Comparative integrated omics analysis of the Hfq regulon in Bordetella pertussis

Bordetella pertussis is a Gram-negative strictly human pathogen of the respiratory tract and the etiological agent of whooping cough (pertussis). Previously, we have shown that RNA chaperone Hfq is required for virulence of B. pertussis and that more than 10% of genes are affected by the lack of Hfq. This study represents the first attempt to characterize the Hfq regulon in bacterial pathogen using an integrative omics approach. Gene expression profiles were analyzed by RNA-seq and protein levels in cell-associated and cell-free fractions were analyzed by LC-MS/MS techniques. Comparative analysis of transcriptomic and proteomic data revealed solid correlation (r2= 0.4) considering the role of Hfq in post-transcriptional control of gene expression. Importantly, our study confirms and further enlightens the role of Hfq in pathogenicity of B. pertussis as it shows that hfq mutant displays strongly impaired expression and in particular secretion of substrates of Type III secretion system (T3SS) and substantially reduced resistance to serum killing. On the other side, significantly increased production of proteins implicated in transport of important metabolites and essential nutrients observed in the mutant seems to compensate for the physiological defect introduced by the deletion of the hfq gene.