4.6 Article

Global coordination of metabolic pathways in Escherichia coli by active and passive regulation

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

Laurent Heirendt et al.

NATURE PROTOCOLS (2019)

Article Multidisciplinary Sciences

Lysine harvesting is an antioxidant strategy and triggers underground polyamine metabolism

Viridiana Olin-Sandoval et al.

NATURE (2019)

Article Biochemistry & Molecular Biology

RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12

Alberto Santos-Zavaleta et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP

Donghyuk Kim et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemical Research Methods

Proteomic Delineation of the ArcA Regulon in Salmonella Typhimurium During Anaerobiosis

Zhen Wang et al.

MOLECULAR & CELLULAR PROTEOMICS (2018)

Article Biochemistry & Molecular Biology

Few regulatory metabolites coordinate expression of central metabolic genes in Escherichia coli

Karl Kochanowski et al.

MOLECULAR SYSTEMS BIOLOGY (2017)

Article Multidisciplinary Sciences

A global resource allocation strategy governs growth transition kinetics of Escherichia coli

David W. Erickson et al.

NATURE (2017)

Article Multidisciplinary Sciences

Optimality and sub-optimality in a bacterial growth law

Benjamin D. Towbin et al.

NATURE COMMUNICATIONS (2017)

Article Biotechnology & Applied Microbiology

The quantitative and condition-dependent Escherichia coli proteome

Alexander Schmidt et al.

NATURE BIOTECHNOLOGY (2016)

Review Biochemistry & Molecular Biology

Metabolic control of methylation and acetylation

Xiaoyang Su et al.

CURRENT OPINION IN CHEMICAL BIOLOGY (2016)

Article Biochemistry & Molecular Biology

Translation elicits a growth rate-dependent, genome-wide, differential protein production in Bacillus subtilis

Olivier Borkowski et al.

MOLECULAR SYSTEMS BIOLOGY (2016)

Article Multidisciplinary Sciences

Systems-level analysis of mechanisms regulating yeast metabolic flux

Sean R. Hackett et al.

SCIENCE (2016)

Article Cell Biology

The Cost of Protein Production

Moshe Kafri et al.

CELL REPORTS (2016)

Article Biochemical Research Methods

Quantification and Classification of E-coli Proteome Utilization and Unused Protein Costs across Environments

Edward J. O'Brien et al.

PLOS COMPUTATIONAL BIOLOGY (2016)

Review Microbiology

Posttranslational regulation of microbial metabolism

Karl Kochanowski et al.

CURRENT OPINION IN MICROBIOLOGY (2015)

Review Microbiology

Post-translational modifications as key regulators of bacterial metabolic fluxes

Tippapha Pisithkul et al.

CURRENT OPINION IN MICROBIOLOGY (2015)

Article Biochemistry & Molecular Biology

How fast-growing bacteria robustly tune their ribosome concentration to approximate growth-rate maximization

Evert Bosdriesz et al.

FEBS JOURNAL (2015)

Article Biochemistry & Molecular Biology

Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria

Sheng Hui et al.

MOLECULAR SYSTEMS BIOLOGY (2015)

Article Multidisciplinary Sciences

Overflow metabolism in Escherichia coli results from efficient proteome allocation

Markus Basan et al.

NATURE (2015)

Article Biotechnology & Applied Microbiology

Use of Adaptive Laboratory Evolution To Discover Key Mutations Enabling Rapid Growth of Escherichia coli K-12 MG1655 on Glucose Minimal Medium

Ryan A. LaCroix et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2015)

Article Biochemistry & Molecular Biology

Ubiquinone accumulation improves osmotic-stress tolerance in Escherichia coli

Daniel C. Sevin et al.

NATURE CHEMICAL BIOLOGY (2014)

Review Microbiology

Coordination of microbial metabolism

Victor Chubukov et al.

NATURE REVIEWS MICROBIOLOGY (2014)

Article Multidisciplinary Sciences

Lost in Transition: Start-Up of Glycolysis Yields Subpopulations of Nongrowing Cells

Johan H. van Heerden et al.

SCIENCE (2014)

Article Biochemical Research Methods

Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism

Elad Noor et al.

PLOS COMPUTATIONAL BIOLOGY (2014)

Article Genetics & Heredity

Determining the Control Circuitry of Redox Metabolism at the Genome-Scale

Stephen Federowicz et al.

PLOS GENETICS (2014)

Review Biochemical Research Methods

Somewhat in control - the role of transcription in regulating microbial metabolic fluxes

Karl Kochanowski et al.

CURRENT OPINION IN BIOTECHNOLOGY (2013)

Review Biochemistry & Molecular Biology

Systematic investigation of protein-small molecule interactions

Xiyan Li et al.

IUBMB LIFE (2013)

Article Biochemistry & Molecular Biology

Escherichia coli achieves faster growth by increasing catalytic and translation rates of proteins

Kaspar Valgepea et al.

MOLECULAR BIOSYSTEMS (2013)

Article Biochemistry & Molecular Biology

Promoters maintain their relative activity levels under different growth conditions

Leeat Keren et al.

MOLECULAR SYSTEMS BIOLOGY (2013)

Article Biochemistry & Molecular Biology

Dissecting specific and global transcriptional regulation of bacterial gene expression

Luca Gerosa et al.

MOLECULAR SYSTEMS BIOLOGY (2013)

Article Biochemistry & Molecular Biology

Transcriptional regulation is insufficient to explain substrate-induced flux changes in Bacillus subtilis

Victor Chubukov et al.

MOLECULAR SYSTEMS BIOLOGY (2013)

Article Biochemistry & Molecular Biology

Indirect and suboptimal control of gene expression is widespread in bacteria

Morgan N. Price et al.

MOLECULAR SYSTEMS BIOLOGY (2013)

Article Multidisciplinary Sciences

Pyrimidine homeostasis is accomplished by directed overflow metabolism

Marshall Louis Reaves et al.

NATURE (2013)

Article Multidisciplinary Sciences

Coordination of bacterial proteome with metabolism by cyclic AMP signalling

Conghui You et al.

NATURE (2013)

Article Biotechnology & Applied Microbiology

Systematic identification of allosteric protein-metabolite interactions that control enzyme activity in vivo

Hannes Link et al.

NATURE BIOTECHNOLOGY (2013)

Article Multidisciplinary Sciences

Functioning of a metabolic flux sensor in Escherichia coli

Karl Kochanowski et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Biotechnology & Applied Microbiology

Biological systems modeling of metabolic and signaling networks

Joseph A. Wayman et al.

CURRENT OPINION IN CHEMICAL ENGINEERING (2013)

Article Biotechnology & Applied Microbiology

Acetate scavenging activity in Escherichia coli: interplay of acetyl-CoA synthetase and the PEP-glyoxylate cycle in chemostat cultures

Sergio Renilla et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2012)

Review Biotechnology & Applied Microbiology

The importance of post-translational modifications in regulating Saccharomyces cerevisiae metabolism

Ana Paula Oliveira et al.

FEMS YEAST RESEARCH (2012)

Article Biochemistry & Molecular Biology

Need-based activation of ammonium uptake in Escherichia coli

Minsu Kim et al.

MOLECULAR SYSTEMS BIOLOGY (2012)

Article Biochemistry & Molecular Biology

Deciphering the transcriptional regulatory logic of amino acid metabolism

Byung-Kwan Cho et al.

NATURE CHEMICAL BIOLOGY (2012)

Article Biotechnology & Applied Microbiology

Extensive exometabolome analysis reveals extended overflow metabolism in various microorganisms

Nicole Paczia et al.

MICROBIAL CELL FACTORIES (2012)

Article Multidisciplinary Sciences

Evolutionary Trade-Offs, Pareto Optimality, and the Geometry of Phenotype Space

O. Shoval et al.

SCIENCE (2012)

Article Mathematical & Computational Biology

Negative auto-regulation increases the input dynamic-range of the arabinose system of Escherichia coli

Daniel Madar et al.

BMC SYSTEMS BIOLOGY (2011)

Article Biochemistry & Molecular Biology

Large-scale 13C-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli

Bart R. B. Haverkorn van Rijsewijk et al.

MOLECULAR SYSTEMS BIOLOGY (2011)

Article Biochemistry & Molecular Biology

A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011

Jeffrey D. Orth et al.

MOLECULAR SYSTEMS BIOLOGY (2011)

Article Biochemistry & Molecular Biology

α-ketoglutarate coordinates carbon and nitrogen utilization via enzyme I inhibition

Christopher D. Doucette et al.

NATURE CHEMICAL BIOLOGY (2011)

Article Biochemical Research Methods

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

Jan Schellenberger et al.

NATURE PROTOCOLS (2011)

Article Multidisciplinary Sciences

Using Genomic Sequencing for Classical Genetics in E. coli K12

Eric Lyons et al.

PLOS ONE (2011)

Article Multidisciplinary Sciences

Direct regulation of Escherichia coli ribosomal protein promoters by the transcription factors ppGpp and DksA

Justin J. Lemke et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Biochemistry & Molecular Biology

Tradeoff between enzyme and metabolite efficiency maintains metabolic homeostasis upon perturbations in enzyme capacity

Sarah-Maria Fendt et al.

MOLECULAR SYSTEMS BIOLOGY (2010)

Article Biochemistry & Molecular Biology

Bacterial adaptation through distributed sensing of metabolic fluxes

Oliver Kotte et al.

MOLECULAR SYSTEMS BIOLOGY (2010)

Article Multidisciplinary Sciences

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

Matthew Scott et al.

SCIENCE (2010)

Article Mathematical & Computational Biology

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

Monica L. Mo et al.

BMC SYSTEMS BIOLOGY (2009)

Article Biochemistry & Molecular Biology

Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli

Jie Yuan et al.

MOLECULAR SYSTEMS BIOLOGY (2009)

Article Biochemical Research Methods

C-13-based metabolic flux analysis

Nicola Zamboni et al.

NATURE PROTOCOLS (2009)

Review Microbiology

(p)ppGpp: Still Magical?

Katarzyna Potrykus et al.

ANNUAL REVIEW OF MICROBIOLOGY (2008)

Article Biochemistry & Molecular Biology

Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli

Robert Schuetz et al.

MOLECULAR SYSTEMS BIOLOGY (2007)

Article Biochemistry & Molecular Biology

Signal integration in the galactose network of Escherichia coli

Szabolcs Semsey et al.

MOLECULAR MICROBIOLOGY (2007)

Article Multidisciplinary Sciences

Combinatorial transcriptional control of the lactose operon of Escherichia coli

Thomas Kuhlman et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Biochemical Research Methods

A comprehensive library of fluorescent transcriptional reporters for Escherichia coli

Alon Zaslaver et al.

NATURE METHODS (2006)

Article Multidisciplinary Sciences

Unraveling the complexity of flux regulation:: A new method demonstrated for nutrient starvation in Saccharomyces cerevisiae

S Rossell et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Biotechnology & Applied Microbiology

Nonlinear dependency of intracellular fluxes on growth rate in miniaturized continuous cultures of Escherichia coli

A Nanchen et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2006)

Article Biochemical Research Methods

FiatFlux -: a software for metabolic flux analysis from 13C-glucose experiments -: art. no. 209

N Zamboni et al.

BMC BIOINFORMATICS (2005)

Article Biochemical Research Methods

High-throughput metabolic flux analysis based on gas chromatography-mass spectrometry derived 13C constraints

E Fischer et al.

ANALYTICAL BIOCHEMISTRY (2004)

Review Biochemistry & Molecular Biology

Catabolite activator protein: DNA binding and transcription activation

CL Lawson et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2004)

Article Multidisciplinary Sciences

Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis

KC Kao et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Article Biotechnology & Applied Microbiology

Correcting mass isotopomer distributions for naturally occurring isotopes

WA van Winden et al.

BIOTECHNOLOGY AND BIOENGINEERING (2002)

Review Microbiology

Revisiting the stringent response, ppGpp and starvation signaling

D Chatterji et al.

CURRENT OPINION IN MICROBIOLOGY (2001)