SlyA directly represses yhcN via a novel binding motif in Salmonella Typhimurium: Implications for motility control

Salmonella Typhimurium is a prevalent foodborne pathogen worldwide. The MarR family transcriptional regulator SlyA acts as a global modulator of gene expression, yet its specific downstream effectors remain poorly defined. RNA-seq analysis identified 211 genes significantly regulated by SlyA. Notably, the yhcN gene, exhibiting the most pronounced differential expression, was found to contain a novel SlyA-binding motif (TTAAAAAGCAGAAACAAT) validated by electrophoretic mobility shift assay (EMSA). Structural analysis supports a "conserved scaffold, variable interface" model, in which inter-domain loop plasticity enables SlyA to accommodate non-canonical promoter architectures. Functional validation confirmed that SlyA directly represses yhcN transcription. Genetic epistasis analysis revealed that deletion of slyA enhanced bacterial swimming motility, whereas deletion of yhcN attenuated it; importantly, the ΔslyAΔyhcN double mutant restored motility to wild-type levels, and complementation of either single mutant with the respective wild-type allele rescued the phenotype. These findings establish a linear regulatory cascade in which SlyA represses yhcN to modulate swimming motility, expanding the known SlyA regulatory network and providing a foundation for understanding bacterial adaptation mechanisms.