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.

  • Review Article
  • Published:

CRISPR-Cas immunity in prokaryotes

Abstract

Prokaryotic organisms are threatened by a large array of viruses and have developed numerous defence strategies. Among these, only clustered, regularly interspaced short palindromic repeat (CRISPR)-Cas systems provide adaptive immunity against foreign elements. Upon viral injection, a small sequence of the viral genome, known as a spacer, is integrated into the CRISPR locus to immunize the host cell. Spacers are transcribed into small RNA guides that direct the cleavage of the viral DNA by Cas nucleases. Immunization through spacer acquisition enables a unique form of evolution whereby a population not only rapidly acquires resistance to its predators but also passes this resistance mechanism vertically to its progeny.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Stages of CRISPR-Cas immunity.
Figure 2: Immunity mechanisms of the different CRISPR-Cas types.
Figure 3: Mechanism of CRISPR immunization.

Similar content being viewed by others

References

  1. Bergh, O., Borsheim, K. Y., Bratbak, G. & Heldal, M. High abundance of viruses found in aquatic environments. Nature 340, 467–468 (1989)

    Article  ADS  CAS  PubMed  Google Scholar 

  2. Chibani-Chennoufi, S., Bruttin, A., Dillmann, M. L. & Brussow, H. Phage-host interaction: an ecological perspective. J. Bacteriol. 186, 3677–3686 (2004)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. d’Herelle, F. Sur un microbe invisible antagoniste des bacilles dysentériques. C.R. Acad. Sci. Paris 165, 373–375 (1917)

    Google Scholar 

  4. Twort, F. W. An investigation on the nature of ultra-microscopic viruses. Lancet 186, 1241–1243 (1915)

    Article  Google Scholar 

  5. Burnet, F. M. Further observations on the nature of bacterial resistance to bacteriophage. J. Pathol. Bacteriol. 32, 349–354 (1929)

    Article  Google Scholar 

  6. Gratia, A. Studies on the D'herelle phenomenon. J. Exp. Med. 34, 115–126 (1921)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Luria, S. E. & Delbruck, M. Mutations of bacteria from virus sensitivity to virus resistance. Genetics 28, 491–511 (1943)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Barrangou, R. et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315, 1709–1712 (2007)A study that demonstrated that CRISPR-Cas loci provide acquired immunity against bacteriophages

    Article  ADS  CAS  PubMed  Google Scholar 

  9. Marraffini, L. A. & Sontheimer, E. J. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322, 1843–1845 (2008)A paper showing that CRISPR-Cas loci target DNA molecules in a sequence-specific manner, highlighting for the first time the potential for the technological applications of these systems

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  10. Andersson, A. F. & Banfield, J. F. Virus population dynamics and acquired virus resistance in natural microbial communities. Science 320, 1047–1050 (2008)This study revealed the arms race between CRISPR-Cas systems and viruses in their natural habitat

    Article  ADS  CAS  PubMed  Google Scholar 

  11. Deveau, H. et al. Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. J. Bacteriol. 190, 1390–1400 (2008)

    Article  CAS  PubMed  Google Scholar 

  12. Childs, L. M., England, W. E., Young, M. J., Weitz, J. S. & Whitaker, R. J. CRISPR-induced distributed immunity in microbial populations. PLoS ONE 9, e101710 (2014)

    Article  ADS  PubMed  PubMed Central  CAS  Google Scholar 

  13. Paez-Espino, D. et al. CRISPR immunity drives rapid phage genome evolution in Streptococcus thermophilus. MBio 6, e00262–15 (2015)

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  14. Weinberger, A. D. et al. Persisting viral sequences shape microbial CRISPR-based immunity. PLOS Comput. Biol. 8, e1002475 (2012)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. 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)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. 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)First description of CRISPR loci as a new family of repetitive sequences in prokaryotes

    Article  CAS  PubMed  Google Scholar 

  17. 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)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  18. 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)First description of cas sequences as a family of genes associated with CRISPR repeats

    Article  CAS  PubMed  Google Scholar 

  19. 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)This paper, along with references 20 and 21, made the discovery that spacer sequences match viruses and plasmids, and suggested a defence function for CRISPR-Cas systems

    Article  CAS  PubMed  Google Scholar 

  20. 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)

    Article  ADS  CAS  PubMed  Google Scholar 

  21. 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)

    Article  CAS  PubMed  Google Scholar 

  22. 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)This work provided the first comprehensive model for the mechanism of CRISPR-Cas immunity

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  23. Brouns, S. J. et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321, 960–964 (2008)Study demonstrating the central role of crRNA guides and Cas ribonucleoproteins in CRISPR immunity

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  24. Pennisi, E. The CRISPR craze. Science 341, 833–836 (2013)

    Article  ADS  CAS  PubMed  Google Scholar 

  25. Makarova, K. S. et al. Evolution and classification of the CRISPR-Cas systems. Nature Rev. Microbiol. 9, 467–477 (2011)

    Article  CAS  Google Scholar 

  26. Haurwitz, R. E., Jinek, M., Wiedenheft, B., Zhou, K. & Doudna, J. A. Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science 329, 1355–1358 (2010)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  27. Jore, M. M. et al. Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nature Struct. Mol. Biol. 18, 529–536 (2011)

    Article  CAS  Google Scholar 

  28. Wiedenheft, B. et al. RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions. Proc. Natl Acad. Sci. USA 108, 10092–10097 (2011)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  29. Sashital, D. G., Wiedenheft, B. & Doudna, J. A. Mechanism of foreign DNA selection in a bacterial adaptive immune system. Mol. Cell 46, 606–615 (2012)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Horvath, P. et al. Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus. J. Bacteriol. 190, 1401–1412 (2008)

    Article  CAS  PubMed  Google Scholar 

  31. Mojica, F. J., Diez-Villasenor, C., Garcia-Martinez, J. & Almendros, C. Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 155, 733–740 (2009)

    Article  CAS  PubMed  Google Scholar 

  32. Semenova, E. et al. Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence. Proc. Natl Acad. Sci. USA 108, 10098–10103 (2011)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  33. Sinkunas, T. et al. In vitro reconstitution of Cascade-mediated CRISPR immunity in Streptococcus thermophilus. EMBO J. 32, 385–394 (2013)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Westra, E. R. et al. CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3. Mol. Cell 46, 595–605 (2012)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Blosser, T. R. et al. Two distinct DNA binding modes guide dual roles of a CRISPR-Cas protein complex. Mol. Cell 58, 60–70 (2015)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Rutkauskas, M. et al. Directional R-loop formation by the CRISPR-Cas surveillance complex cascade provides efficient off-target site rejection. Cell Rep http://dx.doi.org/10.1016/j.celrep.2015.01.067 (2015)

  37. Szczelkun, M. D. et al. Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes. Proc. Natl Acad. Sci. USA 111, 9798–9803 (2014)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  38. Jackson, R. N. et al. Structural biology. Crystal structure of the CRISPR RNA-guided surveillance complex from Escherichia coli. Science 345, 1473–1479 (2014)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  39. Mulepati, S., Heroux, A. & Bailey, S. Structural biology. Crystal structure of a CRISPR RNA-guided surveillance complex bound to a ssDNA target. Science 345, 1479–1484 (2014)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  40. Zhao, H. et al. Crystal structure of the RNA-guided immune surveillance Cascade complex in Escherichia coli. Nature 515, 147–150 (2014)

    Article  ADS  CAS  PubMed  Google Scholar 

  41. Hochstrasser, M. L. et al. CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference. Proc. Natl Acad. Sci. USA 111, 6618–6623 (2014)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  42. Huo, Y. et al. Structures of CRISPR Cas3 offer mechanistic insights into Cascade-activated DNA unwinding and degradation. Nature Struct. Mol. Biol. 21, 771–777 (2014)

    Article  CAS  Google Scholar 

  43. Mulepati, S. & Bailey, S. In vitro reconstitution of an Escherichia coli RNA-guided immune system reveals unidirectional, ATP-dependent degradation of DNA target. J. Biol. Chem. 288, 22184–22192 (2013)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Sinkunas, T. et al. Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system. EMBO J. 30, 1335–1342 (2011)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Sapranauskas, R. et al. The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli. Nucleic Acids Res. 39, 9275–9282 (2011)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Deltcheva, E. et al. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471, 602–607 (2011)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  47. Anders, C., Niewoehner, O., Duerst, A. & Jinek, M. Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature 513, 569–573 (2014)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  48. Jinek, M. et al. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 343, 1247997 (2014)

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  49. Nishimasu, H. et al. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 156, 935–949 (2014)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Garneau, J. E. et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468, 67–71 (2010)This work showed that the crRNA-guided DNA targeting by CRISPR-Cas systems results in sequence-specific DNA cleavage

    Article  ADS  CAS  PubMed  Google Scholar 

  51. Gasiunas, G., Barrangou, R., Horvath, P. & Siksnys, V. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc. Natl Acad. Sci. USA 109, E2579–E2586 (2012)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  52. Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  53. Sternberg, S. H., Redding, S., Jinek, M., Greene, E. C. & Doudna, J. A. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507, 62–67 (2014)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  54. Jiang, W., Bikard, D., Cox, D., Zhang, F. & Marraffini, L. A. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nature Biotechnol. 31, 233–239 (2013)

    Article  CAS  Google Scholar 

  55. Carte, J., Wang, R., Li, H., Terns, R. M. & Terns, M. P. Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes. Genes Dev. 22, 3489–3496 (2008)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Marraffini, L. A. & Sontheimer, E. J. Self versus non-self discrimination during CRISPR RNA-directed immunity. Nature 463, 568–571 (2010)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  57. Sokolowski, R. D., Graham, S. & White, M. F. Cas6 specificity and CRISPR RNA loading in a complex CRISPR-Cas system. Nucleic Acids Res. 42, 6532–6541 (2014)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Hale, C., Kleppe, K., Terns, R. M. & Terns, M. P. Prokaryotic silencing (psi)RNAs in Pyrococcus furiosus. RNA 14, 2572–2579 (2008)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Hatoum-Aslan, A., Maniv, I. & Marraffini, L. A. Mature clustered, regularly interspaced, short palindromic repeats RNA (crRNA) length is measured by a ruler mechanism anchored at the precursor processing site. Proc. Natl Acad. Sci. USA 108, 21218–21222 (2011)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  60. Hatoum-Aslan, A., Samai, P., Maniv, I., Jiang, W. & Marraffini, L. A. A ruler protein in a complex for antiviral defense determines the length of small interfering CRISPR RNAs. J. Biol. Chem. 288, 27888–27897 (2013)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Deng, L., Garrett, R. A., Shah, S. A., Peng, X. & She, Q. A novel interference mechanism by a type IIIB CRISPR-Cmr module in Sulfolobus. Mol. Microbiol. 87, 1088–1099 (2013)

    Article  CAS  PubMed  Google Scholar 

  62. Goldberg, G. W., Jiang, W., Bikard, D. & Marraffini, L. A. Conditional tolerance of temperate phages via transcription-dependent CRISPR-Cas targeting. Nature 514, 633–637 (2014)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  63. Samai, P. et al. Co-transcriptional DNA and RNA cleavage during type III CRISPR-Cas immunity. Cell 161, 1164–1174 (2015)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Hale, C. R. et al. RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell 139, 945–956 (2009)First demonstration that some CRISPR-Cas systems can cleave RNA molecules

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Staals, R. H. et al. RNA targeting by the type III-A CRISPR-Cas Csm complex of Thermus thermophilus. Mol. Cell 56, 518–530 (2014)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Tamulaitis, G. et al. Programmable RNA shredding by the type III-A CRISPR-Cas system of Streptococcus thermophilus. Mol. Cell 56, 506–517 (2014)

    Article  CAS  PubMed  Google Scholar 

  67. Zebec, Z., Manica, A., Zhang, J., White, M. F. & Schleper, C. CRISPR-mediated targeted mRNA degradation in the archaeon Sulfolobus solfataricus. Nucleic Acids Res. 42, 5280–5288 (2014)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Zhang, J. et al. Structure and mechanism of the CMR complex for CRISPR-mediated antiviral immunity. Mol. Cell 45, 303–313 (2012)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Peng, W., Feng, M., Feng, X., Liang, Y. X. & She, Q. An archaeal CRISPR type III-B system exhibiting distinctive RNA targeting features and mediating dual RNA and DNA interference. Nucleic Acids Res. 43, 406–417 (2014)

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  70. Yosef, I., Goren, M. G. & Qimron, U. Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli. Nucleic Acids Res. 40, 5569–5576 (2012)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Oh, J. H. & van Pijkeren, J. P. CRISPR-Cas9-assisted recombineering in Lactobacillus reuteri. Nucleic Acids Res. 42, e131 (2014)

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  72. Jiang, Y. et al. Multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system. Appl. Environ. Microbiol. 81, 2506–2514 (2015)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  73. Huang, H., Zheng, G., Jiang, W., Hu, H. & Lu, Y. One-step high-efficiency CRISPR/Cas9-mediated genome editing in Streptomyces. Acta Biochim. Biophys. Sin. 47, 231–243 (2015)

    Article  CAS  PubMed  Google Scholar 

  74. Bikard, D. et al. Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials. Nature Biotechnol. 32, 1146–1150 (2014)

    Article  CAS  Google Scholar 

  75. Citorik, R. J., Mimee, M. & Lu, T. K. Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases. Nature Biotechnol. 32, 1141–1145 (2014)

    Article  CAS  Google Scholar 

  76. Gomaa, A. A. et al. Programmable removal of bacterial strains by use of genome-targeting CRISPR-Cas systems. MBio 5, e00928–e00913 (2014)

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  77. Díez-Villaseñor, C., Guzman, N. M., Almendros, C., Garcia-Martinez, J. & Mojica, F. J. CRISPR-spacer integration reporter plasmids reveal distinct genuine acquisition specificities among CRISPR-Cas I-E variants of Escherichia coli. RNA Biol. 10, 792–802 (2013)

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  78. Nuñez, J. K. et al. Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity. Nature Struct. Mol. Biol. 21, 528–534 (2014)

    Article  CAS  Google Scholar 

  79. Levy, A. et al. CRISPR adaptation biases explain preference for acquisition of foreign DNA. Nature 520, 505–510 (2015)This paper showed that dsDNA breaks generated during replication trigger spacer acquisition

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  80. El Karoui, M., Biaudet, V., Schbath, S. & Gruss, A. Characteristics of Chi distribution on different bacterial genomes. Res. Microbiol. 150, 579–587 (1999)

    Article  CAS  PubMed  Google Scholar 

  81. Neylon, C., Kralicek, A. V., Hill, T. M. & Dixon, N. E. Replication termination in Escherichia coli: structure and antihelicase activity of the Tus-Ter complex. Microbiol. Mol. Biol. Rev. 69, 501–526 (2005)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Dillingham, M. S. & Kowalczykowski, S. C. RecBCD enzyme and the repair of double-stranded DNA breaks. Microbiol. Mol. Biol. Rev. 72, 642–671 (2008)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Smith, G. R. How RecBCD enzyme and Chi promote DNA break repair and recombination: a molecular biologist’s view. Microbiol. Mol. Biol. Rev. 76, 217–228 (2012)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Heler, R. et al. Cas9 specifies functional viral targets during CRISPR-Cas adaptation. Nature 519, 199–202 (2015)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  85. Wei, Y., Terns, R. M. & Terns, M. P. Cas9 function and host genome sampling in Type II-A CRISPR-Cas adaptation. Genes Dev. 29, 356–361 (2015)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Datsenko, K. A. et al. Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system. Nat. Commun. 3, 945 (2012)This study showed that pre-existing spacers with partial homology to an invader sequence enhance the acquisition of new spacers

    Article  ADS  PubMed  CAS  Google Scholar 

  87. Swarts, D. C., Mosterd, C., van Passel, M. W. & Brouns, S. J. CRISPR interference directs strand specific spacer acquisition. PLoS ONE 7, e35888 (2012)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  88. Goren, M. G., Yosef, I., Auster, O. & Qimron, U. Experimental definition of a clustered regularly interspaced short palindromic duplicon in Escherichia coli. J. Mol. Biol. 423, 14–16 (2012)

    Article  CAS  PubMed  Google Scholar 

  89. Savitskaya, E., Semenova, E., Dedkov, V., Metlitskaya, A. & Severinov, K. High-throughput analysis of type I-E CRISPR/Cas spacer acquisition in E. coli. RNA Biol. 10, 716–725 (2013)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Shmakov, S. et al. Pervasive generation of oppositely oriented spacers during CRISPR adaptation. Nucleic Acids Res. 42, 5907–5916 (2014)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Arslan, Z., Hermanns, V., Wurm, R., Wagner, R. & Pul, U. Detection and characterization of spacer integration intermediates in type I-E CRISPR-Cas system. Nucleic Acids Res. 42, 7884–7893 (2014)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Nuñez, J. K., Lee, A. S., Engelman, A. & Doudna, J. A. Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity. Nature 519, 193–198 (2015)This study showed the molecular mechanism of spacer integration

    Article  ADS  PubMed  PubMed Central  CAS  Google Scholar 

  93. Thomas, C. M. & Nielsen, K. M. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nature Rev. Microbiol. 3, 711–721 (2005)

    Article  CAS  Google Scholar 

  94. Bikard, D., Hatoum-Aslan, A., Mucida, D. & Marraffini, L. A. CRISPR interference can prevent natural transformation and virulence acquisition during in vivo bacterial infection. Cell Host Microbe 12, 177–186 (2012)

    Article  CAS  PubMed  Google Scholar 

  95. Zhang, Y. et al. Processing-independent CRISPR RNAs limit natural transformation in Neisseria meningitidis. Mol. Cell 50, 488–503 (2013)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Jiang, W. et al. Dealing with the evolutionary downside of CRISPR immunity: bacteria and beneficial plasmids. PLoS Genet. 9, e1003844 (2013)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Marraffini, L. A. CRISPR-Cas immunity against phages: its effects on the evolution and survival of bacterial pathogens. PLoS Pathog. 9, e1003765 (2013)

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  98. 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  PubMed  PubMed Central  CAS  Google Scholar 

  99. Gophna, U. et al. No evidence of inhibition of horizontal gene transfer by CRISPR-Cas on evolutionary timescales. ISME J. 9, 2021–2027 (2015)

    Article  PubMed  PubMed Central  Google Scholar 

  100. Makarova, K. S., Wolf, Y. I. & Koonin, E. V. The basic building blocks and evolution of CRISPR-cas systems. Biochem. Soc. Trans. 41, 1392–1400 (2013)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Bondy-Denomy, J., Pawluk, A., Maxwell, K. L. & Davidson, A. R. Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system. Nature 493, 429–432 (2013)

    Article  ADS  CAS  PubMed  Google Scholar 

  102. Sampson, T. R., Saroj, S. D., Llewellyn, A. C., Tzeng, Y. L. & Weiss, D. S. A. CRISPR/Cas system mediates bacterial innate immune evasion and virulence. Nature 497, 254–257 (2013)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  103. Sampson, T. R., Saroj, S. D., Llewellyn, A. C., Tzeng, Y. L. & Weiss, D. S. Corrigendum: A CRISPR/Cas system mediates bacterial innate immune evasion and virulence. Nature 501, 262 (2013)

    Article  ADS  CAS  Google Scholar 

  104. Hale, C. R. et al. Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs. Mol. Cell 45, 292–302 (2012)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Liu, M. et al. Reverse transcriptase-mediated tropism switching in Bordetella bacteriophage. Science 295, 2091–2094 (2002)

    Article  ADS  CAS  PubMed  Google Scholar 

  106. Zaleski, P., Wojciechowski, M. & Piekarowicz, A. The role of Dam methylation in phase variation of Haemophilus influenzae genes involved in defence against phage infection. Microbiology 151, 3361–3369 (2005)

    Article  CAS  PubMed  Google Scholar 

  107. Hanlon, G. W., Denyer, S. P., Olliff, C. J. & Ibrahim, L. J. Reduction in exopolysaccharide viscosity as an aid to bacteriophage penetration through Pseudomonas aeruginosa biofilms. Appl. Environ. Microbiol. 67, 2746–2753 (2001)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  108. Lu, M. J. & Henning, U. Superinfection exclusion by T-even-type coliphages. Trends Microbiol. 2, 137–139 (1994)

    Article  CAS  PubMed  Google Scholar 

  109. Molineux, I. J. Host-parasite interactions: recent developments in the genetics of abortive phage infections. New Biol. 3, 230–236 (1991)

    CAS  PubMed  Google Scholar 

  110. Parma, D. H. et al. The Rex system of bacteriophage lambda: tolerance and altruistic cell death. Genes Dev. 6, 497–510 (1992)

    Article  CAS  PubMed  Google Scholar 

  111. Bingham, R., Ekunwe, S. I., Falk, S., Snyder, L. & Kleanthous, C. The major head protein of bacteriophage T4 binds specifically to elongation factor Tu. J. Biol. Chem. 275, 23219–23226 (2000)

    Article  CAS  PubMed  Google Scholar 

  112. Aizenman, E., Engelberg-Kulka, H. & Glaser, G. An Escherichia coli chromosomal “addiction module” regulated by guanosine 3′,5′-bispyrophosphate: a model for programmed bacterial cell death. Proc. Natl Acad. Sci. USA 93, 6059–6063 (1996)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  113. Fineran, P. C. et al. The phage abortive infection system, ToxIN, functions as a protein-RNA toxin-antitoxin pair. Proc. Natl Acad. Sci. USA 106, 894–899 (2009)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  114. Bickle, T. A. & Kruger, D. H. Biology of DNA restriction. Microbiol. Rev. 57, 434–450 (1993)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Goldfarb, T. et al. BREX is a novel phage resistance system widespread in microbial genomes. EMBO J. 34, 169–183 (2015)

    Article  CAS  PubMed  Google Scholar 

  116. Olovnikov, I., Chan, K., Sachidanandam, R., Newman, D. K. & Aravin, A. A. Bacterial argonaute samples the transcriptome to identify foreign DNA. Mol. Cell 51, 594–605 (2013)

    Article  CAS  PubMed  Google Scholar 

  117. Swarts, D. C. et al. DNA-guided DNA interference by a prokaryotic Argonaute. Nature 507, 258–261 (2014)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  118. Labrie, S. J., Samson, J. E. & Moineau, S. Bacteriophage resistance mechanisms. Nature Rev. Microbiol. 8, 317–327 (2010)

    Article  CAS  Google Scholar 

  119. Doulatov, S. et al. Tropism switching in Bordetella bacteriophage defines a family of diversity-generating retroelements. Nature 431, 476–481 (2004)

    Article  ADS  CAS  PubMed  Google Scholar 

  120. Sutherland, I. W., Hughes, K. A., Skillman, L. C. & Tait, K. The interaction of phage and biofilms. FEMS Microbiol. Lett. 232, 1–6 (2004)

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

L.A.M. is supported by the Rita Allen Scholars Program, an Irma T. Hirschl Award, a Sinsheimer Foundation Award and a NIH Director’s New Innovator Award (1DP2AI104556-01).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Luciano A. Marraffini.

Ethics declarations

Competing interests

The author declares no competing financial interests.

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Marraffini, L. CRISPR-Cas immunity in prokaryotes. Nature 526, 55–61 (2015). https://doi.org/10.1038/nature15386

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature15386

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing Microbiology

Sign up for the Nature Briefing: Microbiology newsletter — what matters in microbiology research, free to your inbox weekly.

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