ArticleNature communications2022
Auxotrophic and prototrophic conditional genetic networks reveal the rewiring of transcription factors in Escherichia coli.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 13 citations in OpenAlex.
- Impact of selective digestive decontamination on the pangenome composition of ESBL-E. coli.The Journal of antimicrobial chemotherapy · 2026Article
- Genome-based insights into metal co-resistance in Amazonian mercury-resistant bacteria: ecological lifestyle and biosafety implications for bioremediation.Microbiology spectrum · 2026Article
- Combining structural modeling and deep learning to calculate the E. coli protein interactome and functional networks.Nature communications · 2026Article
- EefR mutations drive sanguinarine resistance by activating cryptic multidrug efflux pumps in AcrB-NullVirulence · 2025Article
- Transcriptional Regulation in Bacteria.Microorganisms · 2024Article
- A Cryptic Prophage Transcription Factor Drives Phenotypic Changes via Host Gene Regulation.bioRxiv : the preprint server for biology · 2024Article
- Antipsychotic quetiapine alters the mouse fecal resistome by impacting antibiotic efflux, cell membrane, and cell wall synthesis genes.Microbiology spectrum · 2024Article
- Article
- Overview of the Molecular Mechanism of Bacterial Environmental Adaptation by Comprehensive Analysis.International journal of molecular sciences · 2023Article
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Authors and funding
13 authors at 1 institution in 1 country.
Funding
Abstract
Bacterial transcription factors (TFs) are widely studied in Escherichia coli. Yet it remains unclear how individual genes in the underlying pathways of TF machinery operate together during environmental challenge. Here, we address this by applying an unbiased, quantitative synthetic genetic interaction (GI) approach to measure pairwise GIs among all TF genes in E. coli under auxotrophic (rich medium) and prototrophic (minimal medium) static growth conditions. The resulting static and differential GI networks reveal condition-dependent GIs, widespread changes among TF genes in metabolism, and new roles for uncharacterized TFs (yjdC, yneJ, ydiP) as regulators of cell division, putrescine utilization pathway, and cold shock adaptation. Pan-bacterial conservation suggests TF genes with GIs are co-conserved in evolution. Together, our results illuminate the global organization of E. coli TFs, and remodeling of genetic backup systems for TFs under environmental change, which is essential for controlling the bacterial transcriptional regulatory circuits.
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