Transcriptional regulation for genome expression determines growth and adaptation of single-cell bacteria that are directly exposed to environment. The transcriptional apparatus in Escherichia coli K-12 is composed of RNA polymerase core enzyme and two groups of its regulatory proteins, seven species of promoter-recognition subunit sigma and about 300 species of transcription factors. The identification of regulatory targets for all these regulatory proteins is critical toward understanding the genome regulation as a whole. For this purpose, we performed a systematic search in vitro of the whole set of binding sites for each factor by gSELEX system. This review summarizes the accumulated knowledge of regulatory targets for more than 150 TFs from E. coli K-12. Overall TFs could be classified into four families: nucleoid-associated bifunctional TFs; global regulators; local regulators; and single-target regulators, in which the regulatory functions remain uncharacterized for the nucleoid-associated TFs. Here we overview the regulatory targets of two nucleoid-associated TFs, H-NS and its paralog StpA, both together playing the silencing role of a set of non-essential genes. Participation of LeuO and other global regulators have been indicated for the anti-silencing. Finally, we propose the hierarchy of TF network as a key framework of the bacterial genome regulation.

中文翻译：

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大肠杆菌 K-12 转录因子网络的层次结构：H-NS 介导的沉默和全球监管机构的抗沉默

基因组表达的转录调控决定了直接暴露于环境的单细胞细菌的生长和适应。大肠杆菌K-12的转录装置由RNA聚合酶核心酶及其两组调控蛋白、7种启动子识别亚基sigma和约300种转录因子组成。识别所有这些调节蛋白的调节靶点对于理解整个基因组调节至关重要。为此，我们通过 gSELEX 系统对每个因子的整套结合位点进行了体外系统搜索。这篇综述总结了来自大肠杆菌的 150 多个 TF 的监管目标积累知识K-12。总体 TF 可分为四个家族：类核相关双功能 TF；全球监管机构；当地监管机构；和单靶点调节剂，其中与类核素相关的 TF 的调节功能仍未确定。在这里，我们概述了两个类核相关 TF、H-NS 及其旁系同源 StpA 的调节靶标，它们共同发挥了一组非必需基因的沉默作用。LeuO 和其他全球监管机构的参与已被指示用于反沉默。最后，我们提出 TF 网络的层次结构作为细菌基因组调控的关键框架。