Transcriptome analysis of QsvR regulating gene expression of Vibrio parahaemolyticus with different genetic backgrounds

Abstract:

[Background] OpaR is the master quorum sensing regulator of Vibrio parahaemolyticus. QsvR, an AraC-type transcriptional regulator, has reciprocal regulatory activities with OpaR. The regulatory effect of QsvR on gene expression is affected by OpaR, while their relationship in gene regulation remains to be fully elucidated. [Objective] To investigate QsvR regulons in the wild type (WT) and the opaR mutant (ΔopaR), and thus determine the effect of OpaR on the gene regulation of QsvR in V. parahaemolyticus. [Methods] Illumina HiSeq was employed to mine the differentially expressed genes in the qsvR mutant (ΔqsvR) or ΔqsvRΔopaR relative to that in WT or ΔopaR under the biofilm formation growth condition. [Results] QsvR regulated 1 735 genes (regulon 1) in the WT background, including 855 genes activated and 880 genes repressed. QsvR regulated 1 187 genes (regulon 2) in the ΔopaR background, including 533 genes activated and 654 genes repressed. There were 517 common genes shared by regulons 1 and regulons 2, and most of these genes were oppositely regulated by QsvR between the two regulons. According to the results of gene ontology (GO) annotation, 467 and 204 genes from regulons 1 and regulons 2 were respectively annotated to three categories (biological process, molecular function, and cellular component) and thirty sub-categories. The results of Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment showed that 372 and 678 genes from regulons 1 and regulons 2 were respectively enriched in 30 signaling pathways (Q value＜0.05). The genes in regulon 1 were mainly enriched in cellular metabolism, genetic information processing, and environmental information processing, and those in regulon 2 in cellular metabolism. The classification results obtained with the cluster of orthologous groups of proteins (COG) showed that the genes in regulons 1 and regulons 2 were mainly involved in amino acid transport and metabolism, signal transduction mechanisms, energy production and conversion, general function prediction only, and function unknown. In addition, the regulons 1 and regulons 2 contained a large number of regulatory genes and putative c-di-GMP metabolism-associated genes, as well as some polar flagellar genes, capsular polysaccharide genes, exopolysaccharide synthesis genes, type IV pili-associated genes, type III secretion system genes, and type VI secretion system genes. [Conclusion] QsvR was a global regulator in V. parahaemolyticus, controlling the transcription of a large number of genes. OpaR affected the regulatory actions of QsvR on its target genes and the composition of QsvR regulon.