In 1967, in this journal, Evelyn Witkin proposed the existence of a coordinated DNA damage response in Escherichia coli , which later came to be called the “SOS response.” We revisited this response using the replication inhibitor azidothymidine (AZT) and RNA-Seq analysis and identified several features. We confirm the induction of classic Save our ship (SOS) loci and identify several genes, including many of the pyrimidine pathway, that have not been previously demonstrated to be DNA damage-inducible. Despite a strong dependence on LexA, these genes lack LexA boxes and their regulation by LexA is likely to be indirect via unknown factors. We show that the transcription factor “stringent starvation protein” SspA is as important as LexA in the regulation of AZT-induced genes and that the genes activated by SspA change dramatically after AZT exposure. Our experiments identify additional LexA-independent DNA damage inducible genes, including 22 small RNA genes, some of which appear to activated by SspA. Motility and chemotaxis genes are strongly down-regulated by AZT, possibly as a result of one of more of the small RNAs or other transcription factors such as AppY and GadE, whose expression is elevated by AZT. Genes controlling the iron siderophore, enterobactin, and iron homeostasis are also strongly induced, independent of LexA. We confirm that IraD antiadaptor protein is induced independent of LexA and that a second antiadaptor, IraM is likewise strongly AZT-inducible, independent of LexA, suggesting that RpoS stabilization via these antiadaptor proteins is an integral part of replication stress tolerance.

中文翻译：

---

重温大肠杆菌的 DNA 损伤反应：复制抑制后的差异基因表达


1967 年，Evelyn Witkin 在该杂志上提出，大肠杆菌中存在协调的 DNA 损伤反应，后来被称为“SOS 反应”。我们使用复制抑制剂叠氮胸苷 (AZT) 和 RNA 测序分析重新审视了这种反应，并确定了几个特征。我们确认了经典的“拯救我们的船”（SOS）基因座的诱导，并鉴定了几个基因，包括许多嘧啶途径，这些基因之前未被证明是可诱导 DNA 损伤的。尽管对 LexA 具有很强的依赖性，但这些基因缺乏 LexA 盒，并且 LexA 的调节可能是通过未知因素间接进行的。我们发现转录因子“严格饥饿蛋白”SspA 在 AZT 诱导基因的调节中与 LexA 一样重要，并且 SspA 激活的基因在 AZT 暴露后发生显着变化。我们的实验确定了额外的不依赖于 LexA 的 DNA 损伤诱导基因，包括 22 个小 RNA 基因，其中一些似乎被 SspA 激活。 AZT 强烈下调运动性和趋化性基因，这可能是由于 AZT 升高表达的一种或多种小 RNA 或其他转录因子（例如 AppY 和 GadE）的结果。控制铁铁载体、肠杆菌素和铁稳态的基因也被强烈诱导，不依赖于 LexA。我们证实，IraD 抗接头蛋白的诱导独立于 LexA，并且第二种抗接头蛋白 IraM 同样具有强烈的 AZT 诱导性，不依赖于 LexA，这表明通过这些抗接头蛋白实现的 RpoS 稳定是复制应激耐受性的一个组成部分。