1. Home
  2. People Index
  3. Katja Bettenbrock

Katja Bettenbrock

About Katja Bettenbrock:

I am interested in the coupling of global regulation and metabolism in E. coli. To analyze this I construct and analyze defined mutant strains. These strains are characterized in bioreactor experiments of different types (batch, conti, pulse ...) and measurements on the level of metabolites, mRNA, and protein are applied. For all projects there are cooperation partners that use the data in modeling approaches either from the MPI Magdeburg or from the SUMO consortium.

SEEK ID: https://fairdomhub.org/people/31

Location: Germany

Expertise: Regulatory Networks, Molecular Biology, Genetics, Microbiology

Tools: Mutant and Strain Construction; RNA / DNA Techniques; RT-RealTime-PCR; 2D-Gels; Metabolite Analysis; Bioreactor Experiments; Flow Cyometry; ...

ORCID: Not specified

asset_housekeeper
help Katja's tags

This person has not yet tagged anything.

Related items

EraCoBiotech 2 nd call proposal preparation

Glycon proposal preparation

Programme: Model repository for M4 (Make Me My Model) clients of ISBE

Public web page: Not specified

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

Analysis of population heterogeneity in chemostat cultures with limited oxygen supply
SUMO

Cultures grown under standard SUMO conditions were analyzed with respect to heterogeneity in gene expression. To this end GFP reporter strains were constructed and GFP expression at single cell level was monitored by flow cytometry.

Snapshots: No snapshots

Analysis of Escherichia coli with linear electron transport chain
SUMO

The electron transport chain of E. coli is branched. Different NAD Dehydrogenases and terminal oxidases are known to be expressed at different oxygen availabilities. By deleting multiple genes mutant strains were constructed that posses a linear electron transport chain. These mutants were investigated in continous bioreactor experiments with limiting glucose and varying oxygen supply.

Snapshots: No snapshots

Analysis of Escherichia coli strains with linear respiratory chain
SUMO

A set of isogenic mutant strains was constructed which lack NADH Dehydrogenase I as well as two terminal oxidases, resulting in strains with linear respiratory chain. The different strains hence differ in the terminal oxidase and express either cytochrome bo, cytochrome bdI or cytochrome bdII.
The different strains were cultivated in glucose-limited chemostats with defined low levels of oxygen supply. Biomass and by-product formation, gene expression and the phosphorylation state of the important
...

Person responsible: Katja Bettenbrock

Snapshots: No snapshots

Deternination of ArcA phosphroylation level in mutants with linear ETC at different defined aerobiosis levels
SUMO

Mutants with linear respiratory chains were grown under SUMO chemostat conditions at different defined aerobiosis levels. The ArcA phoshorylation state as determined.

Contributor: Katja Bettenbrock

Assay type: Experimental Assay Type

Technology type: Gel Electrophoresis

Snapshots: No snapshots

Gene expression analysis of mutants with linear electron transport chain at different aerobiosis levels
SUMO

Mutant strains with linear electron transport chain were grown in chemostat cultures at different defined aerobiosis levels. Expression of selected genes was determined by Real Time RT-PCR

Contributor: Katja Bettenbrock

Assay type: Experimental Assay Type

Technology type: qRT-PCR

Snapshots: No snapshots

Determination of by-product formation and glucose uptake of mutants with linear respiratory chain at different aerobiosis levels
SUMO

Mutants with a linear respiratory chain consisting of NADH Dehydrogenase II and one of the terminal oxidases cytochrom bo, cytochrome bd I or cytochrome bd II were growth in chemostats with defined oxygen supply. The amounts of biomass formed and of acetate and formate produced were determined.

Contributor: Katja Bettenbrock

Assay type: Experimental Assay Type

Technology type: Chemostat Measurement

Snapshots: No snapshots

PtsG, Man
SUMO

Contributor: Katja Bettenbrock

Provider Name: Not specified

Provider's strain ID: Not specified

Organism: Escherichia coli k-12

Genotypes: del ptsG;del manXYZ

Phenotypes: wild-type

Comment: Not specified

PtsG, Mal
SUMO

Contributor: Katja Bettenbrock

Provider Name: Not specified

Provider's strain ID: Not specified

Organism: Escherichia coli k-12

Genotypes: del ptsG;del malEFG

Phenotypes: wild-type

Comment: Not specified

PtsG, Mgl, GalP
SUMO

Contributor: Katja Bettenbrock

Provider Name: Not specified

Provider's strain ID: Not specified

Organism: Escherichia coli k-12

Genotypes: del ptsG;del mglBAC;del galP

Phenotypes: wild-type

Comment: Not specified

PtsG, Mgl
SUMO

Contributor: Katja Bettenbrock

Provider Name: Not specified

Provider's strain ID: Not specified

Organism: Escherichia coli k-12

Genotypes: del ptsG;del mglBAC

Phenotypes: wild-type

Comment: Not specified

PtsG
SUMO

Contributor: Katja Bettenbrock

Provider Name: Not specified

Provider's strain ID: Not specified

Organism: Escherichia coli k-12

Genotypes: del ptsG

Phenotypes: slow growth with glucose

Comment: Not specified

Man
SUMO

Contributor: Katja Bettenbrock

Provider Name: Not specified

Provider's strain ID: Not specified

Organism: Escherichia coli k-12

Genotypes: del manXYZ

Phenotypes: wild-type

Comment: Not specified

Mal
SUMO

Contributor: Katja Bettenbrock

Provider Name: Not specified

Provider's strain ID: Not specified

Organism: Escherichia coli k-12

Genotypes: del malEFG

Phenotypes: wild-type

Comment: Not specified

Mgl, GalP
SUMO

Contributor: Katja Bettenbrock

Provider Name: Not specified

Provider's strain ID: Not specified

Organism: Escherichia coli k-12

Genotypes: del mglBAC;del galP

Phenotypes: wild-type

Comment: Not specified

GalP
SUMO

Contributor: Katja Bettenbrock

Provider Name: Not specified

Provider's strain ID: Not specified

Organism: Escherichia coli k-12

Genotypes: del galP

Phenotypes: wild-type

Comment: Not specified

Mgl
SUMO

Contributor: Katja Bettenbrock

Provider Name: Not specified

Provider's strain ID: Not specified

Organism: Escherichia coli k-12

Genotypes: del mglBAC

Phenotypes: wild-type

Comment: Not specified

AV36
SUMO

Contributor: Katja Bettenbrock

Provider Name: Not specified

Provider's strain ID: Not specified

Organism: Escherichia coli k-12

Genotypes: del ubiE

Phenotypes: wild-type

Comment: Not specified

AV34
SUMO

Contributor: Katja Bettenbrock

Provider Name: Not specified

Provider's strain ID: Not specified

Organism: Escherichia coli k-12

Genotypes: del menA

Phenotypes: wild-type

Comment: Not specified

AV33
SUMO

Contributor: Katja Bettenbrock

Provider Name: Not specified

Provider's strain ID: Not specified

Organism: Escherichia coli k-12

Genotypes: del ubiCA

Phenotypes: wild-type

Comment: Not specified

TBE042
SUMO

Contributor: Katja Bettenbrock

Provider Name: Not specified

Provider's strain ID: Not specified

Organism: Escherichia coli k-12

Genotypes: del nuoB;del appB;del cyoB

Phenotypes: wild-type

Comment: Not specified

TBE032
SUMO

Contributor: Katja Bettenbrock

Provider Name: Not specified

Provider's strain ID: Not specified

Organism: Escherichia coli k-12

Genotypes: del nuoB;del cydB;del cyoB

Phenotypes: wild-type

Comment: Not specified

TBE031
SUMO

Contributor: Katja Bettenbrock

Provider Name: Not specified

Provider's strain ID: Not specified

Organism: Escherichia coli k-12

Genotypes: del nuoB;del cydAB;del appB

Phenotypes: wild-type

Comment: Not specified

TBE029
SUMO

Contributor: Katja Bettenbrock

Provider Name: Alex terBeek

Provider's strain ID: Not specified

Organism: Escherichia coli k-12

Genotypes: del nuoB

Phenotypes: wild-type

Comment: Not specified

MG1655 SDH- FRD-
SUMO

Contributor: Katja Bettenbrock

Provider Name: Not specified

Provider's strain ID: Not specified

Organism: Escherichia coli k-12

Genotypes: del sdhA;del frdA

Phenotypes: wild-type

Comment: Not specified

MG1655 SucA-s
SUMO

Contributor: Katja Bettenbrock

Provider Name: Not specified

Provider's strain ID: Not specified

Organism: Escherichia coli k-12

Genotypes: del sucA

Phenotypes: faster growing variant

Comment: strain was selected from MG1655 sucA as a faster growing variant

MG1655 SucA
SUMO

Contributor: Katja Bettenbrock

Provider Name: Not specified

Provider's strain ID: Not specified

Organism: Escherichia coli k-12

Genotypes: del sucA

Phenotypes: wild-type

Comment: Not specified

Gene expression rates at different aerobiosis levels via RT-PCR
SUMO

This data file shows results from the different chemostat experiments.Gene expression rates are presented.

Creators: Katja Bettenbrock, Sonja Steinsiek

Contributor: Katja Bettenbrock

Download
Gene expression levels in mutants with linear respiratory chain
SUMO
No description specified

Creator: Katja Bettenbrock

Contributor: Katja Bettenbrock

Download
ETCmutants_metabolites
SUMO

by-product formation rates and glucose uptake rates of mutants with linear electron transport chain at different aerobiosis levels

Creator: Katja Bettenbrock

Contributor: Katja Bettenbrock

Download
ETC_mutants_ArcA
SUMO

The ArcA phosphorylation state was determined for mutants with linear respiratory chain at defined aerobiosis levels.

Creator: Katja Bettenbrock

Contributor: Katja Bettenbrock

Download
ETCmutants_mRNA
SUMO

Gene expression levels in mutants with linear ETC were determined by RealTime RT-PCR

Creator: Katja Bettenbrock

Contributor: Katja Bettenbrock

Download
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.

Authors: None

Date Published: 30th Sep 2014

Journal: PLoS One

Towards a Systems Level Understanding of the Oxygen Response of Escherichia coli
SUMO

Abstract (Expand)

Escherichia coli is a facultatively anaerobic bacterium. With glucose if no external electron acceptors are available, ATP is produced by substrate level phosphorylation. The intracellular redox balance … is maintained by mixed-acid fermentation, that is, the production and excretion of several organic acids. When oxygen is available, E. coli switches to aerobic respiration to achieve redox balance and optimal energy conservation by proton translocation linked to electron transfer. The switch between fermentative and aerobic respiratory growth is driven by extensive changes in gene expression and protein synthesis, resulting in global changes in metabolic fluxes and metabolite concentrations. This oxygen response is determined by the interaction of global and local genetic regulatory mechanisms, as well as by enzymatic regulation. The response is affected by basic physical constraints such as diffusion, thermodynamics and the requirement for a balance of carbon, electrons and energy (predominantly the proton motive force and the ATP pool). A comprehensive systems level understanding of the oxygen response of E. coli requires the integrated interpretation of experimental data that are pertinent to the multiple levels of organization that mediate the response. In the pan-European venture, Systems Biology of Microorganisms (SysMO) and specifically within the project Systems Understanding of Microbial Oxygen Metabolism (SUMO), regulator activities, gene expression, metabolite levels and metabolic flux datasets were obtained using a standardized and reproducible chemostat-based experimental system. These different types and qualities of data were integrated using mathematical models. The approach described here has revealed a much more detailed picture of the aerobic-anaerobic response, especially for the environmentally critical microaerobic range that is located between unlimited oxygen availability and anaerobiosis.

Authors: Katja Bettenbrock, Hao Bai, Michael Ederer, Jeff Green, Klaas Hellingwerf, Michael Holcombe, S. Kunz, Matthew Rolfe, Guido Sanguinetti, Oliver Sawodny, Poonam Sharma, Sonja Steinsiek, Robert Poole

Date Published: 7th May 2014

Journal: Adv Microb Physiol

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.

Authors: None

Date Published: 27th Mar 2014

Journal: Front Microbiol

Analysis of Escherichia coli mutants with a linear respiratory chain
SUMO

Abstract (Expand)

The respiratory chain of E. coli is branched to allow the cells' flexibility to deal with changing environmental conditions. It consists of the NADH:ubiquinone oxidoreductases NADH dehydrogenase I … and II, as well as of three terminal oxidases. They differ with respect to energetic efficiency (proton translocation) and their affinity to the different quinone/quinol species and oxygen. In order to analyze the advantages of the branched electron transport chain over a linear one and to assess how usage of the different terminal oxidases determines growth behavior at varying oxygen concentrations, a set of isogenic mutant strains was created, which lack NADH dehydrogenase I as well as two of the terminal oxidases, resulting in strains with a linear respiratory chain. These strains were analyzed in glucose-limited chemostat experiments with defined oxygen supply, adjusting aerobic, anaerobic and different microaerobic conditions. In contrast to the wild-type strain MG1655, the mutant strains produced acetate even under aerobic conditions. Strain TBE032, lacking NADH dehydrogenase I and expressing cytochrome bd-II as sole terminal oxidase, showed the highest acetate formation rate under aerobic conditions. This supports the idea that cytochrome bd-II terminal oxidase is not able to catalyze the efficient oxidation of the quinol pool at higher oxygen conditions, but is functioning mainly under limiting oxygen conditions. Phosphorylation of ArcA, the regulator of the two-component system ArcBA, besides Fnr the main transcription factor for the response towards different oxygen concentrations, was studied. Its phosphorylation pattern was changed in the mutant strains. Dephosphorylation and therefore inactivation of ArcA started at lower aerobiosis levels than in the wild-type strain. Notably, not only the micro- and aerobic metabolism was affected by the mutations, but also the anaerobic metabolism, where the respiratory chain should not be important.

Authors: None

Date Published: 27th Jan 2014

Journal: PLoS One

Kinase activity of ArcB from Escherichia coli is subject to regulation by both ubiquinone and demethylmenaquinone
SUMO

Abstract (Expand)

Expression of the catabolic network in Escherichia coli is predominantly regulated, via oxygen availability, by the two-component system ArcBA. It has been shown that the kinase activity of ArcB is … controlled by the redox state of two critical pairs of cysteines in dimers of the ArcB sensory kinase. Among the cellular components that control the redox state of these cysteines of ArcB are the quinones from the cytoplasmic membrane of the cell, which function in 'respiratory' electron transfer. This study is an effort to understand how the redox state of the quinone pool(s) is sensed by the cell via the ArcB kinase. We report the relationship between growth, quinone content, ubiquinone redox state, the level of ArcA phosphorylation, and the level of ArcA-dependent gene expression, in a number of mutants of E. coli with specific alterations in their set of quinones, under a range of physiological conditions. Our results provide experimental evidence for a previously formulated hypothesis that not only ubiquinone, but also demethylmenaquinone, can inactivate kinase activity of ArcB. Also, in a mutant strain that only contains demethylmenaquinone, the extent of ArcA phosphorylation can be modulated by the oxygen supply rate, which shows that demethylmenaquinone can also inactivate ArcB in its oxidized form. Furthermore, in batch cultures of a strain that contains ubiquinone as its only quinone species, we observed that the ArcA phosphorylation level closely followed the redox state of the ubiquinone/ubiquinol pool, much more strictly than it does in the wild type strain. Therefore, at low rates of oxygen supply in the wild type strain, the activity of ArcB may be inhibited by demethylmenaquinone, in spite of the fact that the ubiquinones are present in the ubiquinol form.

Authors: P. Sharma, S. Stagge, M. Bekker, K. Bettenbrock, K. J. Hellingwerf

Date Published: 7th Oct 2013

Journal: PLoS One

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.

Authors: None

Date Published: 8th Oct 2012

Journal: Journal of Bacteriology

Characterization of E. coli MG1655 and frdA and sdhC mutants at various aerobiosis levels
SUMO

Abstract

Not specified

Authors: Sonja Steinsiek, S. Frixel, Stefan Stagge, Katja Bettenbrock

Date Published: 1st Jun 2011

Journal: Journal of Biotechnology

Powered by
 (v.1.9.0)
FAIRDOMHub | Funding and Programmes | Credits | Terms & Conditions | Imprint
Copyright © 2008 - 2019 The University of Manchester and HITS gGmbH