Bordetella pertussis is a Gram-negative, strictly human re-emerging respiratory pathogen and the causative agent of whooping cough. The requirement of the RNA chaperone Hfq for the virulence of B. pertussis suggests that Hfq-dependent small regulatory RNAs (sRNAs) are involved in the virulence of this pathogen. To identify their potential mRNA targets, we applied a method combining experimental and computational approaches called RIL-seq. The majority of putative mRNA targets, including several virulence factors, interact with two sRNAs, CT_433 and CT_521, suggesting that these sRNAs may represent central riboregulatory nodes of B. pertussis. Furthermore, our data suggest that CT_532 sRNA can base pair with the 5'UTR region of ompA mRNA encoding outer membrane protein BP0943 (OmpA) and that CT_532, RNase III and Hfq are involved in the control of ompA expression. The CT_532 sRNA shares 60% identity with the E. coli sRNA MicA and its expression is also modulated by Hfq and stress conditions such as heat and cold shocks. Overall, these results suggest that CT_532 represents a MicA homolog. Importantly, the mutant lacking the first 22 nucleotides of CT_532 exhibits reduced cytotoxicity towards human macrophages and impaired biofilm production but increased resistance to complement compared to the wild type strain.

Laboratory of post transcriptional control of gene expression Institute of Microbiology of the Czech Academy of Sciences Prague 14200 Czech Republic

University of Lille CNRS Inserm CHU Lille Institute Pasteur de Lille US 41 UAR 2014 PLBS F 59000Lille France

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