Redefining HexR regulatory landscape in Pseudomonas putida through integrative systems biology [RNA-Seq]

Fine–tuning the regulation of primary carbon metabolism is essential for their successful adaptation, with HexR emerging as a key regulator. While previous studies have assessed HexR binding using in vitro assays and comparative transcriptomics, the in vivo binding sites of HexR and its genome–scale regulon remain undefined.

In this study, we performed comparative expression profiling of P. putida wild-type and hexR mutant strains on distinct growth substrates, including a glycolytic substrate (glucose), gluconeogenic substrates (acetate, succinate), and a substrate inducing both metabolic responses (glycerol). Our findings revealed extensive regulation of HexR in acetate metabolism, which simultaneously deactivates the glycolytic route and upregulates pyruvate metabolism, glyoxylate shunt, gluconeogenesis to support growth.