Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Apartado 1095, Seville 41080, Spain.
Nucleic Acids Res. 2020 Dec 2;48(21):11857-11867. doi: 10.1093/nar/gkaa730.
Expression of Salmonella enterica loci harboring undermethylated GATC sites at promoters or regulatory regions was monitored by single cell analysis. Cell-to-cell differences in expression were detected in ten such loci (carA, dgoR, holA, nanA, ssaN, STM1290, STM3276, STM5308, gtr and opvAB), with concomitant formation of ON and OFF subpopulations. The ON and OFF subpopulation sizes varied depending on the growth conditions, suggesting that the population structure can be modulated by environmental control. All the loci under study except STM5308 displayed altered patterns of expression in strains lacking or overproducing Dam methylase, thereby confirming control by Dam methylation. Bioinformatic analysis identified potential binding sites for transcription factors OxyR, CRP and Fur, and analysis of expression in mutant backgrounds confirmed transcriptional control by one or more of such factors. Surveys of gene expression in pairwise combinations of Dam methylation-dependent loci revealed independent switching, thus predicting the formation of a high number of cell variants. This study expands the list of S. enterica loci under transcriptional control by Dam methylation, and underscores the relevance of the DNA adenine methylome as a source of phenotypic heterogeneity.
通过单细胞分析监测了沙门氏菌 enterica 基因座中在启动子或调控区域含有未甲基化 GATC 位点的表达。在十个这样的基因座（carA、dgoR、holA、nanA、ssaN、STM1290、STM3276、STM5308、gtr 和 opvAB）中检测到了细胞间表达的差异，同时形成了 ON 和 OFF 亚群。ON 和 OFF 亚群的大小取决于生长条件，表明群体结构可以通过环境控制来调节。除了 STM5308 之外，所有研究的基因座在缺乏或过度产生 Dam 甲基酶的菌株中表现出改变的表达模式，从而证实了 Dam 甲基化的控制。生物信息学分析鉴定了转录因子 OxyR、CRP 和 Fur 的潜在结合位点，并且在突变背景下的表达分析证实了一个或多个这样的因子的转录控制。对依赖 Dam 甲基化的基因座进行成对组合的基因表达调查显示出独立的切换，从而预测形成大量细胞变体。本研究扩展了沙门氏菌 enterica 基因座受 Dam 甲基化转录控制的列表，并强调了 DNA 腺嘌呤甲基组作为表型异质性来源的相关性。
