Regulons for many transcription factors have been elucidated in model strains leading to an understanding of their role in producing physiological states. Comparative analysis of a regulon and its target genes between different strains of the same species is lacking. Ferric uptake regulator (Fur), involved in iron homeostasis, is one of the most conserved TFs, and is present in a wide range of bacteria. Using ChIP-exo experiments, we performed a comprehensive study of Fur binding sites in nine Escherichia coli strains with different lifestyles. 79 of the 431 target genes (18%) found belong to Fur core regulon, comprising genes involved in ion transport and metabolism, energy production and conversion, and amino acid metabolism and transport. 179 of the target genes (42%) comprise the accessory regulon, most of which were related to cell wall structure and biogenesis, and virulence factor pathways. The remaining target genes (173 or 40%) were in the unique regulon, with gene functions that were largely unknown. Furthermore, deletion of the fur gene led to distinct phenotypes in growth, motility, antibiotic resistance, and the change of siderophore production. These results provide a more complete understanding of how Fur regulates a set of target genes with surprising variation in closely related bacteria.

中文翻译：

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毛皮泛调节子的重建揭示了大肠杆菌转录调控的复杂性和多样性

已经在模型菌株中阐明了许多转录因子的调节子，从而使人们了解了它们在产生生理状态中的作用。缺乏对相同物种的不同品系之间的调节子及其靶基因的比较分析。参与铁稳态的铁摄取调节剂（Fur）是最保守的TF之一，存在于多种细菌中。使用ChIP-exo实验，我们对9种具有不同生活方式的大肠杆菌菌株的Fur结合位点进行了全面研究。发现的431个靶基因中有79个（占18％）属于毛皮核心调节子，包括与离子转运和代谢，能量产生和转化以及氨基酸代谢和转运有关的基因。179个靶基因（42％）组成了副基因，其中大多数与细胞壁结构和生物发生以及毒力因子途径有关。其余的目标基因（173或40％）位于独特的regulon中，其基因功能很大程度上未知。此外，毛发基因的缺失导致生长，运动性，抗生素抗性和铁载体产生的变化具有明显的表型。这些结果提供了对Fur如何调节一组靶基因以及紧密相关细菌中令人惊讶的变化的更完整的理解。