ArticleNucleic acids research2007
Discovery of Fur binding site clusters in Escherichia coli by information theory models.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
What it found
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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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
62 citing papers in PubMed, 90 citations in OpenAlex.
- Klebsiella pneumoniae employs a type VI secretion system to overcome microbiota-mediated colonization resistance.Nature communications · 2025Article
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- Iron limitation indirectly reduces theMicrobiology spectrum · 2024Article
- Iron uptake pathway ofFrontiers in microbiology · 2024Article
- Different lanthanide elements induce strong gene expression changes in a lanthanide-accumulating methylotroph.Microbiology spectrum · 2023Article
- A critical role for iron and zinc homeostatic systems in the evolutionary adaptation ofMicrobial genomics · 2023Article
- Natural flavonoids disrupt bacterial iron homeostasis to potentiate colistin efficacy.Science advances · 2023Article
- Unusual Relationship between Iron Deprivation and Organophosphate Hydrolase Expression.Applied and environmental microbiology · 2023Article
- Revisiting Fur Regulon Leads to a Comprehensive Understanding of Iron and Fur Regulation.International journal of molecular sciences · 2023Article
- Meddling with Metal Sensors: Fur-Family Proteins as Signaling Hubs.Journal of bacteriology · 2023Review
- Escherichia coli induces DNA repair enzymes to protect itself from low-grade hydrogen peroxide stress.Molecular microbiology · 2022Article
- Extracellular and Intracellular Lanthanide Accumulation in the MethylotrophicApplied and environmental microbiology · 2021Article
- Uncovering Transcriptional Regulators and Targets of sRNAs Using an Integrative Data-Mining Approach: H-NS-Regulated RseX as a Case Study.Frontiers in cellular and infection microbiology · 2021Article
- Biochemical characterization of ferric uptake regulator (Fur) from Aliivibrio salmonicida. Mapping the DNA sequence specificity through binding studies and structural modelling.Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine · 2020Article
- Article
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- sRNA EsrE Is Transcriptionally Regulated by the Ferric Uptake Regulator Fur inJournal of microbiology and biotechnology · 2020Article
- New evolving strategies revealed by transcriptomic analysis of a furMicrobial biotechnology · 2020Article
- Article
- IdeR, a DtxR Family Iron Response Regulator, Controls Iron Homeostasis, Morphological Differentiation, Secondary Metabolism, and the Oxidative Stress Response in Streptomyces avermitilis.Applied and environmental microbiology · 2018Article
2 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 5 institutions in 3 countries.
Funding
Abstract
Fur is a DNA binding protein that represses bacterial iron uptake systems. Eleven footprinted Escherichia coli Fur binding sites were used to create an initial information theory model of Fur binding, which was then refined by adding 13 experimentally confirmed sites. When the refined model was scanned across all available footprinted sequences, sequence walkers, which are visual depictions of predicted binding sites, frequently appeared in clusters that fit the footprints ( approximately 83% coverage). This indicated that the model can accurately predict Fur binding. Within the clusters, individual walkers were separated from their neighbors by exactly 3 or 6 bases, consistent with models in which Fur dimers bind on different faces of the DNA helix. When the E. coli genome was scanned, we found 363 unique clusters, which includes all known Fur-repressed genes that are involved in iron metabolism. In contrast, only a few of the known Fur-activated genes have predicted Fur binding sites at their promoters. These observations suggest that Fur is either a direct repressor or an indirect activator. The Pseudomonas aeruginosa and Bacillus subtilis Fur models are highly similar to the E. coli Fur model, suggesting that the Fur-DNA recognition mechanism may be conserved for even distantly related bacteria.
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What OpenQuestion holds
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.