Sibanda Siphathele, Kwenda Stanford, Tanui Collins K, Shyntum Divine Y, Coutinho Teresa A, Moleleki Lucy N
Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, 0002 Pretoria, South Africa.
Centre for Microbial Ecology and Genomics (CMEG), Faculty of Natural and Agricultural Sciences, University of Pretoria, 0002 Pretoria, South Africa.
Genes (Basel). 2018 Mar 7;9(3):148. doi: 10.3390/genes9030148.
LMG 2665 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. Pairwise comparisons of LMG 2665 in the absence of AHLs (Optical density (OD) = 0.2) and in the presence of AHLs (OD = 0.5) were performed. Additionally, pairwise comparisons of LMG 2665 and its QS mutant at OD = 0.5 were undertaken. In total, 608 genes were differentially expressed between LMG 2665 at OD = 0.5 versus the same strain at OD = 0.2 and 701 genes were differentially expressed between LMG 2665 versus its QS mutant at OD = 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. Functional characterization of the QS regulated genes in LMG 2665 could assist in the formulation of control strategies for this plant pathogen.
LMG 2665合成并利用酰基高丝氨酸内酯（AHLs）进行信号传导。该菌株中受EanI/R群体感应（QS）系统调控的完整基因集仍不完全清楚。在本研究中，利用RNA测序（RNA-seq）来鉴定LMG 2665中的EanI/R调控子。对不存在AHLs（光密度（OD）= 0.2）和存在AHLs（OD = 0.5）的LMG 2665进行了成对比较。此外，还对OD = 0.5时的LMG 2665及其QS突变体进行了成对比较。总共，OD = 0.5的LMG 2665与OD = 0.2的同一菌株之间有608个基因差异表达，OD = 0.5时的LMG 2665与其QS突变体之间有701个基因差异表达。两种方法共有196个基因差异表达。这些基因约占本研究所用实验条件下整个转录组的4.5%。RNA-seq数据通过逆转录定量聚合酶链反应（RT-qPCR）进行了验证。发现受EanI/R QS调控的基因包括编码氧化还原感应、代谢、鞭毛形成、鞭毛依赖性运动、细胞粘附、生物膜形成、调节因子、转运、趋化性、甲基接受蛋白、膜蛋白、细胞壁合成、应激反应以及大量假定蛋白的基因。本研究结果深入了解了LMG 2665中受EanI/R系统调控的基因。对LMG 2665中QS调控基因的功能表征有助于制定针对这种植物病原体的控制策略。
