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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.


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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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