Escherichia coli

Investigation of the regulation and function of the glycogen metabolism within different bacteria with special focus on the phosphoglucomutase enzyme

FUNCEMM is a project bringing together 2 teams from France and Austria focusing on synthetic methylotrophy.

The main objective of SynBio4Flav is to go further in the standardization of high complexity synthetic biological parts, and to demonstrate the development of a standardized, and systematic platform for flavonoids production based on synthetic microbial consortia (SMCs).

Ion and solute homeostasis in enteric bacteria: an integrated view generated from the interface of modelling and biological experimentation

Andrew Millar's research group, University of Edinburgh

Background- Thermophilic organisms are composed of both bacterial and archaeal species. The enzymes isolated from these species and from other extreme habitats are more robust to temperature, organic solvents and proteolysis. They often have unique substrate specificities and originate from novel metabolic pathways. Thermophiles as well as their stable enzymes (‘thermozymes’) are receiving increased attention for biotechnological applications.

The proposed project will establish thermophilic in ...

CEPOPA envisions a sustainable cascade one-pot process for the synthesis of optically pure amines from alcohols and/or alkynes, using enzymes immobilized onto catalytically active nanomaterials. In the framework of the project, efficient chemoenzymatic processes will be developed for the synthesis of a set of amines that can be used as building blocks for pharmaceuticals or biomaterials.

generation of a toggle switch based on a non-cooperative network

Escherichia coli is a well-established and the most widely used organism for the production of recombinant proteins (used in medical and industrial applications, as molecular biology reagents, etc.). Production of proteins is the most resource exhaustive process for the cells and therefore needs to be optimized to achieve maximal productivities. Natural environment of E. coli is much harsher compared to the near optimal growth conditions used in production processes. In order to survive cells ...

"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 ...

This assay describes how to analyze gene expression rates via RT-PCR.

This document describes by-product formation rates measured in MG1655 at steady-state conditions in Infors-Multifors-Bioreactors.

This experiment uses a low-copy plasmid based system (MG1655 Δlac FF(-41.5)/RW50) for measuring FNR activity. Initial acetate calibration of the chemostat with the MG1655 Δlac strain was carried out, with β-galactosidase activity from the FF(-41.5)/RW50 reporter plasmid measured at 100%, 80%, 50%, 20% and 0% aerobiosis levels. Finally, the aerobiosis levels were re-determined by calculating the actual acetate flux in the sampled chemostat runs.

Note: the strain used (MG1655 Δlac) is not the same ...

The task of this assay is to determine the impact of oxygen availability on the concentrations of metabolites from different central metabolic pathways. The focus lies on metabolites connected to glycolysis, tri-carbon-acid-cycle and energy metabolism. All strains have been cultured and analysed according to the SOPs listed below

These files show physiological measurements from the Sheffield Infors chemostat which were made during acetate calibration and also when sampling for the steady-state transcriptional profiles.

This assay involved the determination of transcriptional profiles at 0, 2, 5, 10, 15 and 20 minutes through aerobic to anaerobic gas transitions and anaerobic to aerobic gas transitions. In each case an aerobic or anaerobic steady state was created, RNA sampled (0 min) and then the gas supply changed. RNA samples were then taken from the time at which the gas supply was changed.

For anaerobic conditions 5% CO2, 95% N2 was used.

The full transcriptional dataset is available from ArrayExpress ...

The transcriptional profiles of steady state E. coli cultures at a range of aerobiosis levels were determined. Two biological replicates and two technical replicates were carried out. Microarrays were carried out in a reference style (i.e. RNA vs a gDNA reference).

This assay describes the determination of concentrations and ratio of metabolites of adenine nucleotides (NAD and NADH). These metabolites have been extracted from Escherichia coli MG1655 and isgenic mutant strains.

This assay describes the determination of concentrations and ratio of metabolites of ubiquinones (oxidised and reduced form). These metabolites have been extracted from Escherichia coli MG1655 and isgenic mutant strains.

This .csv file shows the numbers of different cytochrome molecules per cell from steady-state continuously-grown cultures at various aerobiosis levels (0%, 31%, 56%, 85% and 115% AAU).

E. coli MG1655 and ∆sdhC and ∆frdA isogenic mutant strains were characterized in batch growth curves aerobic and anaerobically. Optical density, glucose consumption and by-product accumulation were measured during growth.

The model describes the behaviour of E. coli in a stationary chemostat with different oxygen availability.

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.

ArcA phosphorylation in chemostat cultures grown at different aerobiosis levels was quantitated by Phos-tag SDS-PAGE gel analysis and subsequent immunodetection of ArcA.

First version of enzyme-constrained model (ecModel) for Escherichia coli

The model describes the catabolism of Escherichia coli and its regulation. The metabolic reactions are modeled by the thermokinetic model formalism. The model is simplified by assuming rapid equilibrium of many reactions. Regulation is modeled by phenomenological laws describing the activation or repression of enzymes and genes in dependence of metabolic signals. The model is intended to describe the behavior of E. coli in a chemostat culture in depedence on the oxygen supply.

The model is described ...

This ordinary-differential equation model is a spatially lumped model showing the behaviour of oxygen in the three compartments medium, membrane and cytoplasm and its impact on FNR inactivation, hereby showing the effects of different oxygen concentrations, diffusion coefficients and reaction rates. The model was created with the Matlab SimBiology toolbox.

This partial-differential equations model focuses on the oxygen gradients in consideration of the three-dimensional cell and environment.

Code for joint probabilistic inference of transcription factor behaviour and gene-transcription factor as well as metabolite-transcription factor interaction based on genome and metabolite data.

The model presents the response of E.coli to different levels of oxygen supply, in which the oxidases, Cyo and Cyd, and their regulators, FNR and ArcBA systems, are included. The initial file 0.xml and supporting documents are for the model with FNR only. Four 0.xml files provided are at AAU level 31, 85, 115 and 217 respectively. The ArcBA system can be activated by revising the number of agents, ArcB, ArcA dimer, ArcA monomer, ArcA tetramer and ArcA octamer, in the initial file. The model needs ...

The model describes the electron transport chain (ETC) of Escherichia coli by ordinary differential equations. Also a simplified growth model based on an abstract reducing potential describing the balance of electron donor (glucose) and electron acceptors is coupled to the ETC. The model should reproduce and predict the regulation of the described system for different oxygen availability within the aerobiosis scale (glucose limited continuous culture<=>chemostat). Therefore oxygen is changed ...

A model of E. coli central carbon core metabolism, used as starting point for B. subtilis modelling. It is developed by Chassagnole et al. doi:10.1002/bit.10288.

Simplified model of the electron-transport chain(s) (ETC) of Escherichia coli and its regulation by ArcA and FNR. The goal is to demonstrate a hypothetical design principle in the regulatory structure (->partly qualitative parameter values). Oxygen is changed slowly (100% aerobiosis at 1000000 time units) thus the basis variable is not the time but the oxygen flux voxi.

The agent-based model involves the representation of each individual molecule of interest as an autonomous agent that exists within the cellular environment and interacts with other molecules according to the biochemical situation. FLAME environmet has beem used for agent-based development. The FLAME framework is an enabling tool to create agent-based models that can be run on high performance computers (HPCs). Models are created based upon extended finite state machines that include message input ...