ArticleNucleic acids research2018
Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
64 citing papers in PubMed, 115 citations in OpenAlex.
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- YeiE regulates YeiH to implement sulfite stress resistance inJournal of bacteriology · 2026Article
- Approaches for accelerating microbial gene function discovery using artificial intelligence.Nature microbiology · 2026Review
- A short peptide derived from late embryogenesis abundant proteins enhances acid tolerance in Escherichia coli via modulation of two-component regulatory systems.The FEBS journal · 2026Article
- Historical contingency limits adaptive diversification in a spatially structured environment.Evolution letters · 2026Article
- groovDB in 2026: a community-editable database of small molecule biosensors.Nucleic acids research · 2026Article
- Microgravity reshapes bacteriophage-host coevolution aboard the International Space Station.PLoS biology · 2026Article
- Article
- Novel Regulators of the flhDC Gene Encoding the Flagella Master Regulator in Escherichia Coli K-12.Current microbiology · 2025Article
- Multiscale regulation of nutrient stress responses in Escherichia coli from chromatin structure to small regulatory RNAs.Nucleic acids research · 2025Article
- Transcriptional Regulation in Bacteria.Microorganisms · 2024Article
- Exploring interspecific interaction variability in microbiota: A review.Engineering microbiology · 2024Review
- Evolution of pH-sensitive transcription termination inProceedings of the National Academy of Sciences of the United States of America · 2024Article
- CyuR is a dual regulator for L-cysteine dependent antimicrobial resistance in Escherichia coli.Communications biology · 2024Article
- Transcriptional and post-transcriptional mechanisms modulate cyclopropane fatty acid synthase through small RNAs inJournal of bacteriology · 2024Article
- Evolution of pH-sensitive transcription termination during adaptation to repeated long-term starvation.bioRxiv : the preprint server for biology · 2024Article
- Harnessing regulatory networks in Actinobacteria for natural product discovery.Journal of industrial microbiology & biotechnology · 2024Review
- RegulonDB v12.0: a comprehensive resource of transcriptional regulation in E. coli K-12.Nucleic acids research · 2024Article
- Ribosome profiling reveals the fine-tuned response ofmSystems · 2023Article
4 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
14 authors at 6 institutions in 4 countries.
Funding
Abstract
Transcriptional regulation enables cells to respond to environmental changes. Of the estimated 304 candidate transcription factors (TFs) in Escherichia coli K-12 MG1655, 185 have been experimentally identified, but ChIP methods have been used to fully characterize only a few dozen. Identifying these remaining TFs is key to improving our knowledge of the E. coli transcriptional regulatory network (TRN). Here, we developed an integrated workflow for the computational prediction and comprehensive experimental validation of TFs using a suite of genome-wide experiments. We applied this workflow to (i) identify 16 candidate TFs from over a hundred uncharacterized genes; (ii) capture a total of 255 DNA binding peaks for ten candidate TFs resulting in six high-confidence binding motifs; (iii) reconstruct the regulons of these ten TFs by determining gene expression changes upon deletion of each TF and (iv) identify the regulatory roles of three TFs (YiaJ, YdcI, and YeiE) as regulators of l-ascorbate utilization, proton transfer and acetate metabolism, and iron homeostasis under iron-limited conditions, respectively. Together, these results demonstrate how this workflow can be used to discover, characterize, and elucidate regulatory functions of uncharacterized TFs in parallel.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.