Hfq modulates system-wide regulatory networks controlling biocontrol property in Lysobacter enzymogenes

Abstract

Lysobacter enzymogenes is a beneficial soil bacterium renowned for its potent biocontrol properties, primarily attributed to antimicrobial secondary metabolites such as HSAF and WAP-8294A2, as well as specialized secretion systems. In this study, we investigate the post-transcriptional regulatory roles of the RNA chaperone Hfq in L. enzymogenes OH11 using an integrated multi-omics approach, combining transcriptomic, proteomic, and RNA-binding data. Our comprehensive analysis reveals that Hfq systemically regulates central metabolism and coordinates biocontrol-associated processes, including antimicrobial biosynthesis and secretion systems. Notably, Hfq extensively modulates multiple regulatory pathways involved in HSAF biosynthesis, a well-studied compound with potential applications in combating fungal and oomycete diseases. Additionally, we identify a set of Hfq-associated small RNAs. Through target prediction, we inferred that many of these sRNAs likely influence cellular functions and stress responses, reinforcing Hfq's role as a global regulator of bacterial physiology. These findings provide a systems-level understanding of Hfq's regulatory mechanisms in L. enzymogenes, offering valuable insights for optimizing its biocontrol potential.