ArticleJournal of molecular biology2010
Regulation of aerobic-to-anaerobic transitions by the FNR cycle in Escherichia coli.
Article in Journal of molecular biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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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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
19 citing papers in PubMed, 39 citations in OpenAlex.
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- Isolation of a novel Lactiplantibacillus plantarum strain resistant to nitrite stress and its transcriptome analysis.Journal of microbiology (Seoul, Korea) · 2022Article
- High-efficiency delivery of CRISPR-Cas9 by engineered probiotics enables precise microbiome editing.Molecular systems biology · 2021Article
- Deciphering the Adaptation ofGenes · 2018Article
- Strategies for manipulation of oxygen utilization by the electron transfer chain in microbes for metabolic engineering purposes.Journal of industrial microbiology & biotechnology · 2017Review
- Light-induced gene expression with photocaged IPTG for induction profiling in a high-throughput screening system.Microbial cell factories · 2016Article
- Design Space Toolbox V2: Automated Software Enabling a Novel Phenotype-Centric Modeling Strategy for Natural and Synthetic Biological Systems.Frontiers in genetics · 2016Article
- Design principles of a conditional futile cycle exploited for regulation.Molecular bioSystems · 2015Article
- Fe-S proteins that regulate gene expression.Biochimica et biophysica acta · 2015Review
- Agent-based modeling of oxygen-responsive transcription factors in Escherichia coli.PLoS computational biology · 2014Article
- Metabolic Engineering of Escherichia coli for Production of Mixed-Acid Fermentation End Products.Frontiers in bioengineering and biotechnology · 2014Review
- Computational analyses of transcriptomic data reveal the dynamic organization of the Escherichia coli chromosome under different conditions.Nucleic acids research · 2013Article
- YjcC, a c-di-GMP phosphodiesterase protein, regulates the oxidative stress response and virulence of Klebsiella pneumoniae CG43.PloS one · 2013Article
- Bacterial iron-sulfur regulatory proteins as biological sensor-switches.Antioxidants & redox signaling · 2012Review
- Iron-containing transcription factors and their roles as sensors.Current opinion in chemical biology · 2011Review
- Phenotypic repertoire of the FNR regulatory network in Escherichia coli.Molecular microbiology · 2011Article
- Elucidating the genotype-phenotype map by automatic enumeration and analysis of the phenotypic repertoire.NPJ systems biology and applicationsArticle
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The FNR (fumarate nitrate reduction) protein plays a central role in the global oxygen response of a variety of bacteria. In Escherichia coli, FNR is the master transcriptional regulator of the transition between aerobic and anaerobic growth. Regulation of FNR is achieved by cycling the molecule between three states in a process dependent on oxygen. In an effort to better understand the nature of this post-transcriptional cyclic regulatory mechanism, we formulated a kinetic model of the FNR protein and its regulation in E. coli. The values for the parameters of the model were fit to experimental data for the wild-type organism, and the model was validated by successfully predicting the behavior of fnr mutant strains characterized in the literature. We characterized the steady-state behavior of the FNR system by determining its sensitivity to changes in parameter values and its response to changes in the concentration of iron-sulfur cluster assembly proteins and the protease ClpXP. We also determined the steady-state induction characteristic that provides a direct estimate for the levels of the active form of FNR as a function of oxygen concentration. This result, in combination with reporter assays for expression of FNR target operons, gives an estimate for the equilibrium dissociation constant for the binding of active FNR to its recognition sequences in the DNA. Finally, we predicted the dynamics of the aerobic-to-anaerobic transition and determined distinct contributions to the dynamic profile of regulatory mechanisms operating at the transcriptional and post-translational levels.
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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.