ArticleMolecular microbiology2011
Phenotypic repertoire of the FNR regulatory network in Escherichia coli.
Article in Molecular microbiology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Strategies for manipulation of oxygen utilization by the electron transfer chain in microbes for metabolic engineering purposes.Journal of industrial microbiology & biotechnology · 2017Review
- Rapid Discrimination Among Putative Mechanistic Models of Biochemical Systems.Scientific reports · 2016Article
- Design Space Toolbox V2: Automated Software Enabling a Novel Phenotype-Centric Modeling Strategy for Natural and Synthetic Biological Systems.Frontiers in genetics · 2016Article
- Unrelated toxin-antitoxin systems cooperate to induce persistence.Journal of the Royal Society, Interface · 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
- Strategy revealing phenotypic differences among synthetic oscillator designs.ACS synthetic biology · 2014Article
- The oxygen sensor MgFnr controls magnetite biomineralization by regulation of denitrification in Magnetospirillum gryphiswaldense.BMC microbiology · 2014Article
- Agent-based modeling of oxygen-responsive transcription factors in Escherichia coli.PLoS computational biology · 2014Article
- Molecular mechanisms of multiple toxin-antitoxin systems are coordinated to govern the persister phenotype.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Article
- Bacterial adaptation of respiration from oxic to microoxic and anoxic conditions: redox control.Antioxidants & redox signaling · 2012Review
- Article
- Design of the lac gene circuit revisited.Mathematical biosciences · 2011Review
- Biomedical engineering strategies in system design space.Annals of biomedical engineering · 2011Review
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Authors and funding
2 authors.
Funding
Abstract
The FNR protein in Escherichia coli is an O(2) sensor that modifies global gene expression to adapt the cell to anaerobic growth. Regulation of FNR involves continuous cycling of the protein between its active and inactive states under aerobic conditions without apparent function. This raises the question of what benefit to the overall life cycle might compensate for the cost of cycling and reveals that the role of this process is poorly understood. To address this problem, we introduce the concept of a 'system design space', which provides a rigorous definition of phenotype at the molecular level and a means of visualizing the phenotypic repertoire of the system. Our analysis reveals undesirable and desirable phenotypes with an optimal constellation of parameter values for the system. To facilitate a more concrete understanding of what the design space represents, we analyse mutations that alter the apparent dimerization rate constant of FNR. We show that our estimated wild-type value of this rate constant, which is difficult to measure in situ, is located within this constellation and that the behaviour of the system is compromised in mutants if the value of the apparent dimerization rate constant lies beyond the bounds of this optimal constellation.
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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.