Letter | Published:

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

Nature volume 497, pages 254257 (09 May 2013) | Download Citation

This article has been updated


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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Change history

  • 24 May 2019

    We could not replicate the results in Fig. 2a and g of this Letter, and new information has revealed a flaw in the interpretation of Fig. 2h. As a result, we do not have evidence to support RNA degradation as the mechanism that underlies Cas9-mediated regulation of FTN_1103 mRNA expression; see accompanying Amendment. This has not been corrected online.


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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.

Author information


  1. Microbiology and Molecular Genetics Program, Department of Microbiology and Immunology, Emory University, Atlanta, Georgia 30329, USA

    • Timothy R. Sampson
    •  & Anna C. Llewellyn
  2. Emory Vaccine Center, Emory University, Atlanta, Georgia 30329, USA

    • Timothy R. Sampson
    • , Anna C. Llewellyn
    •  & David S. Weiss
  3. Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA

    • Timothy R. Sampson
    • , Anna C. Llewellyn
    •  & David S. Weiss
  4. Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia 30329, USA

    • Sunil D. Saroj
    • , Yih-Ling Tzeng
    •  & David S. Weiss


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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.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to David S. Weiss.

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    Supplementary Information

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