Cold shock adaptability is a key survival skill of gut bacteria of warm-blooded animals. Escherichia coli cold shock responses are controlled by a complex multi-gene, timely-ordered transcriptional program. We investigated its underlying mechanisms. Having identified short-term, cold shock repressed genes, we show that their responsiveness is unrelated to their transcription factors or global regulators, while their single-cell protein numbers’ variability increases after cold shock. We hypothesized that some cold shock repressed genes could be triggered by high propensity for transcription locking due to changes in DNA supercoiling (likely due to DNA relaxation caused by an overall reduction in negative supercoiling). Concomitantly, we found that nearly half of cold shock repressed genes are also highly responsive to gyrase inhibition (albeit most genes responsive to gyrase inhibition are not cold shock responsive). Further, their response strengths to cold shock and gyrase inhibition correlate. Meanwhile, under cold shock, nucleoid density increases, and gyrases and nucleoid become more colocalized. Moreover, the cellular energy decreases, which may hinder positive supercoils resolution. Overall, we conclude that sensitivity to diminished negative supercoiling is a core feature of E. coli’s short-term, cold shock transcriptional program, and could be used to regulate the temperature sensitivity of synthetic circuits.

中文翻译：

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DNA超螺旋的改变是大肠杆菌短期冷休克抑制基因的触发因素

冷休克适应性是温血动物肠道细菌的一项关键生存技能。大肠杆菌冷休克反应由复杂的多基因、及时排序的转录程序控制。我们研究了它的潜在机制。在确定了短期的冷休克抑制基因后，我们表明它们的反应性与其转录因子或全局调节因子无关，而冷休克后它们的单细胞蛋白数量的变异性增加。我们假设由于 DNA 超螺旋的变化（可能是由于负超螺旋的总体减少引起的 DNA 松弛），转录锁定的高倾向可能会触发一些冷休克抑制基因。同时，我们发现近一半的冷休克抑制基因也对回旋酶抑制有高度反应（尽管大多数对回旋酶抑制有反应的基因对冷休克没有反应）。此外，它们对冷休克和旋转酶抑制的反应强度相关。同时，在冷冲击下，核仁密度增加，回旋酶和核仁变得更加共定位。此外，细胞能量降低，这可能会阻碍正超螺旋的分辨率。总体而言，我们得出结论，对减少负超螺旋的敏感性是大肠杆菌短期冷休克转录程序的核心特征，可用于调节合成电路的温度敏感性。同时，在冷冲击下，核仁密度增加，回旋酶和核仁变得更加共定位。此外，细胞能量降低，这可能会阻碍正超螺旋的分辨率。总体而言，我们得出结论，对减少负超螺旋的敏感性是大肠杆菌短期冷休克转录程序的核心特征，可用于调节合成电路的温度敏感性。同时，在冷冲击下，核仁密度增加，回旋酶和核仁变得更加共定位。此外，细胞能量降低，这可能会阻碍正超螺旋的分辨率。总体而言，我们得出结论，对减少负超螺旋的敏感性是大肠杆菌短期冷休克转录程序的核心特征，可用于调节合成电路的温度敏感性。