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A CRISPR/Cas system mediates bacterial innate immune evasion and virulence

An Author Correction to this article was published on 24 May 2019

A Corrigendum to this article was published on 21 August 2013


CRISPR/Cas (clustered regularly interspaced palindromic repeats/CRISPR-associated) systems are a bacterial defence against invading foreign nucleic acids derived from bacteriophages or exogenous plasmids1,2,3,4. These systems use an array of small CRISPR RNAs (crRNAs) consisting of repetitive sequences flanking unique spacers to recognize their targets, and conserved Cas proteins to mediate target degradation5,6,7,8. Recent studies have suggested that these systems may have broader functions in bacterial physiology, and it is unknown if they regulate expression of endogenous genes9,10. Here we demonstrate that the Cas protein Cas9 of Francisella novicida uses a unique, small, CRISPR/Cas-associated RNA (scaRNA) to repress an endogenous transcript encoding a bacterial lipoprotein. As bacterial lipoproteins trigger a proinflammatory innate immune response aimed at combating pathogens11,12, CRISPR/Cas-mediated repression of bacterial lipoprotein expression is critical for F. novicida to dampen this host response and promote virulence. Because Cas9 proteins are highly enriched in pathogenic and commensal bacteria, our work indicates that CRISPR/Cas-mediated gene regulation may broadly contribute to the regulation of endogenous bacterial genes, particularly during the interaction of such bacteria with eukaryotic hosts.

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Figure 1: Cas9, tracrRNA and scaRNA are necessary for FTN_1103 repression.
Figure 2: Cas9, tracrRNA and scaRNA associate and mediate FTN_1103 degradation.
Figure 3: Cas9, tracrRNA and scaRNA facilitate evasion of TLR2 signalling by temporal repression of FTN_1103.
Figure 4: Cas9, tracrRNA and scaRNA are necessary for virulence.


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

    ADS  CAS  Article  Google Scholar 

  2. Marraffini, L. A. & Sontheimer, E. J. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322, 1843–1845 (2008)

    ADS  CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

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

    ADS  CAS  Article  Google Scholar 

  5. Hale, C. R. et al. RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell 139, 945–956 (2009)

    CAS  Article  Google Scholar 

  6. 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)

    ADS  CAS  Article  Google Scholar 

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

    ADS  CAS  Article  Google Scholar 

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

    ADS  Article  Google Scholar 

  9. Zegans, M. E. et al. Interaction between bacteriophage DMS3 and host CRISPR region inhibits group behaviors of Pseudomonas aeruginosa . J. Bacteriol. 191, 210–219 (2009)

    CAS  Article  Google Scholar 

  10. Babu, M. et al. A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol. Microbiol. 79, 484–502 (2011)

    CAS  Article  Google Scholar 

  11. Aliprantis, A. O. et al. Cell activation and apoptosis by bacterial lipoproteins through toll-like receptor-2. Science 285, 736–739 (1999)

    CAS  Article  Google Scholar 

  12. Brightbill, H. D. et al. Host defense mechanisms triggered by microbial lipoproteins through Toll-like receptors. Science 285, 732–736 (1999)

    CAS  Article  Google Scholar 

  13. Jones, C. L. et al. Subversion of host recognition and defense systems by Francisella spp. Microbiol. Mol. Biol. Rev. 76, 383–404 (2012)

    CAS  Article  Google Scholar 

  14. Malik, M. et al. Toll-like receptor 2 is required for control of pulmonary infection with Francisella tularensis . Infect. Immun. 74, 3657–3662 (2006)

    CAS  Article  Google Scholar 

  15. Abplanalp, A. L., Morris, I. R., Parida, B. K., Teale, J. M. & Berton, M. T. TLR-dependent control of Francisella tularensis infection and host inflammatory responses. PLoS ONE 4, e7920 (2009)

    ADS  Article  Google Scholar 

  16. Jones, C. L., Sampson, T. R., Nakaya, H. I., Pulendran, B. & Weiss, D. S. Repression of bacterial lipoprotein production by Francisella novicida facilitates evasion of innate immune recognition. Cell. Microbiol. 14, 1531–1543 (2012)

    CAS  Article  Google Scholar 

  17. Makarova, K. S., Aravind, L., Wolf, Y. I. & Koonin, E. V. Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biol. Direct 6, 38 (2011)

    CAS  Article  Google Scholar 

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

    ADS  CAS  Article  Google Scholar 

  19. Postic, G. et al. Identification of small RNAs in Francisella tularensis . BMC Genomics 11, 625 (2010)

    Article  Google Scholar 

  20. Bayer, T. S., Booth, L. N., Knudsen, S. M. & Ellington, A. D. Arginine-rich motifs present multiple interfaces for specific binding by RNA. RNA 11, 1848–1857 (2005)

    CAS  Article  Google Scholar 

  21. Stern, A., Keren, L., Wurtzel, O., Amitai, G. & Sorek, R. Self-targeting by CRISPR: gene regulation or autoimmunity? Trends Genet. 26, 335–340 (2010)

    CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

  23. Louwen, R. et al. A novel link between Campylobacter jejuni bacteriophage defence, virulence and Guillain-Barre syndrome. Eur. J. Clin. Microbiol. Infect. Dis. 32, 207–226 (2013)

    CAS  Article  Google Scholar 

  24. Brotcke, A. et al. Identification of MglA-regulated genes reveals novel virulence factors in Francisella tularensis . Infect. Immun. 74, 6642–6655 (2006)

    CAS  Article  Google Scholar 

  25. Janik, A., Juni, E. & Heym, G. A. Genetic transformation as a tool for detection of Neisseria gonorrhoeae . J. Clin. Microbiol. 4, 71–81 (1976)

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Llewellyn, A. C., Jones, C. L., Napier, B. A., Bina, J. E. & Weiss, D. S. Macrophage replication screen identifies a novel Francisella hydroperoxide resistance protein involved in virulence. PLoS ONE 6, e24201 (2011)

    ADS  CAS  Article  Google Scholar 

  27. Kumar, P., Sannigrahi, S., Scoullar, J., Kahler, C. M. & Tzeng, Y. L. Characterization of DsbD in Neisseria meningitidis . Mol. Microbiol. 79, 1557–1573 (2011)

    CAS  Article  Google Scholar 

  28. Schaible, U. E. & Kaufmann, S. H. E. Studying trafficking of intracellular pathogens in antigen-presenting cells. Methods Microbiol. 31, 343–360 (2002)

    CAS  Article  Google Scholar 

  29. Postic, G. et al. Identification of a novel small RNA modulating Francisella tularensis pathogenicity. PLoS ONE 7, e41999 (2012)

    ADS  CAS  Article  Google Scholar 

  30. Janik, A., Juni, E. & Heym, G. A. Genetic transformation as a tool for detection of Neisseria gonorrhoeae . J. Clin. Microbiol. 4, 71–81 (1976)

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Gallagher, L. A., McKevitt, M., Ramage, E. R. & Manoil, C. Genetic dissection of the Francisella novicida restriction barrier. J. Bacteriol. 190, 7830–7837 (2008)

    CAS  Article  Google Scholar 

  32. Bryksin, A. V. & Matsumura, I. Rational design of a plasmid origin that replicates efficiently in both gram-positive and gram-negative bacteria. PLoS ONE 5, e13244 (2010)

    ADS  Article  Google Scholar 

  33. Ménard, R., Sansonetti, P. J. & Parsot, C. Nonpolar mutagenesis of the ipa genes defines IpaB, IpaC, and IpaD as effectors of Shigella flexneri entry into epithelial cells. J. Bacteriol. 175, 5899–5906 (1993)

    Article  Google Scholar 

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We would like to thank R. Ahmed, G. Conn, C. Dunham, C. Moran, B. Napier, D. S. Stephens and the Stephens laboratory, and M. Swanson for discussions and critical reading of this manuscript. The project described was supported by National Institutes of Health (NIH) grant U54-AI057157 from the Southeastern Regional Center of Excellence for Emerging Infections and Biodefense and R56-AI87673 to D.S.W., and R56-AI061031 to Y.-L.T. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the NIH. T.R.S. was supported by the NSF Graduate Research Fellowship, as well as the ARCS Foundation. T.R.S. and D.S.W. have filed a related provisional patent.

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T.R.S. performed the experiments; S.D.S. and Y.-L.T. generated the N. meningitidis cas9 deletion mutant and performed associated experiments; A.C.L. generated the Cas9–Flag expressing strain; T.R.S. and D.S.W. conceived and designed experiments, interpreted data and wrote the manuscript.

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Correspondence to David S. Weiss.

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The authors declare no competing financial interests.

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Sampson, T., Saroj, S., Llewellyn, A. et al. A CRISPR/Cas system mediates bacterial innate immune evasion and virulence. Nature 497, 254–257 (2013).

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