Coordination of microbial metabolism

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

(2013) Karl Kochanowski et al.   CURRENT OPINION IN BIOTECHNOLOGY

A new regulatory principle for in vivo biochemistry: Pleiotropic low affinity regulation by the adenine nucleotides - Illustrated for the glycolytic enzymes of Saccharomyces cerevisiae

(2013) Femke I.C. Mensonides et al.   FEBS LETTERS

Comprehensive Profiling of Protein Lysine Acetylation in Escherichia coli

(2013) Kai Zhang et al.   JOURNAL OF PROTEOME RESEARCH

Nitrogen Assimilation in Escherichia coli: Putting Molecular Data into a Systems Perspective

(2013) W. C. van Heeswijk et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Acetyl-Phosphate Is a Critical Determinant of Lysine Acetylation in E. coli

(2013) Brian T. Weinert et al.   MOLECULAR CELL

Promoters maintain their relative activity levels under different growth conditions

(2013) L. Keren et al.   Molecular Systems Biology

Dissecting specific and global transcriptional regulation of bacterial gene expression

(2013) L. Gerosa et al.   Molecular Systems Biology

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

(2013) V. Chubukov et al.   Molecular Systems Biology

Shared control of gene expression in bacteria by transcription factors and global physiology of the cell

(2013) S. Berthoumieux et al.   Molecular Systems Biology

Coordination of bacterial proteome with metabolism by cyclic AMP signalling

(2013) Conghui You et al.   NATURE

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

(2013) Hannes Link et al.   NATURE BIOTECHNOLOGY

Functioning of a metabolic flux sensor in Escherichia coli

(2013) K. Kochanowski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PII signal transduction proteins are ATPases whose activity is regulated by 2-oxoglutarate

(2013) M. V. Radchenko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional Lysine Modification by an Intrinsically Reactive Primary Glycolytic Metabolite

(2013) R. E. Moellering et al.   SCIENCE

Nitrogen and Carbon Status Are Integrated at the Transcriptional Level by the Nitrogen Regulator NtrC In Vivo

(2013) J. Schumacher et al.   mBio

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Global relative and absolute quantitation in microbial proteomics

(2012) Andreas Otto et al.   CURRENT OPINION IN MICROBIOLOGY

RpoS proteolysis is controlled directly by ATP levels in Escherichia coli

(2012) C. N. Peterson et al.   GENES & DEVELOPMENT

Direct Regulation of GTP Homeostasis by (p)ppGpp: A Critical Component of Viability and Stress Resistance

(2012) Allison Kriel et al.   MOLECULAR CELL

Regulation of Yeast Pyruvate Kinase by Ultrasensitive Allostery Independent of Phosphorylation

(2012) Yi-Fan Xu et al.   MOLECULAR CELL

Regulation of yeast central metabolism by enzyme phosphorylation

(2012) Ana Paula Oliveira et al.   Molecular Systems Biology

Ultrasensitive regulation of anapleurosis via allosteric activation of PEP carboxylase

(2012) Yi-Fan Xu et al.   Nature Chemical Biology

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

(2012) Nicholas T Ingolia et al.   Nature Protocols

ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions

(2012) Terrence S. Furey   NATURE REVIEWS GENETICS

EcoCyc: fusing model organism databases with systems biology

(2012) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Regulatory architecture determines optimal regulation of gene expression in metabolic pathways

(2012) V. Chubukov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Throughput, Accurate Mass Metabolome Profiling of Cellular Extracts by Flow Injection–Time-of-Flight Mass Spectrometry

(2011) Tobias Fuhrer et al.   ANALYTICAL CHEMISTRY

More than just a metabolic regulator - elucidation and validation of new targets of PdhR in Escherichia coli

(2011) Anna-Katharina Göhler et al.   BMC Systems Biology

Pyruvate Kinase Triggers a Metabolic Feedback Loop that Controls Redox Metabolism in Respiring Cells

(2011) Nana-Maria Grüning et al.   Cell Metabolism

Regulation and control of metabolic fluxes in microbes

(2011) Luca Gerosa et al.   CURRENT OPINION IN BIOTECHNOLOGY

A flux-sensing mechanism could regulate the switch between respiration and fermentation

(2011) Daphne H. E. W. Huberts et al.   FEMS YEAST RESEARCH

Target of Rapamycin (TOR) in Nutrient Signaling and Growth Control

(2011) Robbie Loewith et al.   GENETICS

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

(2011) J. D. Orth et al.   Molecular Systems Biology

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

(2011) Christopher D Doucette et al.   Nature Chemical Biology

Deciphering the transcriptional regulatory logic of amino acid metabolism

(2011) Byung-Kwan Cho et al.   Nature Chemical Biology

Optical sensors for measuring dynamic changes of cytosolic metabolite levels in yeast

(2011) Clara Bermejo et al.   Nature Protocols

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

(2011) Jan Schellenberger et al.   Nature Protocols

Novel Roles of cAMP Receptor Protein (CRP) in Regulation of Transport and Metabolism of Carbon Sources

(2011) Tomohiro Shimada et al.   PLoS One

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

(2011) J. J. Lemke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrahigh Performance Liquid Chromatography−Tandem Mass Spectrometry Method for Fast and Robust Quantification of Anionic and Aromatic Metabolites

(2010) Joerg Martin Buescher et al.   ANALYTICAL CHEMISTRY

Systems biology approach reveals that overflow metabolism of acetate in Escherichia coli is triggered by carbon catabolite repression of acetyl-CoA synthetase

(2010) Kaspar Valgepea et al.   BMC Systems Biology

Transcriptional regulation of respiration in yeast metabolizing differently repressive carbon substrates

(2010) Sarah-Maria Fendt et al.   BMC Systems Biology

Extensive In Vivo Metabolite-Protein Interactions Revealed by Large-Scale Systematic Analyses

(2010) Xiyan Li et al.   CELL

Systems biology of microbial metabolism

(2010) Matthias Heinemann et al.   CURRENT OPINION IN MICROBIOLOGY

Intracellular characterization of aerobic glucose metabolism in seven yeast species by 13C flux analysis and metabolomics

(2010) Stefan Christen et al.   FEMS YEAST RESEARCH

Novel Members of the Cra Regulon Involved in Carbon Metabolism in Escherichia coli

(2010) T. Shimada et al.   JOURNAL OF BACTERIOLOGY

Control of AmtB-GlnK Complex Formation by Intracellular Levels of ATP, ADP, and 2-Oxoglutarate

(2010) Martha V. Radchenko et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Metabolic and Transcriptional Response to Cofactor Perturbations in Escherichia coli

(2010) Anders K. Holm et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A systematic screen for protein–lipid interactions in Saccharomyces cerevisiae

(2010) Oriol Gallego et al.   Molecular Systems Biology

Bacterial adaptation through distributed sensing of metabolic fluxes

(2010) Oliver Kotte et al.   Molecular Systems Biology

Generating and navigating proteome maps using mass spectrometry

(2010) Christian H. Ahrens et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Acetylation of Metabolic Enzymes Coordinates Carbon Source Utilization and Metabolic Flux

(2010) Q. Wang et al.   SCIENCE

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

(2010) M. Scott et al.   SCIENCE

The Carbon Assimilation Network in Escherichia coli Is Densely Connected and Largely Sign-Determined by Directions of Metabolic Fluxes

(2010) Valentina Baldazzi et al.   PLoS Computational Biology

Achieving Optimal Growth through Product Feedback Inhibition in Metabolism

(2010) Sidhartha Goyal et al.   PLoS Computational Biology

α-Ketoglutarate Controls the Ability of theEscherichia coliPII Signal Transduction Protein To Regulate the Activities of NRII (NtrB) but Does Not Control the Binding of PII to NRII

(2009) Peng Jiang et al.   BIOCHEMISTRY

Bacterial sensors of oxygen

(2009) Jeffrey Green et al.   CURRENT OPINION IN MICROBIOLOGY

Coordination of gene expression with growth rate: A feedback or a feed-forward strategy?

(2009) Sagi Levy et al.   FEBS LETTERS

Allosteric control of Escherichia coli rRNA promoter complexes by DksA

(2009) S. T. Rutherford et al.   GENES & DEVELOPMENT

The Vam6 GEF Controls TORC1 by Activating the EGO Complex

(2009) Matteo Binda et al.   MOLECULAR CELL

Shifts in growth strategies reflect tradeoffs in cellular economics

(2009) Douwe Molenaar et al.   Molecular Systems Biology

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

(2009) Jie Yuan et al.   Molecular Systems Biology

Growth landscape formed by perception and import of glucose in yeast

(2009) Hyun Youk et al.   NATURE

13C-based metabolic flux analysis

(2009) Nicola Zamboni et al.   Nature Protocols

Predicting Cellular Growth from Gene Expression Signatures

(2009) Edoardo M. Airoldi et al.   PLoS Computational Biology

(p)ppGpp: Still Magical?

(2008) Katarzyna Potrykus et al.   Annual Review of Microbiology

Dissecting Enzyme Regulation by Multiple Allosteric Effectors: Nucleotide Regulation of Aspartate Transcarbamoylase†

(2008) Joshua D. Rabinowitz et al.   BIOCHEMISTRY

Protein abundance profiling of the Escherichia coli cytosol

(2008) Yasushi Ishihama et al.   BMC GENOMICS

Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis

(2008) Anne Goelzer et al.   BMC Systems Biology

Sloppiness, robustness, and evolvability in systems biology

(2008) Bryan C Daniels et al.   CURRENT OPINION IN BIOTECHNOLOGY

Nutrient signals driving cell growth

(2008) Reinhard Dechant et al.   CURRENT OPINION IN CELL BIOLOGY

Carbon Catabolite Repression in Bacillus subtilis: Quantitative Analysis of Repression Exerted by Different Carbon Sources

(2008) K. D. Singh et al.   JOURNAL OF BACTERIOLOGY

Mitochondrial Oxidative Phosphorylation Is Regulated by Fructose 1,6-Bisphosphate

(2008) Rodrigo Díaz-Ruiz et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Diverse Two-Dimensional Input Functions Control Bacterial Sugar Genes

(2008) Shai Kaplan et al.   MOLECULAR CELL

Kinetic flux profiling for quantitation of cellular metabolic fluxes

(2008) Jie Yuan et al.   Nature Protocols

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Carbon catabolite repression in bacteria: many ways to make the most out of nutrients

(2008) Boris Görke et al.   NATURE REVIEWS MICROBIOLOGY

Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli

(2008) B.-K. Cho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coordination of Growth Rate, Cell Cycle, Stress Response, and Metabolic Activity in Yeast

(2007) Matthew J. Brauer et al.   MOLECULAR BIOLOGY OF THE CELL