Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [ChIP-seq]

Oxidative stress that originates from reactive oxygen species (ROS) is an inevitable consequence of aerobic respiration in bacteria. Three transcription factors (TFs), OxyR, SoxR, and SoxS play a critical role in transcriptional regulation of the defense system. However, the full genome-wide regulatory potential of them remains elusive. Here, we comprehensively reconstruct genome-wide OxyR, SoxR, and SoxS transcriptional regulatory networks in Escherichia coli under oxidative stress. Integrative data analysis reveals that OxyR, SoxR, and SoxS regulons are comprised of 38 genes in 28 transcription units (TUs), 11 genes in 10 TUs, and 34 genes in 25 TUs, respectively, significantly expanding the current knowledge of their regulatory networks. Comparison of them to other stress-response regulatory networks highlights minimal overlap between their regulons, indicating that E. coli has a series of relatively distinct stress responses covering the range of different stresses. We also demonstrate that these intricate networks coordinate detoxification process with DNA and protein damage repair, cell wall synthesis, divalent metal ion homeostasis, as well as metabolic robustness to produce overall response of E. coli to oxidative stress.

由活性氧簇（reactive oxygen species, ROS）引发的氧化应激是细菌有氧呼吸不可避免的生理产物。三类转录因子（transcription factors, TFs）——OxyR、SoxR与SoxS，在细菌防御系统的转录调控过程中发挥关键作用。然而，这三类转录因子在全基因组范围内的完整调控潜能仍未明确。本研究于氧化应激条件下，在大肠杆菌（Escherichia coli）中全面重构了OxyR、SoxR与SoxS的全基因组转录调控网络。整合数据分析显示，OxyR、SoxR与SoxS的调控子分别包含28个转录单元（transcription units, TUs）内的38个基因、10个TUs内的11个基因，以及25个TUs内的34个基因，这一结果显著拓展了学界对其调控网络的现有认知。将上述调控网络与其他应激响应调控网络进行比对后发现，它们的调控子之间重叠度极低，这表明大肠杆菌演化出了一系列相对独立的应激响应机制，以应对各类不同的应激刺激。本研究还证实，这些复杂的调控网络将解毒过程与DNA、蛋白质损伤修复、细胞壁合成、二价金属离子稳态以及代谢稳健性进行协同调控，从而使大肠杆菌产生针对氧化应激的整体应答反应。

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该数据集名称为'Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [ChIP-seq]'，但详情页面显示测序数据和图像数据均为零样本，且存在系统错误，导致数据无法访问，因此无法提供具体内容总结。