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N Use By Plants
Nitrate Assimilation
Ammonia Assimilation
Glu, Gln, Asn, Gly, Ser
Aminotransferases
Asp, Ala, GABA
Val, Leu, Ileu, Thr, Lys
Pro, Arg, Orn
Polyamines
Non-protein AAs
Alkaloids
Sulfate Assimilation
Cys, Met, AdoMet, ACC
His, Phe, Tyr, Tryp
Secondary Products
Onium Compounds
Enzymes
Methods
Simulation
References
HORT640 - Metabolic Plant Physiology

References, flux balance analysis or FBA

Almaas E, Kovacs B, Vicsek T, Oltvai ZN, Barabasi AL. Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature 427: 839-843 (2004).

Almaas E, Oltvai ZN, Barabasi AL. The activity reaction core and plasticity of metabolic networks. PLoS Comput. Biol. 1: e68 (2005).

Alper H, Jin YS, Moxley JF, Stephanopoulos G. Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli. Metab. Eng. 7: 155-164 (2005).

Alvarez-Vasquez F, Sims KJ, Cowart LA, Okamoto Y, Voit EO, Hannun YA. Simulation and validation of modelled sphingolipid metabolism in Saccharomyces cerevisiae. Nature 433: 425-430 (2005).

Arai K, Lee K, Berthiaume F, Tompkins RG, Yarmush ML. Intrahepatic amino acid and glucose metabolism in a D-galactosamine-induced rat liver failure model. Hepatology 34: 360-371 (2001).

Azama K, Abe S, Sugimoto H, Davies E. Lysine-containing proteins in maize endosperm: a major contribution from cytoskeleton-associated carbohydrate-metabolizing enzymes. Planta 217: 628-638 (2003).

Baart GJ, Willemsen M, Khatami E, de Haan A, Zomer B, Beuvery EC, Tramper J, Martens DE. Modeling Neisseria meningitidis B metabolism at different specific growth rates. Biotechnol. Bioeng. 101: 1022-1035 (2008).

Bae YM, Crawford IP. The Rhizobium meliloti trpE(G) gene is regulated by attenuation, and its product, anthranilate synthase, is regulated by feedback inhibition. J. Bacteriol. 172: 3318-3327 (1990).

Bais HP, Walker TS, Stermitz FR, Hufbauer RA, Vivanco JM. Enantiomeric-dependent phytotoxic and antimicrobial activity of (+/-)-catechin. A rhizosecreted racemic mixture from spotted knapweed. Plant Physiol. 128: 1173-1179 (2002).

Bardey V, Vallet C, Robas N, Charpentier B, Thouvenot B, Mougin A, Hajnsdorf E, Regnier P, Springer M, Branlant C. Characterization of the molecular mechanisms involved in the differential production of erythrose-4-phosphate dehydrogenase, 3-phosphoglycerate kinase and class II fructose-1,6-bisphosphate aldolase in Escherichia coli. Mol. Microbiol. 57: 1265-1287 (2005).

Beard DA, Liang SD, Qian H. Energy balance for analysis of complex metabolic networks. Biophys. J. 83: 79-86 (2002).

Berthoud H. Multiple neural systems controlling food intake and body weight. Neurosci. Biobehav. Rev. 26: 393 (2002).

Bijlsma RJ, Lambers H. A dynamic whole-plant model of integrated metabolism of nitrogen and carbon. 2. Balanced growth driven by C fluxes and regulated by signals from C and N substrate. Plant & Soil 220: 71-87 (2000).

Bilu Y, Shlomi T, Barkai N, Ruppin E. Conservation of expression and sequence of metabolic genes is reflected by activity across metabolic states. PLoS Comput. Biol. 2: e106 (2006).

Blank LM, Ebert BE, Buhler B, Schmid A. Metabolic capacity estimation of Escherichia coli as a platform for redox biocatalysis: constraint-based modeling and experimental verification. Biotechnol. Bioeng. 100: 1050-1065 (2008).

Blom J, De Mattos MJ, Grivell LA. Redirection of the respiro-fermentative flux distribution in Saccharomyces cerevisiae by overexpression of the transcription factor Hap4p. Appl. Environ. Microbiol. 66: 1970-1973 (2000).

Bonarius HP, Timmerarends B, de Gooijer CD, Tramper J. Metabolite-balancing techniques vs. 13C tracer experiments to determine metabolic fluxes in hybridoma cells. Biotechnol. Bioeng. 58: 258-262 (1998).

Borodina I, Krabben P, Nielsen J. Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism. Genome Res. 15: 820-829 (2005).

Boyle NR, Morgan JA. Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii. BMC Syst. Biol. 3: 4 (2009).

Burgard AP, Maranas CD. Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions. Biotechnol. Bioeng. 74: 364-375 (2001).

Buvinger WE, Stone LC, Heath HE. Biochemical genetics of tryptophan synthesis in Pseudomonas acidovorans. J. Bacteriol. 147: 62-68 (1981).

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Cohn W, Crawford IP. Regulation of enzyme synthesis in the tryptophan pathway of Acinetobacter calcoaceticus. J. Bacteriol. 127: 367-379 (1976).

Covert MW, Palsson BO. Constraints-based models: regulation of gene expression reduces the steady-state solution space. J. Theor. Biol. 221: 309-325 (2003).

Covert MW, Schilling CH, Palsson B. Regulation of gene expression in flux balance models of metabolism. J. Theor. Biol. 213: 73-88 (2001).

Covert MW, Xiao N, Chen TJ, Karr JR. Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli. Bioinformatics 24: 2044-2050 (2008).

Dash RK, Li Y, Kim J, Saidel GM, Cabrera ME. Modeling cellular metabolism and energetics in skeletal muscle: large-scale parameter estimation and sensitivity analysis. IEEE Trans. Biomed. Eng. 55: 1298-1318 (2008).

De RK, Das M, Mukhopadhyay S. Incorporation of enzyme concentrations into FBA and identification of optimal metabolic pathways. BMC Syst. Biol. 2: 65 (2008).

Deutscher D, Meilijson I, Kupiec M, Ruppin E. Multiple knockout analysis of genetic robustness in the yeast metabolic network. Nat. Genet. 38: 993-998 (2006).

Dias JM, Oehmen A, Serafim LS, Lemos PC, Reis MA, Oliveira R. Metabolic modelling of polyhydroxyalkanoate copolymers production by mixed microbial cultures. BMC Syst. Biol. 2: 59 (2008).

Dikicioglu D, Pir P, Onsan ZI, Ulgen KO, Kirdar B, Oliver SG. Integration of metabolic modeling and phenotypic data in the evaluation and improvement of ethanol production using respiratory deficient mutants of Saccharomyces cerevisiae. Appl. Environ. Microbiol. 74: 5809-5816 (2008).

Drysch A, El Massaoudi M, Mack C, Takors R, de Graaf AA, Sahm H. Production process monitoring by serial mapping of microbial carbon flux distributions using a novel Sensor Reactor approach: II--(13)C-labeling-based metabolic flux analysis and L-lysine production. Metab. Eng. 5: 96-107 (2003).

Durmus Tekir S, Cakir T, O Ulgen K. Analysis of enzymopathies in the human red blood cells by constraint-based stoichiometric modeling approaches. Comput. Biol. Chem. 30: 327-338 (2006).

Edwards JS, Covert MW, Palsson BO. Metabolic modelling of microbes: the flux-balance approach. Environ. Microbiol. 4: 133-140 (2002).

Edwards JS, Palsson BO. Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions. BMC Bioinformatics 1: 1-10 (2000).

Edwards JS, Palsson BO. How will bioinformatics influence metabolic engineering? Biotechnol. Bioeng. 58: 162-169 (1998).

Edwards JS, Palsson BO. Systems properties of the Haemophilus influenzae Rd metabolic genotype. J. Biol. Chem. 274: 17410-17416 (1999).

Edwards JS, Palsson BO. Robustness analysis of the Escherichia coli metabolic network. Biotechnol. Prog. 16: 927-939 (2000).

Edwards JS, Ramakrishna R, Palsson BO. Characterizing the metabolic phenotype: a phenotype phase plane analysis. Biotechnol. Bioeng. 77: 27-36 (2002).

Fan W, Zhang Z, Zhang Y. Cloning and molecular characterization of fructose-1,6-bisphosphate aldolase gene regulated by high-salinity and drought in Sesuvium portulacastrum. Plant Cell Rep. 28: 975-984 (2009).

Gambhir A, Korke R, Lee J, Fu PC, Europa A, Hu WS. Analysis of cellular metabolism of hybridoma cells at distinct physiological states. J. Biosci. Bioeng. 95: 317-327 (2003).

Gast DA, Wasserfallen A, Pfister P, Ragettli S, Leisinger T. Characterization of Methanobacterium thermoautotrophicum Marburg mutants defective in regulation of L-tryptophan biosynthesis. J. Bacteriol. 179: 3664-3669 (1997).

Ghim CM, Goh KI, Kahng B. Lethality and synthetic lethality in the genome-wide metabolic network of Escherichia coli. J. Theor. Biol. 237: 401-411 (2005).

Gianchandani EP, Oberhardt MA, Burgard AP, Maranas CD, Papin JA. Predicting biological system objectives de novo from internal state measurements. BMC Bioinformatics 9: 43 (2008).

Gille C, Hoffmann S, Holzhutter HG. Combining bioinformatics resources for the structural modelling of eukaryotic metabolic networks. Genome Inform. Ser. Workshop Genome Inform. 16: 223-232 (2005).

Grafahrend-Belau E, Schreiber F, Koschutzki D, Junker BH. Flux balance analysis of barley seeds: a computational approach to study systemic properties of central metabolism. Plant Physiol. 149: 585-598 (2009).

Granstrom T, Aristidou AA, Leisola M. Metabolic flux analysis of Candida tropicalis growing on xylose in an oxygen-limited chemostat. Metab. Eng. 4: 248-256 (2002).

Grotkjaer T, Christakopoulos P, Nielsen J, Olsson L. Comparative metabolic network analysis of two xylose fermenting recombinant Saccharomyces cerevisiae strains. Metab. Eng. 7: 437-444 (2005).

Heino J, Tunyan K, Calvetti D, Somersalo E. Bayesian flux balance analysis applied to a skeletal muscle metabolic model. J. Theor. Biol. 248: 91-110 (2007).

Heinzle E, Matsuda F, Miyagawa H, Wakasa K, Nishioka T. Estimation of metabolic fluxes, expression levels and metabolite dynamics of a secondary metabolic pathway in potato using label pulse-feeding experiments combined with kinetic network modelling and simulation. Plant J. 50: 176-187 (2007).

Heuett WJ, Beard DA, Qian H. Linear analysis near a steady-state of biochemical networks: control analysis, correlation metrics and circuit theory. BMC Syst. Biol. 2: 44 (2008).

Hjersted JL, Henson MA, Mahadevan R. Genome-scale analysis of Saccharomyces cerevisiae metabolism and ethanol production in fed-batch culture. Biotechnol. Bioeng. 97: 1190-1204 (2007).

Holms H. Flux analysis and control of the central metabolic pathways in Escherichia coli. FEMS Microbiol. Rev. 19: 85-116 (1996).

Hoon Yang T, Wittmann C, Heinzle E. Respirometric (13)C flux analysis. Part II: in vivo flux estimation of lysine-producing Corynebacterium glutamicum. Metab. Eng. 8: 432-446 (2006).

Jin YS, Jeffries TW. Stoichiometric network constraints on xylose metabolism by recombinant Saccharomyces cerevisiae. Metab. Eng. 6: 229-238 (2004).

Joyce AR, Palsson BO. Predicting gene essentiality using genome-scale in silico models. Methods Mol. Biol. 416: 433-457 (2008).

Kauffman KJ, Prakash P, Edwards JS. Advances in flux balance analysis. Curr. Opin. Biotechnol. 14: 491-496 (2003).

Kelleher JK. Flux estimation using isotopic tracers: common ground for metabolic physiology and metabolic engineering. Metab. Eng. 3: 100-110 (2001).

Khannapho C, Zhao H, Bonde BK, Kierzek AM, Avignone-Rossa CA, Bushell ME. Selection of objective function in genome scale flux balance analysis for process feed development in antibiotic production. Metab. Eng. 10: 227-233 (2008).

Kim JI, Varner JD, Ramkrishna D. A hybrid model of anaerobic E. coli GJT001: combination of elementary flux modes and cybernetic variables. Biotechnol. Prog. 24: 993-1006 (2008).

Kinoshita A, Nakayama Y, Tomita M. Towards simulation of whole metabolic pathways in human erythrocyte. Genome Informatics 12: 312-313 (2001).

Kleijn RJ, van Winden WA, van Gulik WM, Heijnen JJ. Revisiting the 13C-label distribution of the non-oxidative branch of the pentose phosphate pathway based upon kinetic and genetic evidence. FEBS J. 272: 4970-4982 (2005).

Kotrebai M, Tyson JF, Block E, Uden PC. High-performance liquid chromatography of selenium compounds utilizing perfluorinated carboxylic acid ion-pairing agents and inductively coupled plasma and electrospray ionization mass spectrometric detection. J. Chromatogr. A. 866: 51-63 (2000).

Kumar S, Punekar NS, SatyaNarayan V, Venkatesh KV. Metabolic fate of glutamate and evaluation of flux through the 4-aminobutyrate (GABA) shunt in Aspergillus niger. Biotechnol. Bioeng. 67: 575-584 (2000).

Lai CT, Katul G, Butnor J, Siqueira M, Ellsworth D, Maier C, Johnsen K, Mckeand S, Oren R. Modelling the limits on the response of net carbon exchange to fertilization in a south-eastern pine forest. Plant Cell Environ. 25: 1095-1119 (2002).

Lee DY, Fan LT, Park S, Lee SY, Shafie S, Bertok B, Friedler F. Complementary identification of multiple flux distributions and multiple metabolic pathways. Metab. Eng. 7: 182-200 (2005).

Lee J, Yun H, Feist AM, Palsson BO, Lee SY. Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network. Appl. Microbiol. Biotechnol. 80: 849-862 (2008).

Lee K, Berthiaume F, Stephanopoulos GN, Yarmush ML. Metabolic flux analysis: a powerful tool for monitoring tissue function. Tissue Eng. 5: 347-368 (1999).

Lee K, Berthiaume F, Stephanopoulos GN, Yarmush ML. Profiling of dynamic changes in hypermetabolic livers. Biotechnol. Bioeng. 83: 400-415 (2003).

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Luo RY, Liao S, Tao GY, Li YY, Zeng S, Li YX, Luo Q. Dynamic analysis of optimality in myocardial energy metabolism under normal and ischemic conditions. Mol. Syst. Biol. 2: 2006.0031 (2006).

Mahadevan R, Edwards JS, Doyle FJ 3rd. Dynamic flux balance analysis of diauxic growth in Escherichia coli. Biophys. J. 83: 1331-1340 (2002).

Min Lee J, Gianchandani EP, Eddy JA, Papin JA. Dynamic analysis of integrated signaling, metabolic, and regulatory networks. PLoS Comput. Biol. 4: e1000086 (2008).

Morgan JA, Rhodes D. Mathematical modeling of plant metabolic pathways. Metab. Eng. 4: 80-89 (2002).

Nissen TL, Schulze U, Nielsen J, Villadsen J. Flux distributions in anaerobic, glucose-limited continuous cultures of Saccharomyces cerevisiae. Microbiology 143: 203-218 (1997).

Nolan RP, Fenley AP, Lee K. Identification of distributed metabolic objectives in the hypermetabolic liver by flux and energy balance analysis. Metab. Eng. 8: 30-45 (2006).

Nookaew I, Jewett MC, Meechai A, Thammarongtham C, Laoteng K, Cheevadhanarak S, Nielsen J, Bhumiratana S. The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism. BMC Syst. Biol. 2: 71 (2008).

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Oliveira AP, Nielsen J, Forster J. Modeling Lactococcus lactis using a genome-scale flux model. BMC Microbiol. 5: 39 (2005).

Oliver SG. From genomes to systems: the path with yeast. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 361: 477-482 (2006).

Pal C, Papp B, Lercher MJ. Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat. Genet. 37: 1372-1375 (2005).

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Number of references = 131

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David Rhodes
Department of Horticulture & Landscape Architecture
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Last Update: 10/01/09