Transcriptomic dissection of the ToxR regulon in Vibrio parahaemolyticus at low cell density

Vibrio parahaemolyticus is a major seafood-borne pathogen whose pathogenesis and environmental fitness depend on the regulator ToxR, but the scope of its regulon has remained undefined. We used RNA-seq to compare the transcriptomes of wild-type RIMD2210633 strain and an isogenic Δ toxR strain at the peak of toxR expression, revealing 603 differentially expressed genes (348 down-regulated and 255 up-regulated in the mutant). ToxR predominantly functions as an activator of gene expression under the tested conditions. The regulon includes 32 regulatory genes, 13 c-di-GMP metabolism genes, the type III secretion system 1 (T3SS1) cluster (up-regulated in the mutant), all detectable T3SS2 genes and tdh2 (down-regulated in the mutant), differentially regulated type VI secretion system (T6SS1/T6SS2) genes, lateral flagellar genes, the scv genes, the mfpABC operon, and multiple porins. These findings establish ToxR as a central hup integrating the expression of genes associated with virulence, stress adaptation, biofilm development, and second-messenger signaling, providing a comprehensive framework for understanding how V. parahaemolyticus orchestrates its complex lifestyle during host colonization and environmental transitions.