Aerobic and anaerobic characterization of MG1655 and mutant strains with regard to growth, by-product formation and cAMP concentrations.

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Glucose transporter mutants were analyzed under aerobic and aerobic conditions in batch cultures with glucose as substrate. Acetate formation rates and glucose consumption rates were measured, as well as extracellular cAMP concentrations.

SEEK ID: https://fairdomhub.org/assays/211

Class: Experimental assay

Projects: SUMO

Investigation: Analysis of the glucose transport in Escherichia coli under aerobic and anaerobic conditions

Study: Characterization of mutant strains with defects in sugar transport systems

Assay position:

Assay type: Extracellular Metabolite Concentration

Technology type: Technology Type

Organisms: Escherichia coli : MG1655 (del LAM;del rph-1 / pyrimidine starvation )

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Sonja Steinsiek

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Views: 4093

Created: 17th Jan 2013 at 12:18

Last updated: 8th Nov 2017 at 14:21

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Programmes (1)
Projects (1)
Investigations (1)
Studies (1)
Strains (1)
Data files (2)
SOPs (1+1)
Publications (3)

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Sonja Steinsiek

Projects: SUMO

Institutions: Max Planck Institute for Dynamics of Complex Technical Systems

Expertise: Microbiology, Molecular Biology, E. coli, Biotechnology

Tools: qRT-PCR, Bioreactor experiments/Fermentation (batch, Chemostat), Enzyme assays, 2D-PAGE

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SysMO

SysMO is a European transnational funding and research initiative on "Systems Biology of Microorganisms".

The goal pursued by SysMO was to record and describe the dynamic molecular processes going on in unicellular microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models.

Systems biology will raise biomedical and biotechnological research to a new quality level and contribute markedly to progress in understanding. Pooling European research ...

Projects: BaCell-SysMO, COSMIC, SUMO, KOSMOBAC, SysMO-LAB, PSYSMO, SCaRAB, MOSES, TRANSLUCENT, STREAM, SulfoSys, SysMO DB, SysMO Funders, SilicoTryp, Noisy-Strep

Web page: http://sysmo.net/

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SUMO

"Systems Understanding of Microbial Oxygen responses" (SUMO) investigates how Escherichia coli senses oxygen, or the associated changes in oxidation/reduction balance, via the Fnr and ArcA proteins, how these systems interact with other regulatory systems, and how the redox response of an E. coli population is generated from the responses of single cells. There are five sub-projects to determine system properties and behaviour and three sub-projects to employ different and complementary modelling ...

Programme: SysMO

Public web page: http://www.sysmo.net/index.php?index=55

Organisms: Escherichia coli, Escherichia coli K-12

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Analysis of the glucose transport in Escherichia coli under aerobic and anaerobic conditions

SUMO

All creators

Sonja Steinsiek

In Escherichia coli several systems are known to transport glucose into the cytoplasm. A series of mutant strains were constructed, which lack one or more of these uptake systems. These were analyzed in aerobic and anaerobic batch cultures, as well as glucose limited continuous cultivations.

Submitter: Sonja Steinsiek

Studies: Characterization of mutant strains with defects in sugar transport systems

Assays: Aerobic and anaerobic characterization of MG1655 and mutant strains with..., Aerobic and anaerobic characterization of MG1655 and mutant strains with..., Characterization of MG1655 and mutant strains under conditions of glucos..., TFinfer2

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Created: 17th Jan 2013 at 11:58

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Characterization of mutant strains with defects in sugar transport systems

SUMO

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Sonja Steinsiek

Mutant strains in which one or more of the potential glucose uptake systems was deleted have been analyzed in aerobic and anaerobic batch cultures, as well as aerobic chemostat cultures.

Submitter: Sonja Steinsiek

Investigation: Analysis of the glucose transport in Escherichi...

Snapshots: No snapshots

Created: 17th Jan 2013 at 12:03

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MG1655

Submitter: Not available

Provider Name: Yale CGSC

Provider's strain ID: CGSC#: 6300

Organism: Escherichia coli

Genotypes: del LAM;del rph-1

Phenotypes: pyrimidine starvation

Comment: This culture was grown from lyophil Oct. 2003 and it tested Fnr+. The previous working culture was mixed fnr-/fnr+.

Created: 10th May 2012 at 11:16, Last updated: 18th May 2012 at 15:55

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Growth, by-product formation and glucose consumption rates and cAMP-concentrations under aerobic conditions

SUMO

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Sonja Steinsiek

Measurement of by-product formation rates, substrate consumption rates and extracellular concentrations of cAMP under aerobic batch conditions with glucose as substrate.

Creator: Sonja Steinsiek

Submitter: Sonja Steinsiek

Relationship type: Not specified

Investigations: Analysis of the glucose transport in Escherichi...

Studies: Characterization of mutant strains with defects...

Assays: Aerobic and anaerobic characterization of MG165...

Created: 17th Jan 2013 at 12:25, Last updated: 17th Jan 2013 at 13:11

Growth, yield and cAMP excretion under anaerobic conditions

SUMO

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Sonja Steinsiek

Measurement of by-product formation rates, substrate consumption rates and extracellular concentrations of cAMP under anaerobic batch conditions with glucose as substrate.

Creator: Sonja Steinsiek

Submitter: Sonja Steinsiek

Relationship type: Not specified

Investigations: Analysis of the glucose transport in Escherichi...

Studies: Characterization of mutant strains with defects...

Assays: Aerobic and anaerobic characterization of MG165...

Created: 17th Jan 2013 at 12:27, Last updated: 17th Jan 2013 at 12:29

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Measurement of extracellular metabolites

SUMO

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Sonja Steinsiek

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Creator: Sonja Steinsiek

Submitter: The JERM Harvester

Investigations: Analysis of Escherichia coli with linear electr..., Analysis of the glucose transport in Escherichi..., Steady state studies for different oxygen avail...

Studies: Analysis of Escherichia coli strains with linea..., Characterization of mutant strains with defects..., Determination of the impact of specific enzyme ...

Assays: Aerobic and anaerobic characterization of MG165..., Analysis of by-product formation rates in MG1655, Characterization of E. coli MG1655 and ∆sdhC an..., Determination of by-product formation and gluco...

Created: 16th Mar 2010 at 17:13

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Basic Regulatory Principles of Escherichia coli's Electron Transport Chain for Varying Oxygen Conditions

SUMO

Abstract (Expand)

For adaptation between anaerobic, micro-aerobic and aerobic conditions Escherichia coli's metabolism and in particular its electron transport chain (ETC) is highly regulated. Although it is known … that the global transcriptional regulators FNR and ArcA are involved in oxygen response it is unclear how they interplay in the regulation of ETC enzymes under micro-aerobic chemostat conditions. Also, there are diverse results which and how quinones (oxidised/reduced, ubiquinone/other quinones) are controlling the ArcBA two-component system. In the following a mathematical model of the E. coli ETC linked to basic modules for substrate uptake, fermentation product excretion and biomass formation is introduced. The kinetic modelling focusses on regulatory principles of the ETC for varying oxygen conditions in glucose-limited continuous cultures. The model is based on the balance of electron donation (glucose) and acceptance (oxygen or other acceptors). Also, it is able to account for different chemostat conditions due to changed substrate concentrations and dilution rates. The parameter identification process is divided into an estimation and a validation step based on previously published and new experimental data. The model shows that experimentally observed, qualitatively different behaviour of the ubiquinone redox state and the ArcA activity profile in the micro-aerobic range for different experimental conditions can emerge from a single network structure. The network structure features a strong feed-forward effect from the FNR regulatory system to the ArcBA regulatory system via a common control of the dehydrogenases of the ETC. The model supports the hypothesis that ubiquinone but not ubiquinol plays a key role in determining the activity of ArcBA in a glucose-limited chemostat at micro-aerobic conditions.

Editor:

Date Published: 30th Sep 2014

Publication Type: Not specified

PubMed ID: 25268772

Citation:

Created: 7th Oct 2014 at 15:28, Last updated: 8th Dec 2022 at 17:26

A mathematical model of metabolism and regulation provides a systems-level view of how Escherichia coli responds to oxygen

SUMO

Abstract (Expand)

The efficient redesign of bacteria for biotechnological purposes, such as biofuel production, waste disposal or specific biocatalytic functions, requires a quantitative systems-level understanding of … energy supply, carbon, and redox metabolism. The measurement of transcript levels, metabolite concentrations and metabolic fluxes per se gives an incomplete picture. An appreciation of the interdependencies between the different measurement values is essential for systems-level understanding. Mathematical modeling has the potential to provide a coherent and quantitative description of the interplay between gene expression, metabolite concentrations, and metabolic fluxes. Escherichia coli undergoes major adaptations in central metabolism when the availability of oxygen changes. Thus, an integrated description of the oxygen response provides a benchmark of our understanding of carbon, energy, and redox metabolism. We present the first comprehensive model of the central metabolism of E. coli that describes steady-state metabolism at different levels of oxygen availability. Variables of the model are metabolite concentrations, gene expression levels, transcription factor activities, metabolic fluxes, and biomass concentration. We analyze the model with respect to the production capabilities of central metabolism of E. coli. In particular, we predict how precursor and biomass concentration are affected by product formation.

Editor:

Date Published: 27th Mar 2014

Publication Type: Not specified

PubMed ID: 24723921

Citation:

Created: 7th Oct 2014 at 15:32, Last updated: 8th Dec 2022 at 17:26

Glucose Transport in Escherichia coli Mutant Strains with Defects in Sugar Transport Systems

SUMO

Abstract (Expand)

In Escherichia coli several systems are known to transport glucose into the cytoplasm. The main glucose uptake system under batch conditions is the glucose phosphoenolpyruvate:carbohydrate phosphotransferase … system (glucose-PTS), but also the mannose-PTS, as well as the galactose and maltose transporters can translocate glucose. Mutant strains which lack the EIIBC protein of the glucose-PTS have been previously investigated because their lower rate of acetate formation offers advantages in industrial applications. Nevertheless, a systematic study to analyze the impact of the different glucose uptake systems has not been undertaken. Specifically, how the bacteria cope with the deletion of the major glucose uptake system and which alternative transporters react to compensate for this deficit has not been studied in detail. Therefore, a series of mutant strains were analyzed in aerobic and anaerobic batch cultures, as well as in glucose limited continuous cultivations. Deletion of EIIBC, disturbs glucose transport severely. cAMP-CRP levels rise, induction of the mgl-operon occurs. Nevertheless mgl transcription is not essential, as deletion of this transporter did not affect growth rate; the activities of the remaining transporters seems to be sufficient by induction of the galactose and maltose transporters. Despite the strong up-regulation of mgl under glucose limitations, deletion of this transport-system did not lead to further changes.

Editor:

Date Published: 8th Oct 2012

Publication Type: Not specified

DOI: 10.1128/JB.01502-12

Citation:

Created: 19th Dec 2012 at 08:10, Last updated: 8th Dec 2022 at 17:26