A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity

  • Nature volume 494, pages 489491 (28 February 2013)
  • doi:10.1038/nature11927
  • Download Citation


Bacteriophages (or phages) are the most abundant biological entities on earth, and are estimated to outnumber their bacterial prey by tenfold1. The constant threat of phage predation has led to the evolution of a broad range of bacterial immunity mechanisms that in turn result in the evolution of diverse phage immune evasion strategies, leading to a dynamic co-evolutionary arms race2,3. Although bacterial innate immune mechanisms against phage abound, the only documented bacterial adaptive immune system is the CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins) system, which provides sequence-specific protection from invading nucleic acids, including phage4,5,6,7,8,9,10,11. Here we show a remarkable turn of events, in which a phage-encoded CRISPR/Cas system is used to counteract a phage inhibitory chromosomal island of the bacterial host. A successful lytic infection by the phage is dependent on sequence identity between CRISPR spacers and the target chromosomal island. In the absence of such targeting, the phage-encoded CRISPR/Cas system can acquire new spacers to evolve rapidly and ensure effective targeting of the chromosomal island to restore phage replication.

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Primary accessions

Data deposits

The sequences for the CRISPR/Cas system in ICP1_2011_A and ICP1_2006_E have been deposited at GenBank (accession numbers KC152959 and KC152958, respectively). The sequences for the V. cholerae PLEs identified in clinical isolates from the ICDDR,B have been deposited at GenBank/EMBL/DDBJ under the accession numbers KC152960 (PLE1) and KC152961 (PLE2).


  1. 1.

    & Phage genomics: small is beautiful. Cell 108, 13–16 (2002)

  2. 2.

    , & Bacteriophage resistance mechanisms. Nature Rev. Microbiol. 8, 317–327 (2010)

  3. 3.

    & The phage-host arms race: shaping the evolution of microbes. Bioessays 33, 43–51 (2011)

  4. 4.

    & CRISPR/Cas, the immune system of bacteria and archaea. Science 327, 167–170 (2010)

  5. 5.

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

  6. 6.

    & CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322, 1843–1845 (2008)

  7. 7.

    , & CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. Annu. Rev. Genet. 45, 273–297 (2011)

  8. 8.

    , , , & CRISPR-based adaptive and heritable immunity in prokaryotes. Trends Biochem. Sci. 34, 401–407 (2009)

  9. 9.

    & The CRISPR system: small RNA-guided defense in bacteria and archaea. Mol. Cell 37, 7–19 (2010)

  10. 10.

    et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468, 67–71 (2010)

  11. 11.

    & CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nature Rev. Genet. 11, 181–190 (2010)

  12. 12.

    et al. Self-limiting nature of seasonal cholera epidemics: role of host-mediated amplification of phage. Proc. Natl Acad. Sci. USA 102, 6119–6124 (2005)

  13. 13.

    , , , & Cholera transmission: the host, pathogen and bacteriophage dynamic. Nature Rev. Microbiol. 7, 693–702 (2009)

  14. 14.

    et al. Evidence of a dominant lineage of Vibrio cholerae-specific lytic bacteriophages shed by cholera patients over a 10-year period in Dhaka, Bangladesh. MBio 2, e00334–10 (2011)

  15. 15.

    et al. Phase variable O antigen biosynthetic genes control expression of the major protective antigen and bacteriophage receptor in Vibrio cholerae O1. PLoS Pathog. 8, e1002917 (2012)

  16. 16.

    , & The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics 8, 172 (2007)

  17. 17.

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

  18. 18.

    et al. Epidemic and endemic cholera trends over a 33-year period in Bangladesh. J. Infect. Dis. 186, 246–251 (2002)

  19. 19.

    , , & Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 155, 733–740 (2009)

  20. 20.

    , & The phage-related chromosomal islands of Gram-positive bacteria. Nature Rev. Microbiol. 8, 541–551 (2010)

  21. 21.

    et al. Staphylococcal pathogenicity island interference with helper phage reproduction is a paradigm of molecular parasitism. Proc. Natl Acad. Sci. USA 109, 16300–16305 (2012)

  22. 22.

    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)

  23. 23.

    et al. Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system. Nature Commun. 3, 945–947 (2012)

  24. 24.

    , , & CRISPR interference directs strand specific spacer acquisition. PLoS ONE 7, e35888 (2012)

  25. 25.

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

  26. 26.

    et al. The human gut virome: inter-individual variation and dynamic response to diet. Genome Res. 21, 1616–1625 (2011)

  27. 27.

    et al. Reconstructing viral genomes from the environment using fosmid clones: the case of haloviruses. PLoS ONE 7, e33802 (2012)

  28. 28.

    & Homopolymer tail-mediated ligation PCR: a streamlined and highly efficient method for DNA cloning and library construction. Biotechniques 54, 25–34 (2013)

  29. 29.

    , , & WebLogo: a sequence logo generator. Genome Res. 14, 1188–1190 (2004)

  30. 30.

    & Genetic manipulation of Vibrio cholerae by combining natural transformation with FLP recombination. Plasmid 64, 186–195 (2010)

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The authors thank the Tufts University Core Facility for sequencing and computational support. This work was supported by US National Institutes of Health grants AI055058 (A.C.), AI045746 (A.C.) and AI058935 (S.B.C.). A.C. is a Howard Hughes Medical Institute Investigator.

Author information


  1. Howard Hughes Medical Institute and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA

    • Kimberley D. Seed
    • , David W. Lazinski
    •  & Andrew Camilli
  2. Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts 02114, USA

    • Stephen B. Calderwood
  3. Harvard Medical School, Boston, Massachusetts 02114, USA

    • Stephen B. Calderwood


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K.D.S. and D.W.L. performed experiments. K.D.S., D.W.L. and A.C. designed experiments. K.D.S. and A.C. wrote the manuscript. S.B.C. provided materials. All authors discussed the results and commented on the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Andrew Camilli.

Supplementary information

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    Supplementary Information

    This file contains Supplementary Figures 1-5 and Supplementary Tables 1-3.


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