Transcriptome Profiling Reveals the EanI/R Quorum Sensing Regulon in Pantoea Ananatis LMG 2665(T)

Pantoea ananatis LMG 2665(T) synthesizes and utilizes acyl homoserine lactones (AHLs) for signalling. The complete set of genes regulated by the EanI/R quorum sensing (QS) system in this strain is still not fully known. In this study, RNA-sequencing (RNA-seq) was used to identify the EanI/R regulon in LMG 2665(T). Pairwise comparisons of LMG 2665(T) in the absence of AHLs (Optical density (OD)(600) = 0.2) and in the presence of AHLs (OD(600) = 0.5) were performed. Additionally, pairwise comparisons of LMG 2665(T) and its QS mutant at OD(600) = 0.5 were undertaken. In total, 608 genes were differentially expressed between LMG 2665(T) at OD(600) = 0.5 versus the same strain at OD(600) = 0.2 and 701 genes were differentially expressed between LMG 2665(T) versus its QS mutant at OD(600) = 0.5. A total of 196 genes were commonly differentially expressed between the two approaches. These constituted approximately 4.5% of the whole transcriptome under the experimental conditions used in this study. The RNA-seq data was validated by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR). Genes found to be regulated by EanI/R QS were those coding for redox sensing, metabolism, flagella formation, flagella dependent motility, cell adhesion, biofilm formation, regulators, transport, chemotaxis, methyl accepting proteins, membrane proteins, cell wall synthesis, stress response and a large number of hypothetical proteins. The results of this study give insight into the genes that are regulated by the EanI/R system in LMG 2665(T). Functional characterization of the QS regulated genes in LMG 2665(T) could assist in the formulation of control strategies for this plant pathogen.