAS  Article  Google Scholar 

  47. 47

    Peng, X. et al. Genus-specific protein binding to the large clusters of DNA repeats (short regularly spaced repeats) present in Sulfolobus genomes. J. Bacteriol. 185, 2410–2417 (2003).

    CAS  Article  Google Scholar 

  48. 48

    Viswanathan, P., Murphy, K., Julien, B., Garza, A. G. & Kroos, L. Regulation of dev, an operon that includes genes essential for Myxococcus xanthus development and CRISPR-associated genes and repeats. J. Bacteriol. 189, 3738–3750 (2007).

    CAS  Article  Google Scholar 

  49. 49

    Edgar, R. C. PILER-CR: fast and accurate identification of CRISPR repeats. BMC Bioinformatics 8, 18 (2007).

    Article  Google Scholar 

  50. 50

    Bland, C. et al. CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics 8, 209 (2007).

    Article  Google Scholar 

  51. 51

    Grissa, I., Vergnaud, G. & Pourcel, C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 35, W52–W57 (2007).

    Article  Google Scholar 

  52. 52

    Durand, P., Mahé, F., Valin, A. S. & Nicolas, J. Browsing repeats in genomes: Pygram and an application to non-coding region analysis. BMC Bioinformatics 7, 477 (2006).

    Article  Google Scholar 

Download references

Acknowledgements

The authors thank H. Garcia Martin, M. J. Blow, A. Visel and G. Tyson for helpful discussions. This work was performed under the auspices of the US Department of Energy, Office of Science, Biological and Environmental Research Program at the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344 and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396.

Author information

Affiliations

Authors

Corresponding author

Correspondence to Rotem Sorek.

Related links

Related links

DATABASES

Entrez Genome Project

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj

Campylobacter jejuni

Clostridium difficile

Corynebacterium diphtheriae

Escherichia coli

Haloferax volcanii

Methanocaldococcus jannaschii

Mycobacterium avium

Mycobacterium tuberculosis

Myxococcus xanthus

Pyrococcus abyssii

Streptococcus thermophilus

Sulfolobus acidocaldarius

Thermotoga maritima

Thermotoga neapolitana

Verminephrobacter eiseniae

NCBI COGs

cas1

FURTHER INFORMATION

Rotem Sorek's homepage

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Sorek, R., Kunin, V. & Hugenholtz, P. CRISPR — a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat Rev Microbiol 6, 181–186 (2008). https://doi.org/10.1038/nrmicro1793

Download citation

Further reading

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing