Department of Microbiology, Pusan National University, Busan 609-735, Korea.
Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea.
Plant Pathol J. 2013 Sep;29(3):249-59. doi: 10.5423/PPJ.OA.04.2013.0044.
Burkholderia glumae causes rice grain rot and sheath rot by producing toxoflavin, the expression of which is regulated by quorum sensing (QS). The QS systems of B. glumae rely on N-octanoyl homoserine lactone, synthesized by TofI and its cognate receptor TofR, to activate the genes for toxoflavin biosynthesis and an IclR-type transcriptional regulator gene, qsmR. To understand genome-wide transcriptional profiling of QS signaling, we employed RNAseq of the wild-type B. glumae BGR1 with QS-defective mutant, BGS2 (BGR1 tofI::Ω) and QS-dependent transcriptional regulator mutant, BGS9 (BGR1 qsmR::Ω). A comparison of gene expression profiling among the wild-type BGR1 and the two mutants before and after QS onset as well as gene ontology (GO) enrichment analysis from differential expressed genes (DEGs) revealed that genes involved in motility were highly enriched in TofI-dependent DEGs, whereas genes for transport and DNA polymerase were highly enriched in QsmR-dependent DEGs. Further, a combination of pathways with these DEGs and phenotype analysis of mutants pointed to a couple of metabolic processes, which are dependent on QS in B. glumae, that were directly or indirectly related with bacterial motility. The consistency of observed bacterial phenotypes with GOs or metabolic pathways in QS-regulated genes implied that integration RNAseq with GO enrichment or pathways would be useful to study bacterial physiology and phenotypes.
产毒黄素是引起稻粒腐病和叶鞘腐病的主要原因，其表达受群体感应（QS）调控。该菌的 QS 系统依赖于 N-辛酰高丝氨酸内酯，由 TofI 及其同源受体 TofR 合成，激活产毒黄素生物合成和 IclR 型转录调节因子基因 qsmR 的表达。为了了解 QS 信号的全基因组转录谱，我们采用 RNAseq 技术对野生型 B. glumae BGR1 及其 QS 缺陷突变株 BGS2（BGR1 tofI::Ω）和 QS 依赖型转录调节因子突变株 BGS9（BGR1 qsmR::Ω）进行了研究。比较 QS 起始前后野生型 BGR1 和两种突变株的基因表达谱，并对差异表达基因（DEGs）进行基因本体论（GO）富集分析，结果表明，运动相关基因在 TofI 依赖性 DEGs 中高度富集，而运输和 DNA 聚合酶相关基因在 QsmR 依赖性 DEGs 中高度富集。此外，通过对这些 DEGs 相关通路的组合分析以及突变体的表型分析，我们发现了一些代谢过程与细菌的运动能力直接或间接相关，这些过程依赖于 B. glumae 的 QS。QS 调控基因的表型观察与 GO 或代谢通路的一致性表明，将 RNAseq 与 GO 富集或通路分析相结合，将有助于研究细菌的生理学和表型。
