qsmR encoding an IclR-family transcriptional factor is a core pathogenic determinant of Burkholderia glumae beyond the acyl-homoserine lactone-mediated quorum-sensing system

The plant pathogenic bacterium Burkholderia glumae causes bacterial panicle blight (BPB) in rice-growing areas worldwide. It has been widely accepted that an acyl-homoserine lactone (AHL)-type quorum sensing (QS) system encoded by tofI and tofR genes (TofIR QS) is a key regulatory mechanism underlying the bacterial pathogenesis of B. glumae. In addition, qsmR, which encodes an IclR-family regulatory protein, has been considered an important part of TofIR QS. However, the present study with three strains of B. glumae representing different pathogenic strains revealed that this currently accepted paradigm should be modified. We characterized the regulatory function of TofIR QS and qsmR in three different strains of B. glumae, 336gr-1 (virulent), 411gr-6 (hypervirulent) and 257sh-1 (avirulent). In 336gr-1, both TofIR QS and qsmR were critical for the pathogenesis, being consistent with previous studies. However, in the hypervirulent strain 411gr-6, TofIR QS only partially contributes to the virulence, whereas qsmR was critical for pathogenesis like in 336gr-1. Furthermore, we found that a single nucleotide polymorphism causing T50K substitution in the qsmR coding sequence was the cause of the non-pathogenic trait of the naturally avirulent strain 257sh-1. Subsequent analyses of gene expression and transcriptome revealed that TofIR QS is partially controlled by qsmR at the transcriptional level in both virulent strains. Further genetic tests of additional B. glumae strains showed that 11 out of 20 virulent strains retained the ability to produce toxoflavin even after removing the tofI/tofM/tofR QS gene cluster like 411gr-6. In contrast, all the virulent strains tested lost the function almost completely upon deletion of the qsmR gene. Taking these results together, qsmR, rather than TofIR QS, is a master regulator that determines the pathogenic trait of B. glumae thus a more appropriate pathogen target for successful management of BPB. Author summaryBacterial cell-to-cell communication, called quorum-sensing, systems mediated by homoserine lactone (HSL)-type signaling molecules play pivotal roles in the virulence-related functions of diverse plant and animal pathogenic Gram-negative bacteria. Burkholderia glumae is the chief causal agent for bacterial panicle blight, a devastating rice disease worldwide. In this pathogen, the HSL-type quorum-sensing system dependent on the tofI and tofR genes had long been thought to be the core regulatory/signaling system essential for virulence. However, we discovered in this study that a highly virulent strain of B. glumae, 411gr-6, retained its virulence even after the tofI/tofR-dependent quorum-sensing function was disabled. We also found that more than a half of the natural strains of this pathogen species tested in this study also exhibited their virulence function in the absence of the tofI/tofR-dependent quorum-sensing system. Then we characterized the qsmR gene as an essential regulatory/signaling element for the bacterial pathogenesis regardless of the genetic variations among the strains of B. glumae. This study indicates that the qsmR gene, rather than the tofI/tofR-dependent quorum-sensing system, should be considered as an essential master regulatory/signaling factor for the virulence of B. glumae and, thus, a promising target for suppressing bacterial panicle blight.