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Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli

Cite this dataset

Palma, Cristina et al. (2022). Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli [Dataset]. Dryad.


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.


Collection and data generation are described in the section 'Materials and Methods' of the main manuscript and Sections I-III of Supplementary Information.

Data processing methods and the software packages used are described in Supplementary Information.


Jane and Aatos Erkko Foundation, Award: 10-10524-38

Suomalainen Tiedeakatemia

Finnish Cultural Foundation, Award: 00200193

Finnish Cultural Foundation, Award: 00212591

Finnish Cultural Foundation, Award: 50201300

EDUFI Fellowship, Award: TM-19-11105

Tampere University Graduate Program

Finnish Cultural Foundation, Award: 00210818

EDUFI Fellowship, Award: TM-21-11655