Global analysis of the Hfq-mediated RNA interactome discovers a MicA homolog of Bordetella pertussis

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. Our RIL-seq analysis revealed putative targets of several sRNAs including CT_532. This sRNA can interact with 5´UTR regions of mRNAs encoding the outer membrane proteins BP0840 and BP0943 (OmpA). The CT_532 sRNA shares 60% identity with the E. coli sRNA MicA and its expression is modulated by the heat and cold shocks as well as by osmotic stress. Collectively, these results suggest that CT_532 represents a MicA homolog. Importantly, the mutant lacking the first 22 nucleotides of CT_532 as well as its complemented variant overproducing CT_532 displayed reduced cytotoxicity towards human macrophages and impaired biofilm production compared to the wt strain. In addition, proteomic analysis revealed that CT_532 mutant produces increased amounts of OmpA protein.