GSE53639
OpaR Controls a Network of Downstream Transcription Factors in Vibrio parahaemolyticus BB22
Vibrio parahaemolyticus an emerging pathogen that is a causative agent of foodborne gastroenteritis when raw or undercooked seafood is consumed.   Previous microarray data using a Vibrio parahaemolyticus RIMD2210633 chip has shown the master quorum-sensing regulator OpaR controls virulence, type III and type VI secretion systems, and flagellar and capsule production genes.  In a parallel study, RNA-Seq was used to comparatively study the transcriptome changes of wild type Vibrio parahaemolyticus BB22 and a ?opaR strain directly. Differences in mRNA expression were analyzed using next generation Illumina sequencing and bioinformatics techniques to align and count reads.  A comparison with the previous microarray data showed good correlation between the shared genes.  The RNA-Seq offered an insight into control of genes specific to the Vibrio parahaemolyticus BB22 strain as well as a new look at the sRNAs that are expressed.  Eleven transcriptional regulators with greater than 4 fold regulation in the previous microarray study and 2 fold regulation in the RNA-Seq analysis, were chosen to validate the data using qRT-PCR and further characterized with electrophoretic mobility shift assays (EMSAs) to determine if they are direct targets of OpaR.   The transcription factors chosen play key roles in virulence, surface motility, cell to cell interactions, and cell surface characteristics.  One small RNA was identified in the RNA-Seq data to be quorum-sensing controlled and unidentified by other programs.  The RNA-Seq data has aided in understanding and elucidating the hierarchy of quorum-sensing control of OpaR in Vibrio parahaemolyticus. Overall design: The wild type Vibrio parahaemolyticus BB22 strain LM5312 and an opaR deletion strain LM5674 were analyzed for mRNA expression using RNA-Seq.