ArticlePloS one2013
Transcription factors in Escherichia coli prefer the holo conformation.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 15 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
15 citing papers in PubMed, 24 citations in OpenAlex.
- A transcriptional Regulator Gar Regulates the Growth and Virulence of Xanthomonas oryzae pv. oryzae.Current microbiology · 2023Article
- The transcription factor network of E. coli steers global responses to shifts in RNAP concentration.Nucleic acids research · 2022Article
- Homology-based reconstruction of regulatory networks for bacterial and archaeal genomes.Frontiers in microbiology · 2022Article
- Sensory Systems and Transcriptional Regulation inFrontiers in bioengineering and biotechnology · 2022Review
- Article
- Dissecting the Repertoire of DNA-Binding Transcription Factors of the Archaeon Pyrococcus furiosus DSM 3638.Life (Basel, Switzerland) · 2018Article
- Single-target regulators form a minor group of transcription factors in Escherichia coli K-12.Nucleic acids research · 2018Article
- Using RegulonDB, the Escherichia coli K-12 Gene Regulatory Transcriptional Network Database.Current protocols in bioinformatics · 2018Article
- Abundance, diversity and domain architecture variability in prokaryotic DNA-binding transcription factors.PloS one · 2018Article
- Functional Prediction of Hypothetical Transcription Factors ofComputational and structural biotechnology journal · 2018Article
- Transcription profile of Escherichia coli: genomic SELEX search for regulatory targets of transcription factors.Nucleic acids research · 2016Article
- Transcription Factors Exhibit Differential Conservation in Bacteria with Reduced Genomes.PloS one · 2016Article
- The metabolic regulator CodY links Listeria monocytogenes metabolism to virulence by directly activating the virulence regulatory gene prfA.Molecular microbiology · 2015Article
- Intracellular concentrations of 65 species of transcription factors with known regulatory functions in Escherichia coli.Journal of bacteriology · 2014Article
- COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia.Nucleic acids research · 2014Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
The transcriptional regulatory network of Escherichia coli K-12 is among the best studied gene networks of any living cell. Transcription factors bind to DNA either with their effector bound (holo conformation), or as a free protein (apo conformation) regulating transcription initiation. By using RegulonDB, the functional conformations (holo or apo) of transcription factors, and their mode of regulation (activator, repressor, or dual) were exhaustively analyzed. We report a striking discovery in the architecture of the regulatory network, finding a strong under-representation of the apo conformation (without allosteric metabolite) of transcription factors when binding to their DNA sites to activate transcription. This observation is supported at the level of individual regulatory interactions on promoters, even if we exclude the promoters regulated by global transcription factors, where three-quarters of the known promoters are regulated by a transcription factor in holo conformation. This genome-scale analysis enables us to ask what are the implications of these observations for the physiology and for our understanding of the ecology of E. coli. We discuss these ideas within the framework of the demand theory of gene regulation.
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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.