ArticleNucleic acids research2022
Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 18 citations in OpenAlex.
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- The Absence of E. coli Nucleoid-Associated Protein FIS at Low Temperature Leads to an Adaptation Response That Causes a Shift Towards Genome Compaction in Small Rods.Molecular microbiology · 2026Article
- Bacterial 3D genome architecture: organization, regulation, and synthetic biology applications.Genome biology · 2026Review
- Dam-dependent epigenetic memory regulates prophage reintegration in Salmonella.Nucleic acids research · 2025Article
- Changes in Spo0A~P pulsing frequency control biofilm matrix deactivation.PLoS computational biology · 2025Article
- Dynamics of bacterial operons during genome-wide stresses is influenced by premature terminations and internal promoters.Science advances · 2025Article
- Physical communication pathways in bacteria: an extra layer to quorum sensing.Biophysical reviews · 2025Review
- Modularity of Zorya defense systems during phage inhibition.Nature communications · 2025Article
- Bimodality in E. coli gene expression: Sources and robustness to genome-wide stresses.PLoS computational biology · 2025Article
- Article
- Temperature Matters: Bacterial Response to Temperature Change.Journal of microbiology (Seoul, Korea) · 2023Review
- The transcription factor network of E. coli steers global responses to shifts in RNAP concentration.Nucleic acids research · 2022Article
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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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