BIOREACTION NETWORK FLUX ANALYSIS FOR INDUSTRIAL MICROORGANISMS: A REVIEW

[1]  J Villadsen,et al.  Metabolic flux distributions in Penicillium chrysogenum during fed‐batch cultivations , 1995, Biotechnology and bioengineering.

[2]  P. Çalık,et al.  Mass flux balance-based model and metabolic flux analysis for collagen synthesis in the fibrogenesis process of human liver. , 2000, Medical hypotheses.

[3]  Gregory Stephanopoulos,et al.  Carbon Flux Distributions at the Glucose 6‐Phosphate Branch Point in Corynebacterium glutamicum during Lysine Overproduction , 1994 .

[4]  G. Dervakos,et al.  On the topological features of optimal metabolic pathway regimes , 1996, Applied biochemistry and biotechnology.

[5]  H Sahm,et al.  Determination of full 13C isotopomer distributions for metabolic flux analysis using heteronuclear spin echo difference NMR spectroscopy. , 2000, Journal of biotechnology.

[6]  Amit Varma,et al.  Parametric sensitivity of stoichiometric flux balance models applied to wild‐type Escherichia coli metabolism , 1995, Biotechnology and bioengineering.

[7]  E O Voit,et al.  Optimization of nonlinear biotechnological processes with linear programming: Application to citric acid production by Aspergillus niger , 2000, Biotechnology and bioengineering.

[8]  Muriel Cocaign-Bousquet,et al.  Pyruvate overflow and carbon flux within the central metabolic pathways of Corynebacterium glutamicum during growth on lactate , 1995 .

[9]  T. Szyperski.  Biosynthetically directed fractional 13C-labeling of proteinogenic amino acids. An efficient analytical tool to investigate intermediary metabolism. , 1995, European journal of biochemistry.

[10]  U. Sauer,et al.  Altered regulation of pyruvate kinase or co-overexpression of phosphofructokinase increases glycolytic fluxes in resting Escherichia coli. , 2000, Biotechnology and bioengineering.

[11]  M. Reuss,et al.  In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae : I. Experimental observations. , 1997, Biotechnology and bioengineering.

[12]  A. D. de Graaf,et al.  Quantitative Determination of Metabolic Fluxes during Coutilization of Two Carbon Sources: Comparative Analyses withCorynebacterium glutamicum during Growth on Acetate and/or Glucose , 2000, Journal of bacteriology.

[13]  P. Çalık,et al.  Oxygen-transfer strategy and its regulation effects in serine alkaline protease production by Bacillus licheniformis. , 2000, Biotechnology and bioengineering.

[14]  Stefan Schuster.  Biotechnology in silico: metabolic proteomics of Haemophilus influenzae , 2000 .

[15]  G. Stephanopoulos,et al.  Metabolic flux distributions in Corynebacterium glutamicum during growth and lysine overproduction , 2000, Biotechnology and bioengineering.

[16]  J E Bailey,et al.  Metabolic flux analysis with a comprehensive isotopomer model in Bacillus subtilis. , 2001, Biotechnology and bioengineering.

[17]  Sahm,et al.  13C tracer experiments and metabolite balancing for metabolic flux analysis: comparing two approaches , 1998, Biotechnology and bioengineering.

[18]  B O Palsson,et al.  Optimal selection of metabolic fluxes for in vivo measurement. I. Development of mathematical methods. , 1992, Journal of theoretical biology.

[19]  J. Nielsen,et al.  Quantitative analysis of metabolic fluxes in Escherichia coli, using two-dimensional NMR spectroscopy and complete isotopomer models. , 1999, Journal of biotechnology.

[20]  M A Aon,et al.  Fluxes of carbon, phosphorylation, and redox intermediates during growth of saccharomyces cerevisiae on different carbon sources , 1995, Biotechnology and bioengineering.

[21]  K. Shimizu,et al.  Metabolic flux analysis for efficient pyruvate fermentation using vitamin-auxotrophic yeast of Torulopsis glabrata. , 1999, Journal of bioscience and bioengineering.

[22]  P. Verheijen,et al.  Possible pitfalls of flux calculations based on (13)C-labeling. , 2001, Metabolic engineering.

[23]  J. Edwards,et al.  Systems Properties of the Haemophilus influenzaeRd Metabolic Genotype* , 1999, The Journal of Biological Chemistry.

[24]  A P Ison,et al.  Classification and sensitivity analysis of a proposed primary metabolic reaction network for Streptomyces lividans. , 1999, Metabolic engineering.

[25]  N. Torres,et al.  Metabolism of citric acid production by Aspergillus niger: model definition, steady-state analysis and constrained optimization of citric acid production rate. , 2000, Biotechnology and bioengineering.

[26]  H J Cruz,et al.  Metabolic shifts by nutrient manipulation in continuous cultures of BHK cells. , 1999, Biotechnology and bioengineering.

[27]  F. Mavituna,et al.  Metabolic flux distribution for the optimized production of l-glutamate , 1998 .

[28]  U. Sauer,et al.  Metabolic Flux Ratio Analysis of Genetic and Environmental Modulations of Escherichia coli Central Carbon Metabolism , 1999, Journal of bacteriology.

[29]  Gregory Stephanopoulos,et al.  Carbon Flux Distributions at the Pyruvate Branch Point in Corynebacterium glutamicum during Lysine Overproduction , 1994 .

[30]  T Szyperski,et al.  13C-NMR, MS and metabolic flux balancing in biotechnology research , 1998, Quarterly Reviews of Biophysics.

[31]  A. Fiechter.  Die kontinuierliche Züchtung von Mikroorganismen als apparatives problem , 1965 .

[32]  G. Stephanopoulos,et al.  Network rigidity and metabolic engineering in metabolite overproduction , 1991, Science.

[33]  P. Çalık,et al.  Metabolic flux analysis for human therapeutic protein productions and hypothesis for new therapeutical strategies in medicine , 2002 .

[34]  M. Reuss,et al.  In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae: II. Mathematical model. , 1997, Biotechnology and bioengineering.

[35]  E. Papoutsakis,et al.  Fermentation equations for propionic‐acid bacteria and production of assorted oxychemicals from various sugars , 1985, Biotechnology and bioengineering.

[36]  S Shioya,et al.  A maximum production strategy of lysine based on a simplified model derived from a metabolic reaction network. , 1999, Metabolic engineering.

[37]  W. Wiechert,et al.  In Vivo Quantification of Parallel and Bidirectional Fluxes in the Anaplerosis of Corynebacterium glutamicum * , 2000, The Journal of Biological Chemistry.

[38]  M M Ataai,et al.  Analysis of metabolic fluxes in batch and continuous cultures of Bacillus subtilis , 1993, Biotechnology and bioengineering.

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

[40]  N. Torres,et al.  Modeling approach to control of carbohydrate metabolism during citric acid accumulation by Aspergillus niger: II. Sensitivity analysis , 1994, Biotechnology and bioengineering.

[41]  J. Heijnen,et al.  Application of metabolic flux analysis for the identification of metabolic bottlenecks in the biosynthesis of penicillin-G. , 2000, Biotechnology and bioengineering.

[42]  H Sahm,et al.  Determination of the fluxes in the central metabolism of Corynebacterium glutamicum by nuclear magnetic resonance spectroscopy combined with metabolite balancing , 1996, Biotechnology and bioengineering.

[43]  B. Palsson,et al.  Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems. , 2000, Biotechnology and bioengineering.

[44]  M. Domach,et al.  Simple constrained‐optimization view of acetate overflow in E. coli , 1990, Biotechnology and bioengineering.

[45]  J Tramper,et al.  Metabolic flux analysis of hybridoma cells in different culture media using mass balances , 1996, Biotechnology and bioengineering.

[46]  K. Shimizu,et al.  Metabolic flux distributions in recombinant Saccharomyces cerevisiae during foreign protein production. , 1997, Journal of biotechnology.

[47]  M. Domach,et al.  Suppressed Acid Formation By Cofeeding of Glucose and Citrate in Bacillus Cultures: Emergence of Pyruvate Kinase as a Potential Metabolic Engineering Site , 1995, Biotechnology progress.

[48]  W. Wiechert,et al.  13C NMR studies of the fluxes in the central metabolism of Corynebacterium glutamicum during growth and overproduction of amino acids in batch cultures , 1995, Applied Microbiology and Biotechnology.

[49]  M. A. Eiteman,et al.  Metabolic Analysis of Escherichia coliin the Presence and Absence of the Carboxylating Enzymes Phosphoenolpyruvate Carboxylase and Pyruvate Carboxylase , 2000, Applied and Environmental Microbiology.

[50]  N. Torres,et al.  Modeling approach to control of carbohydrate metabolism during citric acid accumulation by Aspergillus niger: I. Model definition and stability of the steady state , 1994, Biotechnology and bioengineering.

[51]  B. Palsson,et al.  Toward Metabolic Phenomics: Analysis of Genomic Data Using Flux Balances , 1999, Biotechnology progress.

[52]  E. Papoutsakis,et al.  Equations and calculations of product yields and preferred pathways for butanediol and mixed‐acid fermentations , 1985, Biotechnology and bioengineering.

[53]  J. Bailey,et al.  13C NMR Flux Ratio Analysis of Escherichia coli Central Carbon Metabolism in Microaerobic Bioprocesses , 1999 .

[54]  A. D. de Graaf,et al.  Flux partitioning in the split pathway of lysine synthesis in Corynebacterium glutamicum. Quantification by 13C- and 1H-NMR spectroscopy. , 1993, European journal of biochemistry.

[55]  P. Çalık,et al.  Metabolic flux analysis for serine alkaline protease fermentation by Bacillus licheniformis in a defined medium: Effects of the oxygen transfer rate , 1999 .

[56]  G. Stephanopoulos,et al.  Computer‐aided synthesis of biochemical pathways , 1990, Biotechnology and bioengineering.

[57]  B. Palsson,et al.  Network analysis of intermediary metabolism using linear optimization. II. Interpretation of hybridoma cell metabolism. , 1992, Journal of theoretical biology.

[58]  J. Edwards,et al.  Robustness Analysis of the Escherichiacoli Metabolic Network , 2000, Biotechnology progress.

[59]  W. Holms,et al.  The central metabolic pathways of Escherichia coli: relationship between flux and control at a branch point, efficiency of conversion to biomass, and excretion of acetate. , 1986, Current topics in cellular regulation.

[60]  G. Stephanopoulos,et al.  Intracellular flux analysis in hybridomas using mass balances and in vitro 13C nmr , 1995, Biotechnology and bioengineering.

[61]  Wright.,et al.  Flux Analysis of Glucose Metabolism in Rhizopus oryzae for the Purpose of Increasing Lactate Yields , 1997, Fungal genetics and biology : FG & B.

[62]  B. Palsson,et al.  Metabolic capabilities of Escherichia coli: I. synthesis of biosynthetic precursors and cofactors. , 1993, Journal of theoretical biology.

[63]  H Sahm,et al.  Response of the central metabolism in Corynebacterium glutamicum to the use of an NADH-dependent glutamate dehydrogenase. , 1999, Metabolic engineering.

[64]  Potential metabolic limitations in lysine production by Corynebacterium glutamicum as revealed by metabolic network analysis , 1994, Applied Microbiology and Biotechnology.

[65]  H. Brunengraber,et al.  Isotopomer Analysis of Citric Acid Cycle and Gluconeogenesis in Rat Liver , 1995, The Journal of Biological Chemistry.

[66]  J. Nikawa,et al.  Effect of modifying metabolic network on poly-3-hydroxybutyrate biosynthesis in recombinant Escherichia coli. , 1999, Journal of bioscience and bioengineering.

[67]  N. Lindley,et al.  Metabolic analysis of glutamate production by Corynebacterium glutamicum. , 1999, Metabolic engineering.

[68]  J. Heijnen,et al.  A metabolic network stoichiometry analysis of microbial growth and product formation , 1995, Biotechnology and bioengineering.

[69]  G. Bennett,et al.  Metabolic flux analysis of Escherichia coli expressing the Bacillus subtilis acetolactate synthase in batch and continuous cultures. , 1999, Biotechnology and bioengineering.

[70]  B. Palsson,et al.  Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalism. , 1992, Journal of theoretical biology.

[71]  B. Palsson,et al.  Metabolic Capabilities of Escherichia coli II. Optimal Growth Patterns , 1993 .

[72]  J. Nielsen,et al.  Metabolic network analysis of Penicillium chrysogenum using (13)C-labeled glucose. , 2000, Biotechnology and bioengineering.

[73]  C. Rosiers,et al.  A 13C Mass Isotopomer Study of Anaplerotic Pyruvate Carboxylation in Perfused Rat Hearts* , 1997, The Journal of Biological Chemistry.

[74]  P. Çalık,et al.  Mass flux balance-based model and metabolic pathway engineering analysis for serine alkaline protease synthesis by , 1999 .

[75]  D. Fell,et al.  Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. , 1999, Trends in biotechnology.

[76]  J E Bailey,et al.  Metabolic capacity of Bacillus subtilis for the production of purine nucleosides, riboflavin, and folic acid. , 1998, Biotechnology and bioengineering.

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

[78]  J Tramper,et al.  Metabolite-balancing techniques vs. 13C tracer experiments to determine metabolic fluxes in hybridoma cells. , 1998, Biotechnology and bioengineering.

[79]  Metabolic flux in glucose/citrate co-fermentation by lactic acid bacteria as measured by isotopic ratio analysis. , 2000, FEMS microbiology letters.

[80]  G. Stephanopoulos,et al.  Elucidation of anaplerotic pathways in Corynebacterium glutamicum via 13C-NMR spectroscopy and GC-MS , 1997, Applied Microbiology and Biotechnology.

[81]  Jens Nielsen,et al.  Identification of Enzymes and Quantification of Metabolic Fluxes in the Wild Type and in a Recombinant Aspergillus oryzae Strain , 1999, Applied and Environmental Microbiology.

[82]  U. Sauer,et al.  Metabolic fluxes in riboflavin-producing Bacillus subtilis , 1997, Nature Biotechnology.

[83]  E. Papoutsakis,et al.  Stoichiometric modeling of Clostridium acetobutylicum fermentations with non-linear constraints. , 1999, Journal of biotechnology.

[84]  B. Palsson,et al.  Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis. , 2000, Journal of theoretical biology.

[85]  David Jenkins,et al.  Development and validation of a flux-based stoichiometric model for enhanced biological phosphorus removal metabolism , 1999 .

[86]  P. Loubière,et al.  The Metabolic Network of Lactococcus lactis: Distribution of 14C-Labeled Substrates between Catabolic and Anabolic Pathways , 2000, Journal of bacteriology.

[87]  B O Palsson,et al.  Optimal selection of metabolic fluxes for in vivo measurement. II. Application to Escherichia coli and hybridoma cell metabolism. , 1992, Journal of theoretical biology.

[88]  E. Heinzle,et al.  Mass spectrometry for metabolic flux analysis. , 1999, Biotechnology and bioengineering.

[89]  J. Nielsen,et al.  Growth energetics and metabolic fluxes in continuous cultures of Penicillium chrysogenum. , 1996, Journal of biotechnology.

[90]  W. Wiechert,et al.  Metabolic state of Zymomonas mobilis in glucose-, fructose-, and xylose-fed continuous cultures as analysed by 13C- and 31P-NMR spectroscopy , 1999, Archives of Microbiology.

[91]  J. Nielsen,et al.  Flux distributions in anaerobic, glucose-limited continuous cultures of Saccharomyces cerevisiae. , 1997, Microbiology.

[92]  H. Brunengraber,et al.  Rates of gluconeogenesis and citric acid cycle in perfused livers, assessed from the mass spectrometric assay of the 13C labeling pattern of glutamate. , 1993, The Journal of biological chemistry.

[93]  M M Ataai,et al.  Metabolic fluxes, pools, and enzyme measurements suggest a tighter coupling of energetics and biosynthetic reactions associated with reduced pyruvate kinase flux. , 1999, Biotechnology and bioengineering.

[94]  Shuichi Aiba,et al.  Identification of metabolic model: Citrate production from glucose by Candida lipolytica , 1979 .

[95]  B. Palsson,et al.  In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data , 2001, Nature Biotechnology.

[96]  F. Naeimpoor,et al.  Metabolic flux analysis in Streptomyces coelicolor under various nutrient limitations. , 2000, Metabolic engineering.

[97]  P. Çalık,et al.  Carbon sources affect metabolic capacities of Bacillus species for the production of industrial enzymes: theoretical analyses for serine and neutral proteases and alpha-amylase. , 2001, Biochemical engineering journal.

[98]  Johannes Tramper,et al.  Metabolic-flux analysis of hybridoma cells under oxidative and reductive stress using mass balances , 2000, Cytotechnology.

[99]  J. Heijnen,et al.  Statistical reconciliation of the elemental and molecular biomass composition of Saccharomyces cerevisiae. , 2001, Biotechnology and bioengineering.

[100]  G. Bennett,et al.  Effect of inactivation of nuo and ackA-pta on redistribution of metabolic fluxes in Escherichia coli. , 1999, Biotechnology and bioengineering.

[101]  G Stephanopoulos,et al.  Metabolic flux analysis of hybridoma continuous culture steady state multiplicity. , 1999, Biotechnology and bioengineering.

[102]  U. Sauer,et al.  Physiology and metabolic fluxes of wild-type and riboflavin-producing Bacillus subtilis , 1996, Applied and environmental microbiology.

[103]  B. Palsson,et al.  Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. , 2000, Journal of theoretical biology.

[104]  G. Bennett,et al.  Effect of glucose analog supplementation on metabolic flux distribution in anaerobic chemostat cultures of Escherichia coli. , 2000, Metabolic engineering.

[105]  G Stephanopoulos,et al.  Effect of reversible reactions on isotope label redistribution--analysis of the pentose phosphate pathway. , 1998, European journal of biochemistry.

[106]  W. Wiechert.  13C metabolic flux analysis. , 2001, Metabolic engineering.

[107]  D. Ramkrishna,et al.  Mathematical models of metabolic pathways. , 1999, Current opinion in biotechnology.

[108]  A J Sinskey,et al.  Metabolic and physiological studies of Corynebacterium glutamicum mutants. , 1997, Biotechnology and bioengineering.

[109]  R. Heinrich,et al.  Metabolic Pathway Analysis: Basic Concepts and Scientific Applications in the Post‐genomic Era , 1999, Biotechnology progress.

[110]  E. Papoutsakis.  Equations and calculations for fermentations of butyric acid bacteria , 1984, Biotechnology and bioengineering.

[111]  George N. Bennett,et al.  Metabolic Flux Analysis ofEscherichia coliDeficient in the Acetate Production Pathway and Expressing theBacillus subtilisAcetolactate Synthase , 1999 .

[112]  M. Ataai,et al.  Utilization of glucose and amino acids in insect cell cultures: Quantifying the metabolic flows within the primary pathways and medium development , 1993, Biotechnology and bioengineering.

[113]  Takáč,et al.  Metabolic flux analyses for serine alkaline protease production. , 2000, Enzyme and microbial technology.

[114]  C. Dussap,et al.  Metabolic flux distribution in Corynebacterium melassecola ATCC 17965 for various carbon sources , 1996, Biotechnology and bioengineering.

[115]  E. Papoutsakis,et al.  Metabolic flux analysis elucidates the importance of the acid-formation pathways in regulating solvent production by Clostridium acetobutylicum. , 1999, Metabolic engineering.