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| Status |
Public on Jul 20, 2022 |
| Title |
Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli |
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
Examination of genome-wide responses over time (optimal and CS temperature) and under the effects of Novobicion (50 ng/μl). Data contains three samples per condition.
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| Contributor(s) |
Dash S, Palma CD, Baptista IC, Almeida BB, Bahrudeen MM, Chauhan V, Jagadeesan R, Ribeiro AS |
| Citation(s) |
35920318 |
| |
| Submission date |
Jan 19, 2022 |
| Last update date |
Aug 31, 2022 |
| Contact name |
Andre Ribeiro |
| E-mail(s) |
andre.sanchesribeiro@tuni.fi
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| Organization name |
Tampere University
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| Department |
Faculty of Medicine and Health Technology
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| Lab |
Laboratory of Biosystem Dynamics
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| Street address |
Arvo Ylpön katu 34
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| City |
Tampere |
| ZIP/Postal code |
33520 |
| Country |
Finland |
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| Platforms (2) |
| GPL24659 |
Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655) |
| GPL26592 |
Illumina NovaSeq 6000 (Escherichia coli str. K-12 substr. MG1655) |
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| Samples (15)
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| Relations |
| BioProject |
PRJNA798769 |
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