Systematic identification of metabolites controlling gene expression in E. coli

[1]  M. Zampieri,et al.  Metabolomics-Driven Exploration of the Chemical Drug Space to Predict Combination Antimicrobial Therapies , 2019, Molecular cell.

[2]  Uwe Sauer,et al.  Biological insights through omics data integration , 2019, Current Opinion in Systems Biology.

[3]  Markus M. Rinschen,et al.  Identification of bioactive metabolites using activity metabolomics , 2019, Nature Reviews Molecular Cell Biology.

[4]  M. Zampieri,et al.  Metabolic profiling of cancer cells reveals genome-wide crosstalk between transcriptional regulators and metabolism , 2019, Nature Communications.

[5]  H. Link,et al.  Allosteric Feedback Inhibition Enables Robust Amino Acid Biosynthesis in E. coli by Enforcing Enzyme Overabundance , 2019, Cell systems.

[6]  Matthias Heinemann,et al.  Assessment of the interaction between the flux‐signaling metabolite fructose‐1,6‐bisphosphate and the bacterial transcription factors CggR and Cra , 2018, Molecular microbiology.

[7]  U. Sauer,et al.  A Map of Protein-Metabolite Interactions Reveals Principles of Chemical Communication , 2018, Cell.

[8]  H. Link,et al.  Crosstalk between transcription and metabolism: how much enzyme is enough for a cell? , 2018, Wiley interdisciplinary reviews. Systems biology and medicine.

[9]  Emma A. Briars,et al.  Genome-Scale Architecture of Small Molecule Regulatory Networks and the Fundamental Trade-Off between Regulation and Enzymatic Activity. , 2017, Cell reports.

[10]  James T. Yurkovich,et al.  Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities , 2017, Proceedings of the National Academy of Sciences.

[11]  R. Phillips,et al.  Tuning Transcriptional Regulation through Signaling: A Predictive Theory of Allosteric Induction , 2017, bioRxiv.

[12]  Kristala L. J. Prather,et al.  Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit , 2017, Nature Biotechnology.

[13]  Shinya Kuroda,et al.  Metabolism-Centric Trans-Omics. , 2017, Cell systems.

[14]  H. Link,et al.  Time-Optimized Isotope Ratio LC-MS/MS for High-Throughput Quantification of Primary Metabolites. , 2017, Analytical chemistry.

[15]  Simon F Brunner,et al.  Few regulatory metabolites coordinate expression of central metabolic genes in Escherichia coli , 2017, Molecular systems biology.

[16]  Peter D. Karp,et al.  The EcoCyc database: reflecting new knowledge about Escherichia coli K-12 , 2016, Nucleic Acids Res..

[17]  Zhixia Ye,et al.  Large-scale bioprocess competitiveness: the potential of dynamic metabolic control in two-stage fermentations , 2016 .

[18]  John D. Storey,et al.  Systems-level analysis of mechanisms regulating yeast metabolic flux , 2016, Science.

[19]  S. Busby,et al.  Local and global regulation of transcription initiation in bacteria , 2016, Nature Reviews Microbiology.

[20]  M. Mann,et al.  L-Arginine Modulates T Cell Metabolism and Enhances Survival and Anti-tumor Activity , 2016, Cell.

[21]  Markus Ralser,et al.  Methionine Metabolism Alters Oxidative Stress Resistance via the Pentose Phosphate Pathway , 2016, Antioxidants & redox signaling.

[22]  Fabio Rinaldi,et al.  RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond , 2015, Nucleic Acids Res..

[23]  Shuai Li,et al.  ASD v3.0: unraveling allosteric regulation with structural mechanisms and biological networks , 2015, Nucleic Acids Res..

[24]  U. Sauer,et al.  Real-time metabolome profiling of the metabolic switch between starvation and growth , 2015, Nature Methods.

[25]  Donghyuk Kim,et al.  Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655. , 2015, Cell reports.

[26]  Amit Pathania,et al.  Distinct Paths for Basic Amino Acid Export in Escherichia coli: YbjE (LysO) Mediates Export of l-Lysine , 2015, Journal of bacteriology.

[27]  U. Sauer,et al.  Coordination of microbial metabolism , 2014, Nature Reviews Microbiology.

[28]  R. Milo,et al.  Glycolytic strategy as a tradeoff between energy yield and protein cost , 2013, Proceedings of the National Academy of Sciences.

[29]  Joerg M. Buescher,et al.  Global Network Reorganization During Dynamic Adaptations of Bacillus subtilis Metabolism , 2012, Science.

[30]  Adam M. Feist,et al.  A comprehensive genome-scale reconstruction of Escherichia coli metabolism—2011 , 2011, Molecular systems biology.

[31]  Dieter Braun,et al.  Molecular interaction studies using microscale thermophoresis. , 2011, Assay and drug development technologies.

[32]  Ivan G. Costa,et al.  Detection and interpretation of metabolite–transcript coresponses using combined profiling data , 2011, Bioinform..

[33]  B. Palsson,et al.  Deciphering the transcriptional regulatory logic of amino acid metabolism. , 2011, Nature chemical biology.

[34]  D. Chatterji,et al.  Transcriptional switching in Escherichia coli during stress and starvation by modulation of sigma activity. , 2010, FEMS microbiology reviews.

[35]  L. Reitzer,et al.  Genetics and Regulation of the Major Enzymes of Alanine Synthesis in Escherichia coli , 2010, Journal of bacteriology.

[36]  J. Selbig,et al.  Metabolomic and transcriptomic stress response of Escherichia coli , 2010, Molecular systems biology.

[37]  Olga G. Troyanskaya,et al.  Coordinated Concentration Changes of Transcripts and Metabolites in Saccharomyces cerevisiae , 2009, PLoS Comput. Biol..

[38]  S. Gottesman,et al.  The Novel Transcription Factor SgrR Coordinates the Response to Glucose-Phosphate Stress , 2007, Journal of bacteriology.

[39]  J. Pronk,et al.  When transcriptome meets metabolome: fast cellular responses of yeast to sudden relief of glucose limitation , 2006, Molecular systems biology.

[40]  H. Mori,et al.  Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. , 2006, DNA research : an international journal for rapid publication of reports on genes and genomes.

[41]  A. Lustig,et al.  Escherichia coli dihydroxyacetone kinase controls gene expression by binding to transcription factor DhaR , 2005, The EMBO journal.

[42]  Katy C. Kao,et al.  Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[43]  Chiara Sabatti,et al.  Network component analysis: Reconstruction of regulatory signals in biological systems , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[44]  Kinetic Studies of cAMP-induced Allosteric Changes in Cyclic AMP Receptor Protein from Escherichia coli * , 2000, The Journal of Biological Chemistry.

[45]  H. Buc,et al.  Transcriptional regulation by cAMP and its receptor protein. , 1993, Annual review of biochemistry.

[46]  R. Gunsalus,et al.  Interaction of the Escherichia coli trp aporepressor with its ligand, L-tryptophan. , 1986, The Journal of biological chemistry.

[47]  B. Peterkofsky,et al.  N-Succinyl-L-diaminopimelic-glutamic transaminase. , 1961, The Journal of biological chemistry.