Regulatory small RNA, Qrr2, is expressed independently of sigma factor-54 and functions autonomously in Vibrio parahaemolyticus to control quorum sensing

Abstract

Bacterial cells alter gene expression in response to changes in population density in a process called quorum sensing (QS). In Vibrio harveyi, LuxO, a low cell density activator of sigma factor-54 (RpoN), is required for transcription of five non-coding regulatory sRNAs, Qrr1-Qrr5, which each repress translation of the master QS regulator LuxR. Vibrio parahaemolyticus, the leading cause of bacterial seafood-borne gastroenteritis, also contains five Qrr sRNAs that control OpaR (the LuxR homolog), required for capsule polysaccharide (CPS) and biofilm production, motility, and metabolism. We show that in a ΔluxO deletion mutant, opaR was de-repressed and CPS and biofilm were produced. However, in a ΔrpoN mutant, opaR was repressed, no CPS was produced, and less biofilm production was observed compared to wild type. To determine why opaR was repressed, expression analysis in ΔluxO showed all five qrr genes were repressed, while in ΔrpoN the qrr2 gene was significantly de-repressed. Reporter assays and mutant analysis showed Qrr2 sRNA can act autonomously to control OpaR. Bioinformatics analysis identified a sigma-70 (RpoD) -35 -10 promoter overlapping the canonical sigma-54 (RpoN) promoter in the qrr2 regulatory region. Mutagenesis of the sigma-70 -10 promoter site in the ΔrpoN mutant background, resulted in repression of qrr2. Analysis of qrr quadruple deletion mutants, in which only a single qrr gene is present, showed that only Qrr2 sRNA can act autonomously to regulate opaR. Mutant and expression data also demonstrated that RpoN and the global regulator Fis act additively to repress qrr2. Our data has uncovered a new mechanism of qrr expression and shows that Qrr2 sRNA is sufficient for OpaR regulation. Importance The quorum sensing non-coding sRNAs are present in all Vibrio species but vary in number and regulatory roles among species. In the Harveyi clade, all species contain five qrr genes that, in V. harveyi, are additive in function to control LuxR. In the Cholerae clade, four qrr genes are present, and in V. cholerae the qrr genes are redundant in function to control HapR (the LuxR homolog). Here, we show that in V. parahaemolyticus, only qrr2 can function autonomously to control OpaR, and it is controlled by two overlapping promoters. The qrr2 sigma-70 promoter is present in all strains of V. parahaemolyticus and in other members of the Harveyi clade suggesting a conserved mechanism of regulation.