Genome-wide RNA-seq analysis of quorum sensing-dependent regulons in the plant-associated Burkholderia glumae strain PG1

Abstract

Burkholderia glumae PG1 is a soil-associated motile plant pathogenic bacterium possessing a cell density-dependent regulatory mechanism called quorum sensing (QS). Its genome encodes three distinct putative autoinducer-1 synthase genes, here designated bgaI1-3, which are responsible for synthesizing the N-acyl-homoserine lactones (AHL). In this study, all three bgaI genes were characterized as the functional AHL synthase genes using AHL bioreporters A. tumefaciens NTL4 and C. violaceum CV026. To elucidate functions of these QS systems, B. glumae PG1 ΔbgaI1-3 mutants were generated through allelic exchange. The deletion of each bgaI gene resulted in the strong reduction in motility, extracellular lipolytic activity, plant maceration and rice pathogenicity and colony morphology variation. To further identify the QS-regulated genes, the genome-wide transcriptome analysis of three ΔbgaI mutants vs. the parental strain was performed in the transition from exponential to stationary growth phase. In comparison with the parental strain, 481 of these genes were regulated in mutant ΔbgaI1, 213 in ΔbgaI2, and 367 in ΔbgaI3. In total, a set of 745 QS-regulated genes was identified. Among them, the majority of the QS-regulated genes linked to metabolic activities and the most pronounced regulation was observed for the genes involved in rhamnolipid, Flp pili, lipase, flagella, type VI secretion system and genes linked to a CRIPSR-Cas system. Notably, a cross-species analysis of QS-regulated genes revealed that B. glumae PG1 has more similarities with B. thailandensis than with the other two Bptm members, B. pseudomallei and B. mallei in lifestyle.