Elucidation of the RpoD and RpoS sigmulons in Klebsiella pneumoniae MGH 78578 reveals distinct growth phase-specific gene regulation

Abstract The proliferation of multidrug-resistant Klebsiella pneumoniae strains underscores the urgent need to decipher the transcriptional mechanisms governing their pathogenicity and resistance. This study characterizes the genome-wide regulatory architecture of K. pneumoniae MGH 78578 by mapping the binding landscapes of the housekeeping sigma factor RpoD and the general stress response sigma factor RpoS using high-resolution chromatin immunoprecipitation with exonuclease treatment (ChIP-exo). Contrasting with prior low-resolution studies, RpoD was identified as the dominant transcriptional orchestrator, encompassing a larger sigmulon than RpoS across both mid-exponential and stationary phases. While RpoS exhibited a high number of binding sites, it displayed relaxed promoter specificity characterized by the absence of a conserved −35 motif, reflecting a poised and plastic regulatory potential. A distinct evolutionary signature was observed on plasmids, where sigma factor binding density matched or exceeded that of the chromosome, but a smaller proportion of these binding events occurred at regulatory positions, indicating that these horizontally acquired sequences are not yet fully adapted to the host’s sigma factor recognition patterns. In the context of pathogenicity, distinct binding patterns were observed: RpoD was predominantly associated with core antimicrobial resistance determinants, including plasmid-encoded β-lactamases, whereas RpoS was preferentially linked to surface-remodeling virulence factors. These findings provide a high-resolution reconstruction of the K. pneumoniae transcriptional network, revealing how evolutionary history and sigma factor specificity coordinate the complex interplay between multidrug resistance and virulence.