RNA interactome of hypervirulentKlebsiella pneumoniaereveals a small RNA inhibitor of capsular mucoviscosity and virulence

ABSTRACT Hypervirulent Klebsiella pneumoniae (HvKP) is an emerging bacterial pathogen causing invasive infection in immune-competent humans. The hypervirulence is strongly linked to the overproduction of hypermucovisous capsule, but the underlining regulatory mechanism of hypermucoviscosity (HMV) has been elusive, especially at the post-transcriptional level mediated by small noncoding RNAs (sRNAs). Using a recently developed RNA interactome profiling approach, we interrogate the Hfq-associated sRNA regulatory network and establish the intracellular RNA-RNA interactome in HvKP. Our data reveal numerous interactions between sRNAs and HMV-related mRNAs, and identify a plethora of sRNAs that repress or promote HMV. One of the strongest repressors of HMV is ArcZ, which is activated by catabolite regulator CRP and targets many HMV-related genes including mlaA and fbp . We discover that MlaA and its function in phospholipid transport is crucial for capsule retention and HMV, inactivation of which abolished Klebsiella virulence in mice. ArcZ overexpression significantly reduced bacterial burden in mice and reduced HMV in multiple carbapenem-resistant and hypervirulent clinical isolates with diverse genetic background, indicating it is a potent RNA inhibitor of bacterial pneumonia with therapeutic potential. In summary, our work unravels a comprehensive map of the RNA-RNA interaction network of HvKP and identifies a novel CRP-ArcZ-MlaA regulatory circuit of HMV, providing mechanistic insights into the posttranscriptional virulence control in a superbug of global concern. HIGHLIGHTS Global RNA-RNA interactome map in hypervirulent Klebsiella pneumoniae Hfq and multiple small RNAs regulate capsular hypermucoviscosity ArcZ targets mlaA that is required for lipid transport, hypermucoviscosity and virulence Crp is a transcriptional activator of ArcZ governing a new virulence circuit