Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland.
Center of Technology and Systems (CTS-Uninova), NOVA University of Lisbon 2829-516, Monte de Caparica, Portugal.
Nucleic Acids Res. 2022 Aug 26;50(15):8512-8528. doi: 10.1093/nar/gkac643.
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.
冷休克适应性是温血动物肠道细菌的一项关键生存技能。大肠杆菌的冷休克反应受一个复杂的多基因、有序的转录程序控制。我们研究了其潜在的机制。在确定了短期的冷休克受抑制基因后，我们表明它们的响应性与它们的转录因子或全局调节剂无关，而它们的单细胞蛋白数量的可变性在冷休克后增加。我们假设，由于 DNA 超螺旋的变化（可能是由于整体负超螺旋减少导致的 DNA 松弛），一些冷休克受抑制的基因可能由于转录锁定的高倾向而被触发。同时，我们发现近一半的冷休克受抑制基因对拓扑异构酶抑制也有高度响应（尽管拓扑异构酶抑制响应的大多数基因对冷休克没有响应）。此外，它们对冷休克和拓扑异构酶抑制的响应强度相关。同时，在冷休克下，核质密度增加，拓扑异构酶和核质变得更加共定位。此外，细胞能量减少，这可能阻碍正超螺旋的解决。总的来说，我们得出结论，对负超螺旋减少的敏感性是大肠杆菌短期冷休克转录程序的核心特征，可用于调节合成回路的温度敏感性。
