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Background    Vibrio parahaemolyticus  is a leading cause of infectious diarrhea and enterogastritis via the fecal-oral route.  V. harveyi  is a pathogen of fishes and invertebrates, and has been used as a model for quorum sensing (QS) studies. LuxR is the master QS regulator (MQSR) of  V. harveyi , and LuxR-dependent expression of its own gene,  qrr2–4  and  aphA  have been established in  V. harveyi . Molecular regulation of target genes by the  V. parahaemolyticus  MQSR OpaR is still poorly understood.    Methodology/Principal Findings  The bioinformatics analysis indicated that V.  parahaemolyticus  OpaR,  V. harveyi  LuxR,  V. vulnificu  SmcR, and  V. alginolyticus  ValR were extremely conserved, and that these four MQSRs appeared to recognize the same conserved  cis -acting signals, which was represented by the consensus constructs manifesting as a position frequency matrix and as a 20 bp box, within their target promoters. The MQSR box-like sequences were found within the upstream DNA regions of  opaR ,  qrr2–4  and  aphA  in  V. parahaemolyticus , and the direct transcriptional regulation of these target genes by OpaR were further confirmed by multiple biochemical experiments including primer extension assay, gel mobility shift assay, and DNase I footprinting analysis. Translation and transcription starts, core promoter elements for sigma factor recognition, Shine-Dalgarno sequences for ribosome recognition, and OpaR-binding sites were determined for the five target genes of OpaR, which gave a structural map of the OpaR-dependent promoters. Further computational promoter analysis indicated the above regulatory circuits were shared by several other closely related Vibrios but with slight exceptions.    Conclusions/Significance  This study gave a comprehensive computational and characterization of the direct transcriptional regulation of five target genes,  opaR ,  qrr2–4  and  ahpA , by OpaR in  V. parahaemolyticus . These characterized regulatory circuits were conserved in  V. harveyi  and  V. parahaemolyticus .

Transcriptional Regulation of opaR, qrr2–4 and aphA by the Master Quorum-Sensing Regulator OpaR in Vibrio parahaemolyticus