ArticleOpen biology2012
Systems analysis of transcription factor activities in environments with stable and dynamic oxygen concentrations.
Article in Open biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 30 citations in OpenAlex.
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- Rapid Sampling of Escherichia coli After Changing Oxygen Conditions Reveals Transcriptional Dynamics.Genes · 2017Article
- Modeling and simulation of the redox regulation of the metabolism inBiotechnology for biofuels · 2017Article
- Homeostasis of metabolites inRoyal Society open science · 2016Article
- Characterization of acetic acid-detoxifying Escherichia coli evolved under phosphate starvation conditions.Microbial cell factories · 2016Article
- Oscillation Kinetics of Post-illumination Increase in Chl Fluorescence in Cyanobacterium Synechocystis PCC 6803.Frontiers in plant science · 2016Article
- Three Pseudomonas putida FNR Family Proteins with Different Sensitivities to O2.The Journal of biological chemistry · 2015Article
- Adaptation of anaerobic cultures of Escherichia coli K-12 in response to environmental trimethylamine-N-oxide.Environmental microbiology · 2015Article
- 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
- A mathematical model of metabolism and regulation provides a systems-level view of how Escherichia coli responds to oxygen.Frontiers in microbiology · 2014Article
- "Affect of anaerobiosis on the antibiotic susceptibility of H. influenzae".BMC research notes · 2013Article
- The bacterial response regulator ArcA uses a diverse binding site architecture to regulate carbon oxidation globally.PLoS genetics · 2013Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
Abstract
Understanding gene regulation requires knowledge of changes in transcription factor (TF) activities. Simultaneous direct measurement of numerous TF activities is currently impossible. Nevertheless, statistical approaches to infer TF activities have yielded non-trivial and verifiable predictions for individual TFs. Here, global statistical modelling identifies changes in TF activities from transcript profiles of Escherichia coli growing in stable (fixed oxygen availabilities) and dynamic (changing oxygen availability) environments. A core oxygen-responsive TF network, supplemented by additional TFs acting under specific conditions, was identified. The activities of the cytoplasmic oxygen-responsive TF, FNR, and the membrane-bound terminal oxidases implied that, even on the scale of the bacterial cell, spatial effects significantly influence oxygen-sensing. Several transcripts exhibited asymmetrical patterns of abundance in aerobic to anaerobic and anaerobic to aerobic transitions. One of these transcripts, ndh, encodes a major component of the aerobic respiratory chain and is regulated by oxygen-responsive TFs ArcA and FNR. Kinetic modelling indicated that ArcA and FNR behaviour could not explain the ndh transcript profile, leading to the identification of another TF, PdhR, as the source of the asymmetry. Thus, this approach illustrates how systematic examination of regulatory responses in stable and dynamic environments yields new mechanistic insights into adaptive processes.
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Registered trials
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