Effect of iclR and arcA knockouts on biomass formation and metabolic fluxes in Escherichia coli K12 and its implications on understanding the metabolism of Escherichia coli BL21 (DE3)

[1]  M. De Mey,et al.  Validation study of 24 deepwell microtiterplates to screen libraries of strains in metabolic engineering. , 2010, Journal of bioscience and bioengineering.

[2]  Vivek K. Mutalik,et al.  Predicting strength and function for promoters of the Escherichia coli alternative sigma factor, σE , 2010, Proceedings of the National Academy of Sciences.

[3]  R. Lenski,et al.  Genome sequences of Escherichia coli B strains REL606 and BL21(DE3). , 2009, Journal of molecular biology.

[4]  R. Lenski,et al.  Understanding the differences between genome sequences of Escherichia coli B strains REL606 and BL21(DE3) and comparison of the E. coli B and K-12 genomes. , 2009, Journal of molecular biology.

[5]  U. Sauer,et al.  13C-based metabolic flux analysis , 2009, Nature Protocols.

[6]  Pei Yee Ho,et al.  Effects of arcA and arcB genes knockout on the metabolism in Escherichia coli under aerobic condition , 2009 .

[7]  Peter D. Karp,et al.  EcoCyc: A comprehensive view of Escherichia coli biology , 2008, Nucleic Acids Res..

[8]  K. Shimizu,et al.  Effect of cra gene knockout together with other genes knockouts on the improvement of substrate consumption rate in Escherichia coli under microaerobic condition , 2008 .

[9]  M. Reuss,et al.  Global Transcription and Metabolic Flux Analysis of Escherichia coli in Glucose-Limited Fed-Batch Cultivations , 2008, Applied and Environmental Microbiology.

[10]  M. Araúzo-Bravo,et al.  Effect of cra gene knockout together with edd and iclR genes knockout on the metabolism in Escherichia coli , 2008, Archives of Microbiology.

[11]  U. Sauer,et al.  Cyclic AMP-Dependent Catabolite Repression Is the Dominant Control Mechanism of Metabolic Fluxes under Glucose Limitation in Escherichia coli , 2008, Journal of bacteriology.

[12]  Matthias Reuss,et al.  Topology of the global regulatory network of carbon limitation in Escherichia coli. , 2007, Journal of biotechnology.

[13]  Jo Maertens,et al.  Construction and model-based analysis of a promoter library for E. coli: an indispensable tool for metabolic engineering , 2007, BMC biotechnology.

[14]  Alexey Bochkarev,et al.  Glyoxylate and Pyruvate Are Antagonistic Effectors of the Escherichia coli IclR Transcriptional Regulator* , 2007, Journal of Biological Chemistry.

[15]  Pei Yee Ho,et al.  Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations , 2007, Science.

[16]  G. Bennett,et al.  Effect of the global redox sensing/regulation networks on Escherichia coli and metabolic flux distribution based on C-13 labeling experiments. , 2006, Metabolic engineering.

[17]  Mansi El-Mansi,et al.  Control of carbon flux through enzymes of central and intermediary metabolism during growth of Escherichia coli on acetate. , 2006, Current opinion in microbiology.

[18]  Antoine Danchin,et al.  Codon Usage Domains over Bacterial Chromosomes , 2006, PLoS Comput. Biol..

[19]  Annik Nanchen,et al.  Nonlinear Dependency of Intracellular Fluxes on Growth Rate in Miniaturized Continuous Cultures of Escherichia coli , 2006, Applied and Environmental Microbiology.

[20]  S. Busby,et al.  Investigations of the modular structure of bacterial promoters. , 2006, Biochemical Society symposium.

[21]  Dequan Chen,et al.  Low-usage codons and rare codons of Escherichia coli Mini Review , 2006 .

[22]  G. Bennett,et al.  Effect of ArcA and FNR on the expression of genes related to the oxygen regulation and the glycolysis pathway in Escherichia coli under microaerobic growth conditions. , 2005, Biotechnology and bioengineering.

[23]  Nicola Zamboni,et al.  FiatFlux – a software for metabolic flux analysis from 13C-glucose experiments , 2005, BMC Bioinformatics.

[24]  Alan J Wolfe,et al.  Glucose metabolism at high density growth of E. coli B and E. coli K: differences in metabolic pathways are responsible for efficient glucose utilization in E. coli B as determined by microarrays and Northern blot analyses. , 2005, Biotechnology and bioengineering.

[25]  U. Sauer,et al.  Impact of Global Transcriptional Regulation by ArcA, ArcB, Cra, Crp, Cya, Fnr, and Mlc on Glucose Catabolism in Escherichia coli , 2005, Journal of bacteriology.

[26]  Ka-Yiu San,et al.  Effect of oxygen on the Escherichia coli ArcA and FNR regulation systems and metabolic responses. , 2005, Biotechnology and bioengineering.

[27]  Volker Hecht,et al.  Metabolic flux analysis of Escherichia coli in glucose-limited continuous culture. I. Growth-rate-dependent metabolic efficiency at steady state. , 2005, Microbiology.

[28]  T. Ferenci,et al.  The role of isocitrate lyase and the glyoxylate cycle in Escherichia coli growing under glucose limitation. , 2005, Research in microbiology.

[29]  S. Ball,et al.  Role of the Escherichia coli glgX Gene in Glycogen Metabolism , 2005, Journal of bacteriology.

[30]  Milton H. Saier,et al.  Functional Interactions between the Carbon and Iron Utilization Regulators, Crp and Fur, in Escherichia coli , 2005, Journal of bacteriology.

[31]  Pierre Baldi,et al.  Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA. , 2005, The Journal of biological chemistry.

[32]  Milton H. Saier,et al.  Transcriptome Analysis of Crp-Dependent Catabolite Control of Gene Expression in Escherichia coli , 2004, Journal of bacteriology.

[33]  Joseph Shiloach,et al.  Transcription levels of key metabolic genes are the cause for different glucose utilization pathways in E. coli B (BL21) and E. coli K (JM109). , 2004, Journal of biotechnology.

[34]  Xueqiao Liu,et al.  Probing the ArcA-P Modulon of Escherichia coli by Whole Genome Transcriptional Analysis and Sequence Recognition Profiling* , 2004, Journal of Biological Chemistry.

[35]  Wouter A. Duetz,et al.  Oxygen transfer by orbital shaking of square vessels and deepwell microtiter plates of various dimensions , 2004 .

[36]  U. Sauer,et al.  High-throughput metabolic flux analysis based on gas chromatography-mass spectrometry derived 13C constraints. , 2004, Analytical biochemistry.

[37]  S. Pirt.  Maintenance energy: a general model for energy-limited and energy-sufficient growth , 1982, Archives of Microbiology.

[38]  Chrystala Constantinidou,et al.  Identification of the CRP regulon using in vitro and in vivo transcriptional profiling. , 2004, Nucleic acids research.

[39]  U. Sauer,et al.  A Novel Metabolic Cycle Catalyzes Glucose Oxidation and Anaplerosis in Hungry Escherichia coli* , 2003, Journal of Biological Chemistry.

[40]  J. Collado-Vides,et al.  Identifying global regulators in transcriptional regulatory networks in bacteria. , 2003, Current opinion in microbiology.

[41]  G. W. Hatfield,et al.  Global Gene Expression Profiling in Escherichia coli K12 , 2003, Journal of Biological Chemistry.

[42]  U. Sauer,et al.  Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS. , 2003, European journal of biochemistry.

[43]  Svetlana Alexeeva,et al.  Requirement of ArcA for Redox Regulation in Escherichia coli under Microaerobic but Not Anaerobic or Aerobic Conditions , 2003, Journal of bacteriology.

[44]  Akira Ishihama,et al.  Two different modes of transcription repression of the Escherichia coli acetate operon by IclR , 2002, Molecular microbiology.

[45]  A. Goldberg,et al.  Trehalose synthesis is induced upon exposure of Escherichia coli to cold and is essential for viability at low temperatures , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[46]  U. Sauer,et al.  Metabolic Flux Responses to Pyruvate Kinase Knockout in Escherichia coli , 2002, Journal of bacteriology.

[47]  M. Quadroni,et al.  Short- and long-term changes in proteome composition and kinetic properties in a culture of Escherichia coli during transition from glucose-excess to glucose-limited growth conditions in continuous culture and vice versa. , 2001, Environmental microbiology.

[48]  B. Wanner,et al.  One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[49]  J. Shiloach,et al.  Investigation of the TCA cycle and the glyoxylate shunt in Escherichia coli BL21 and JM109 using 13C‐NMR/MS , 2000, Biotechnology and bioengineering.

[50]  R. Ebright,et al.  Transcription activation by catabolite activator protein (CAP). , 1999, Journal of molecular biology.

[51]  Juan Aguilar,et al.  Cross-induction of glc and ace Operons ofEscherichia coli Attributable to Pathway Intersection , 1999, The Journal of Biological Chemistry.

[52]  J. Keasling,et al.  Effect of Escherichia coli biomass composition on central metabolic fluxes predicted by a stoichiometric model. , 1998, Biotechnology and bioengineering.

[53]  K. Hammer,et al.  The Sequence of Spacers between the Consensus Sequences Modulates the Strength of Prokaryotic Promoters , 1998, Applied and Environmental Microbiology.

[54]  A. Cozzone,et al.  Regulation of acetate metabolism by protein phosphorylation in enteric bacteria. , 1998, Annual review of microbiology.

[55]  J. Guest,et al.  Transcriptional regulation of the aconitase genes (acnA and acnB) of Escherichia coli. , 1997, Microbiology.

[56]  J. Keasling,et al.  Stoichiometric model of Escherichia coli metabolism: incorporation of growth-rate dependent biomass composition and mechanistic energy requirements. , 1997, Biotechnology and bioengineering.

[57]  N. W. Davis,et al.  The complete genome sequence of Escherichia coli K-12. , 1997, Science.

[58]  S. Park,et al.  Aerobic regulation of isocitrate dehydrogenase gene (icd) expression in Escherichia coli by the arcA and fnr gene products , 1997, Journal of bacteriology.

[59]  T. Ferenci,et al.  The relationship between external glucose concentration and cAMP levels inside Escherichia coli: implications for models of phosphotransferase-mediated regulation of adenylate cyclase. , 1997, Microbiology.

[60]  J. François,et al.  A simplified procedure for a rapid and reliable assay of both glycogen and trehalose in whole yeast cells. , 1997, Analytical biochemistry.

[61]  A. Steinbüchel,et al.  Accumulation of storage lipids in species of Rhodococcus and Nocardia and effect of inhibitors and polyethylene glycol , 1997 .

[62]  A. S. Lynch,et al.  Transcriptional control mediated by the ArcA two-component response regulator protein of Escherichia coli: characterization of DNA binding at target promoters , 1996, Journal of bacteriology.

[63]  M. Madigan,et al.  Brock Biology of Microorganisms , 1996 .

[64]  R. Goody,et al.  Escherichia coli isocitrate dehydrogenase kinase/phosphatase. Overproduction and kinetics of interaction with its substrates by using intrinsic fluorescence and fluorescent nucleotide analogues. , 1996, European journal of biochemistry.

[65]  H. Yang,et al.  Coordinate genetic regulation of glycogen catabolism and biosynthesis in Escherichia coli via the CsrA gene product , 1996, Journal of bacteriology.

[66]  J. Russell,et al.  Energetics of bacterial growth: balance of anabolic and catabolic reactions. , 1995, Microbiological reviews.

[67]  Gideon Schreiber,et al.  Expression of the genes coding for the Escherichia coli integration host factor are controlled by growth phase, rpoS, ppGpp and by autoregulation , 1994, Molecular microbiology.

[68]  H. Bujard,et al.  Context-dependent effects of upstream A-tracts. Stimulation or inhibition of Escherichia coli promoter function. , 1994, Journal of molecular biology.

[69]  R. E. Wolf,et al.  Determination of the growth rate-regulated steps in expression of the Escherichia coli K-12 gnd gene , 1994, Journal of bacteriology.

[70]  B. Palsson,et al.  Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates , 1993, Applied and environmental microbiology.

[71]  B. Palsson,et al.  Biochemical production capabilities of escherichia coli , 1993, Biotechnology and bioengineering.

[72]  D. Tempest,et al.  Physiological and energetic aspects of bacterial metabolite overproduction. , 1992, FEMS microbiology letters.

[73]  W. Boos,et al.  Trehalose synthesis genes are controlled by the putative sigma factor encoded by rpoS and are involved in stationary-phase thermotolerance in Escherichia coli , 1991, Journal of bacteriology.

[74]  G Perrière,et al.  Regulation of the acetate operon in Escherichia coli: purification and functional characterization of the IclR repressor. , 1991, The EMBO journal.

[75]  E. Lin,et al.  The arcB gene of Escherichia coli encodes a sensor‐regulator protein for anaerobic repression of the arc modulon , 1990, Molecular microbiology.

[76]  A. Strøm,et al.  Biochemical and genetic characterization of osmoregulatory trehalose synthesis in Escherichia coli , 1988, Journal of bacteriology.

[77]  E. Lin,et al.  arcA (dye), a global regulatory gene in Escherichia coli mediating repression of enzymes in aerobic pathways. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[78]  S. Iuchi,et al.  arcA(dye),大腸菌において好気経路の酵素を抑える働きをする全体的な制御遺伝子 , 1988 .

[79]  J. Russell.  Heat production by ruminal bacteria in continuous culture and its relationship to maintenance energy , 1986, Journal of bacteriology.

[80]  S. Gottesman.  Bacterial regulation: global regulatory networks. , 1984, Annual review of genetics.

[81]  S. Maloy,et al.  Elevated levels of glyoxylate shunt enzymes in Escherichia coli strains constitutive for fatty acid degradation , 1980, Journal of bacteriology.

[82]  R. E. Wolf,et al.  Growth-rate-dependent alteration of 6-phosphogluconate dehydrogenase and glucose 6-phosphate dehydrogenase levels in Escherichia coli K-12 , 1979, Journal of bacteriology.

[83]  W. Hempfling,et al.  Effects of varying the carbon source limiting growth on yield and maintenance characteristics of Escherichia coli in continuous culture , 1975, Journal of bacteriology.

[84]  J. Wiame,et al.  Purification et caractérisation partielle des deux malate synthases d'Escherichia coli , 1973 .

[85]  J. Wiame,et al.  [Purification and partial characterization of two malate synthases of Echerichia coli]. , 1973, European journal of biochemistry.

[86]  S. Pirt.  The maintenance energy of bacteria in growing cultures , 1965, Proceedings of the Royal Society of London. Series B. Biological Sciences.