ArticlePloS one2015
GntR Family of Bacterial Transcription Factors and Their DNA Binding Motifs: Structure, Positioning and Co-Evolution.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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Who cites it
65 citing papers in PubMed, 111 citations in OpenAlex.
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- Regulation of DMSP organosulfur cycling in ubiquitous Roseobacter marine bacteria.The EMBO journal · 2026Article
- Molecular Strategies of Carbohydrate Binding to Intrinsically Disordered Regions in Bacterial Transcription Factors.International journal of molecular sciences · 2026Article
- Contribution of theMicrobiology spectrum · 2026Article
- A novel GntR-ABC efflux system mediates oxidative stress response, drug resistance, motility and virulence inFrontiers in microbiology · 2026Article
- High-performance genetically-encoded green and red fluorescent biosensors for pyruvate.bioRxiv : the preprint server for biology · 2025Article
- Functional consequences of genetic variations in DgoR, a GntR/FadR family transcriptional repressor of D-galactonate metabolism inJournal of bacteriology · 2025Article
- Molecular Characterization of a Transcriptional Regulator GntR for Gluconate Metabolism in Industrial 2-Ketogluconate ProducerMicroorganisms · 2025Article
- Genomic insights into Neopusillimonas aestuarii sp. nov., a novel estuarine bacterium with adaptations for ectoine biosynthesis and stress tolerance.Antonie van Leeuwenhoek · 2025Article
- The GntR/VanR transcription regulator AlkR represses AlkB2 monooxygenase expression and regulatesmLife · 2025Article
- Molecular mechanisms underlying allosteric behavior of Escherichia coli DgoR, a GntR/FadR family transcriptional regulator.Nucleic acids research · 2025Article
- Bacterial Metallostasis: Metal Sensing, Metalloproteome Remodeling, and Metal Trafficking.Chemical reviews · 2024Review
- Predicting bacterial transcription factor binding sites through machine learning and structural characterization based on DNA duplex stability.Briefings in bioinformatics · 2024Article
- Inference and prioritization of tissue-specific regulons inaBIOTECH · 2024Article
- Transcriptional and post-transcriptional mechanisms modulate cyclopropane fatty acid synthase through small RNAs inJournal of bacteriology · 2024Article
- Comprehensive network of stress-induced responses in Zymomonas mobilis during bioethanol production: from physiological and molecular responses to the effects of system metabolic engineering.Microbial cell factories · 2024Review
- Article
- Genetic disruption of the bacterialProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Evolution of molecular switches for regulation of transgene expression by clinically licensed gluconate.Nucleic acids research · 2023Article
5 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The GNTR family of transcription factors (TFs) is a large group of proteins present in diverse bacteria and regulating various biological processes. Here we use the comparative genomics approach to reconstruct regulons and identify binding motifs of regulators from three subfamilies of the GNTR family, FADR, HUTC, and YTRA. Using these data, we attempt to predict DNA-protein contacts by analyzing correlations between binding motifs in DNA and amino acid sequences of TFs. We identify pairs of positions with high correlation between amino acids and nucleotides for FADR, HUTC, and YTRA subfamilies and show that the most predicted DNA-protein interactions are quite similar in all subfamilies and conform well to the experimentally identified contacts formed by FadR from E. coli and AraR from B. subtilis. The most frequent predicted contacts in the analyzed subfamilies are Arg-G, Asn-A, Asp-C. We also analyze the divergon structure and preferred site positions relative to regulated genes in the FADR and HUTC subfamilies. A single site in a divergon usually regulates both operons and is approximately in the middle of the intergenic area. Double sites are either involved in the co-operative regulation of both operons and then are in the center of the intergenic area, or each site in the pair independently regulates its own operon and tends to be near it. We also identify additional candidate TF-binding boxes near palindromic binding sites of TFs from the FADR, HUTC, and YTRA subfamilies, which may play role in the binding of additional TF-subunits.
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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.