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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, glycolysis

Agrawal GK, Hajduch M, Graham K, Thelen JJ. In-depth investigation of soybean seed-filling proteome and comparison with a parallel study of rapeseed. Plant Physiol. 148: 504-518 (2008).

Ainscow EK, Brand MD. Top-down control analysis of ATP turnover, glycolysis and oxidative phosphorylation in rat hepatocytes. Eur. J. Biochem. 263: 671-685 (1999).

Albrecht G, Mustroph A. Localization of sucrose synthase in wheat roots: increased in situ activity of sucrose synthase correlates with cell wall thickening by cellulose deposition under hypoxia. Planta 217: 252-260 (2003).

Albrecht G, Mustroph A, Fox TC. Sugar and fructan accumulation during metabolic adjustment between respiration and fermentation under low oxygen conditions in wheat roots. Physiol. Plant. 120: 93-105 (2004).

Alonso AP, Raymond P, Rolin D, Dieuaide-Noubhani M. Substrate cycles in the central metabolism of maize root tips under hypoxia. Phytochemistry 68: 2222-2231 (2007).

Anderson LE, Carol AA. Enzyme co-localization in the pea leaf cytosol: 3-P-glycerate kinase, glyceraldehyde-3-P dehydrogenase, triose-P isomerase and aldolase. Plant Sci. 169: 620-628 (2005).

Anderson LE, Goldhaber-Gordon IM, Li D, Tang XY, Xiang M, Prakash N. Enzyme-enzyme interaction in the chloroplast: glyceraldehyde-3-phosphate dehydrogenase, triose phosphate isomerase and aldolase. Planta 196: 245-255 (1995).

Andre C, Froehlich JE, Moll MR, Benning C. A heteromeric plastidic pyruvate kinase complex involved in seed oil biosynthesis in Arabidopsis. Plant Cell 19: 2006-2022 (2007).

Andrews DL, Cobb BG, Johnson JR, Drew MC. Hypoxic and anoxic induction of alcohol dehydrogenase in roots and shoots of seedlings of Zea mays. ADH transcripts and enzyme activity. Plant Physiol. 101: 407-414 (1993).

Antoniewicz MR, Kraynie DF, Laffend LA, González-Lergier J, Kelleher JK, Stephanopoulos G. Metabolic flux analysis in a nonstationary system: fed-batch fermentation of a high yielding strain of E. coli producing 1,3-propanediol. Metab. Eng. 9: 277-292 (2007).

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).

Armengaud P, Sulpice R, Miller AJ, Stitt M, Amtmann A, Gibon Y. Multilevel analysis of primary metabolism provides new insights into the role of potassium nutrition for glycolysis and nitrogen assimilation in Arabidopsis roots. Plant Physiol. 150: 772-785 (2009).

Bago B, Pfeffer PE, Douds Jr DD, Brouillette J, Becard G, Shachar-Hill Y. Carbon metabolism in spores of the arbuscular mycorrhizal fungus Glomus intraradices as revealed by nuclear magnetic resonance spectroscopy. Plant Physiol. 121: 263-272 (1999).

Bakker BM, Michels PAM, Opperdoes FR, Westerhoff HV. Glycolysis in bloodstream form Trypanosoma brucei can be understood in terms of the kinetics of the glycolytic enzymes. J. Biol. Chem. 272: 3207-3215 (1997).

Bakker BM, Westerhoff HV, Opperdoes FR, Michels PA. Metabolic control analysis of glycolysis in trypanosomes as an approach to improve selectivity and effectiveness of drugs. Mol. Biochem. Parasitol. 106: 1-10 (2000).

Bali M, Thomas SR. A modelling study of feedforward activation in human erythrocyte glycolysis. C. R. Acad. Sci. III 324: 185-199 (2001).

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).

Baud S, Mendoza MS, To A, Harscoet E, Lepiniec L, Dubreucq B. WRINKLED1 specifies the regulatory action of LEAFY COTYLEDON2 towards fatty acid metabolism during seed maturation in Arabidopsis. Plant J. 50: 825-838 (2007).

Baxter CJ, Redestig H, Schauer N, Repsilber D, Patil KR, Nielsen J, Selbig J, Liu J, Fernie AR, Sweetlove LJ. The metabolic response of heterotrophic Arabidopsis cells to oxidative stress. Plant Physiol. 143: 312-325 (2007).

Becker J, Klopprogge C, Zelder O, Heinzle E, Wittmann C. Amplified expression of fructose 1,6-bisphosphatase in Corynebacterium glutamicum increases in vivo flux through the pentose phosphate pathway and lysine production on different carbon sources. Appl. Environ. Microbiol. 71: 8587-8596 (2005).

Bernal V, Carinhas N, Yokomizo AY, Carrondo MJ, Alves PM. Cell density effect in the baculovirus-insect cells system: a quantitative analysis of energetic metabolism. Biotechnol. Bioeng. 104: 162-180 (2009).

Betts GF, Srivastava DK. The rationalization of high enzyme concentration in metabolic pathways such as glycolysis. J. Theor. Biol. 151: 155-167 (1991).

Biemelt S, Hajirezaei MR, Melzer M, Albrecht G, Sonnewald U. Sucrose synthase activity does not restrict glycolysis in roots of transgenic potato plants under hypoxic conditions. Planta 210: 41-49 (1999).

Blume A, Fitzen M, Benie AJ, Peters T. Specificity of ligand binding to yeast hexokinase PII studied by STD-NMR. Carbohydr. Res. 344: 1567-1574 (2009).

Boles E, Gohlmann HW, Zimmermann FK. Cloning of a second gene encoding 5-phosphofructo-2-kinase in yeast, and characterization of mutant strains without fructose-2,6-bisphosphate. Mol. Microbiol. 20: 65-76 (1996).

Bolten CJ, Heinzle E, Müller R, Wittmann C. Investigation of the central carbon metabolism of Sorangium cellulosum: metabolic network reconstruction and quantification of pathway fluxes. J. Microbiol. Biotechnol. 19: 23-36 (2009).

Bonarius HP, Ozemre A, Timmerarends B, Skrabal P, Tramper J, Schmid G, Heinzle E. Metabolic-flux analysis of continuously cultured hybridoma cells using (13)CO(2) mass spectrometry in combination with (13)C-lactate nuclear magnetic resonance spectroscopy and metabolite balancing. Biotechnol. Bioeng. 74: 528-538 (2001).

Borodina I, Siebring J, Zhang J, Smith CP, van Keulen G, Dijkhuizen L, Nielsen J. Antibiotic overproduction in Streptomyces coelicolor A3(2) mediated by phosphofructokinase deletion. J. Biol. Chem. 283: 25186-25199 (2008).

Boulanger Y, Legault P, Tejedor A, Vinay P, Theriault Y. Biochemical characterization and osmolytes in papillary collecting ducts from pig and dog kidneys. Can. J. Physiol. Pharmacol. 66: 1282-1290 (1988).

Brouquisse R, Rolin D, Cortes S, Gaudillere M, Evrard A, Roby C. A metabolic study of the regulation of proteolysis by sugars in maize root tips: effects of glycerol and dihydroxyacetone. Planta 225: 693-709 (2007).

Buchinger S, Strosser J, Rehm N, Hanssler E, Hans S, Bathe B, Schomburg D, Kramer R, Burkovski A. A combination of metabolome and transcriptome analyses reveals new targets of the Corynebacterium glutamicum nitrogen regulator AmtR. J. Biotechnol. 140: 68-74 (2009).

Cabrera ME, Saidel GM, Kalhan SC. Role of O2 in regulation of lactate dynamics during hypoxia: mathematical model and analysis. Ann. Biomed. Eng. 26: 1-27 (1998).

Cabrera ME, Saidel GM, Kalhan SC. Lactate metabolism during exercise: analysis by an integrative systems model. Am. J. Physiol. 277: R1522-R1536 (1999).

Calik P, Akbay A. Mass flux balance-based model and metabolic flux analysis for collagen synthesis in the fibrogenesis process of human liver. Med. Hypotheses 55: 5-14 (2000).

Canelas AB, van Gulik WM, Heijnen JJ. Determination of the cytosolic free NAD/NADH ratio in Saccharomyces cerevisiae under steady-state and highly dynamic conditions. Biotechnol. Bioeng. 100: 734-743 (2008).

Casu RE, Grof CP, Rae AL, McIntyre CL, Dimmock CM, Manners JM. Identification of a novel sugar transporter homologue strongly expressed in maturing stem vascular tissues of sugarcane by expressed sequence tag and microarray analysis. Plant Mol. Biol. 52: 371-386 (2003).

Causse M, Duffe P, Gomez MC, Buret M, Damidaux R, Zamir D, Gur A, Chevalier C, Lemaire-Chamley M, Rothan C. A genetic map of candidate genes and QTLs involved in tomato fruit size and composition. J. Exp. Bot. 55: 1671-1685 (2004).

Centeno DC, Oliver SN, Nunes-Nesi A, Geigenberger P, Machado DN, Loureiro ME, Silva MA, Fernie AR. Metabolic regulation of pathways of carbohydrate oxidation in potato (Solanum tuberosum) tubers. Physiol. Plant. 133: 744-754 (2008).

Cernac A, Andre C, Hoffmann-Benning S, Benning C. WRI1 is required for seed germination and seedling establishment. Plant Physiol. 141: 745-757 (2006).

Cernac A, Benning C. WRINKLED1 encodes an AP2/EREB domain protein involved in the control of storage compound biosynthesis in Arabidopsis. Plant J. 40: 575-585 (2004).

Chan C, Berthiaume F, Lee K, Yarmush ML. Metabolic flux analysis of cultured hepatocytes exposed to plasma. Biotechnol. Bioeng. 81: 33-49 (2003).

Chase JR, Rothman DL, Shulman RG. Flux control in the rat gastrocnemius glycogen synthesis pathway by in vivo 13C/31P NMR spectroscopy. Am. J. Physiol. Endocrinol. Metab. 280: E598-E607 (2001).

Chassagnole C, Noisommit-Rizzi N, Schmid JW, Mauch K, Reuss M. Dynamic modeling of the central carbon metabolism of Escherichia coli. Biotechnol. Bioeng. 79: 53-73 (2002).

Chatham JC, Forder JR, Glickson JD, Chance EM. Calculation of absolute metabolic flux and the elucidation of the pathways of glutamate labeling in perfused rat heart by 13C NMR spectroscopy and nonlinear least squares analysis. J. Biol. Chem. 270: 7999-8008 (1995).

Chen M, Mooney BP, Hajduch M, Joshi T, Zhou M, Xu D, Thelen JJ. System analysis of an Arabidopsis mutant altered in de novo fatty acid synthesis reveals diverse changes in seed composition and metabolism. Plant Physiol. 150: 27-41 (2009).

Chico E, Olavarria JS, Nunez de Castro I. L-Alanine as an end product of glycolysis in Saccharomyces cerevisiae growing under different hypoxic conditions. Antonie Van Leeuwenhoek 44: 193-201 (1978).

Churchill TA, Kneteman NM. Investigation of a primary requirement of organ preservation solutions: supplemental buffering agents improve hepatic energy production during cold storage. Transplantation 65: 551-559 (1998).

Clayton H, Ap Rees T. Respiratory metabolism of the bundle sheath of maize leaves. J. Plant Physiol. 139: 350-354 (1992).

Cline GW, LePine RL, Papas KK, Kibbey RG, Shulman GI. 13C-NMR isotopomer analysis of anaplerotic pathways in INS-1 cells. J. Biol. Chem. 279: 44370-44375 (2004).

Cloutier M, Perrier M, Jolicoeur M. Dynamic flux cartography of hairy roots primary metabolism. Phytochemistry 68: 2393-2404 (2007).

Cohen DM, Bergman RN. Estimation of metabolic flux from dominant rate constants in vivo: application to brain and heart. Metab. Eng. 6: 59-74 (2004).

Colebatch G, Desbrosses G, Ott T, Krusell L, Montanari O, Kloska S, Kopka J, Udvardi MK. Global changes in transcription orchestrate metabolic differentiation during symbiotic nitrogen fixation in Lotus japonicus. Plant J. 39: 487-512 (2004).

Colebatch G, Kloska S, Trevaskis B, Freund S, Altmann T, Udvardi MK. Novel aspects of symbiotic nitrogen fixation uncovered by transcript profiling with cDNA arrays. Mol. Plant Microbe Interact. 15: 411-420 (2002).

Cordwell SJ. Microbial genomes and "missing" enzymes: redefining biochemical pathways. Arch. Microbiol. 172: 269-279 (1999).

Cornish-Bowden A, Cardenas ML. Information transfer in metabolic pathways. Effects of irreversible steps in computer models. Eur. J. Biochem. 268: 6616-6624 (2001).

Cox SJ, Shalel Levanon S, Bennett GN, San KY. Genetically constrained metabolic flux analysis. Metab. Eng. 7: 445-456 (2005).

Curioni PM, Hartwig UA, Nosberger J, Schuller KA. Glycolytic flux is adjusted to nitrogenase activity in nodules of detopped and argon-treated alfalfa plants. Plant Physiol. 119: 445-454 (1999).

Cushman JC, Bohnert HJ. Crassulacean acid metabolism: molecular genetics. Annu. Rev. Plant Physiol. Plant Mol. Biol. 50: 305-332 (1999).

Cushman JC, Tillett RL, Wood JA, Branco JM, Schlauch KA. Large-scale mRNA expression profiling in the common ice plant, Mesembryanthemum crystallinum, performing C3 photosynthesis and Crassulacean acid metabolism (CAM). J. Exp. Bot. 59: 1875-1894 (2008).

Dafoe NJ, Constabel CP. Proteomic analysis of hybrid poplar xylem sap. Phytochemistry 70: 856-863 (2009).

Dandekar T, Schuster S, Snel B, Huynen M, Bork P. Pathway alignment: application to the comparative analysis of glycolytic enzymes. Biochem. J. 343: 115-124 (1999).

Dauner M, Bailey JE, Sauer U. Metabolic flux analysis with a comprehensive isotopomer model in Bacillus subtilis. Biotechnol. Bioeng. 76: 144-156 (2001).

Dauner M, Sauer U. GC-MS analysis of amino acids rapidly provides rich information for isotopomer balancing. Biotechnol. Prog. 16: 642-649 (2000).

Davies SE, Brindle KM. Effects of overexpression of phosphofructokinase on glycolysis in the yeast Saccharomyces cerevisiae. Biochemistry 31: 4729-4735 (1992).

Desvaux M. Clostridium cellulolyticum: model organism of mesophilic cellulolytic clostridia. FEMS Microbiol. Rev. 29: 741-764 (2005).

deZengotita VM, Abston LR, Schmelzer AE, Shaw S, Miller WM. Selected amino acids protect hybridoma and CHO cells from elevated carbon dioxide and osmolality. Biotechnol. Bioeng. 78: 741-752 (2002).

Dian W, Jiang H, Chen Q, Liu F, Wu P. Cloning and characterization of the granule-bound starch synthase II gene in rice: gene expression is regulated by the nitrogen level, sugar and circadian rhythm. Planta 218: 261-268 (2003).

Dieuaide-Noubhani M, Alonso AP, Rolin D, Eisenreich W, Raymond P. Metabolic flux analysis: recent advances in carbon metabolism in plants. EXS 97: 213-243 (2007).

Dieuaide-Noubhani M, Canioni P, Raymond P. Sugar starvation induced changes of carbon metabolism in excised maize root tips. Plant Physiol. 115: 1505-1513 (1997).

Dieuaide-Noubhani M, Raffard G, Canioni P, Pradet A, Raymond P. Quantification of compartmented metabolic fluxes in maize root tips using isotope distribution from 13C- or 14C-labeled glucose. J. Biol. Chem. 270: 13147-13159 (1995).

Dijkema C, Kester HC, Visser J. 13C NMR studies of carbon metabolism in the hyphal fungus Aspergillus nidulans. Proc. Natl. Acad. Sci. U.S.A. 82: 14-18 (1985).

Dominguez H, Rollin C, Guyonvarch A, Guerquin-Kern JL, Cocaign-Bousquet M, Lindley ND. Carbon-flux distribution in the central metabolic pathways of Corynebacterium glutamicum during growth on fructose. Eur. J. Biochem. 254: 96-102 (1998).

Drews M, Doverskog M, Ohman L, Chapman BE, Jacobsson U, Kuchel PW, Haggstrom L. Pathways of glutamine metabolism in Spodoptera frugiperda (Sf9) insect cells: evidence for the presence of the nitrogen assimilation system, and a metabolic switch by 1H/15N NMR. J. Biotechnol. 78: 23-37 (2000).

Dupriez VJ, Rousseau GG. Glucose response elements in a gene that codes for 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase. DNA Cell Biol. 16: 1075-1085 (1997).

Durante P, Gueuning MA, Darville MI, Hue L, Rousseau GG. Apoptosis induced by growth factor withdrawal in fibroblasts overproducing fructose 2,6-bisphosphate. FEBS Lett. 448: 239-243 (1999).

Eastmond PJ, Graham IA. Trehalose metabolism: a regulatory role for trehalose-6-phosphate? Curr. Opin. Plant Biol. 6: 231-235 (2003).

Eastmond PJ, van Dijken AJ, Spielman M, Kerr A, Tissier AF, Dickinson HG, Jones JD, Smeekens SC, Graham IA. Trehalose-6-phosphate synthase 1, which catalyses the first step in trehalose synthesis, is essential for Arabidopsis embryo maturation. Plant J. 29: 225-235 (2002).

Ebenhoh O, Heinrich R. Evolutionary optimization of metabolic pathways. Theoretical reconstruction of the stoichiometry of ATP and NADH producing systems. Bull. Math. Biol. 63: 21-55 (2001).

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. Robustness analysis of the Escherichia coli metabolic network. Biotechnol. Prog. 16: 927-939 (2000).

Eisenthal R, Cornish-Bowden A. Prospects for antiparasitic drugs. The case of Trypanosoma brucei, the causative agent of African sleeping sickness. J. Biol. Chem. 273: 5500-5505 (1998).

Elbing K, Stahlberg A, Hohmann S, Gustafsson L. Transcriptional responses to glucose at different glycolytic rates in Saccharomyces cerevisiae. Eur. J. Biochem. 271: 4855-4864 (2004).

Emelyanov VV. Mitochondrial connection to the origin of the eukaryotic cell. Eur. J. Biochem. 270: 1599-1618 (2003).

Erecinska M, Nelson D, Nissim I, Daikhin Y, Yudkoff M. Cerebral alanine transport and alanine aminotransferase reaction: alanine as a source of neuronal glutamate. J. Neurochem. 62: 1953-1964 (1994).

Ettenhuber C, Radykewicz T, Kofer W, Koop HU, Bacher A, Eisenreich W. Metabolic flux analysis in complex isotopolog space. Recycling of glucose in tobacco plants. Phytochemistry 66: 323-335 (2005).

Even S, Garrigues C, Loubiere P, Lindley ND, Cocaign-Bousquet M. Pyruvate metabolism in Lactococcus lactis is dependent upon glyceraldehyde-3-phosphate dehydrogenase activity. Metab. Eng. 1: 198-205 (1999).

Even S, Lindley ND, Cocaign-Bousquet M. Molecular physiology of sugar catabolism in Lactococcus lactis IL1403. J. Bacteriol. 183: 3817-3824 (2001).

Even S, Lindley ND, Loubiere P, Cocaign-Bousquet M. Dynamic response of catabolic pathways to autoacidification in Lactococcus lactis: transcript profiling and stability in relation to metabolic and energetic constraints. Mol. Microbiol. 45: 1143-1152 (2002).

Fan TWM, Higashi RM, Frenkiel TA, Lane AN. Anaerobic nitrate and ammonium metabolism in flood-tolerant rice coleoptiles. J. Exp. Bot. 48: 1655-1666 (1997).

Farre EM, Bachmann A, Willmitzer L, Trethewey RN. Acceleration of potato tuber sprouting by the expression of a bacterial pyrophosphatase. Nat. Biotechnol. 19: 268-272 (2001).

Fell DA, Snell K. Control analysis of mammalian serine biosynthesis. Feedback inhibition on the final step. Biochem. J. 256: 97-101 (1988).

Fell DA, Wagner A. The small world of metabolism. Nat. Biotechnol. 18: 1121-1122 (2000).

Fernie AR, Carrari F, Sweetlove LJ. Respiratory metabolism: glycolysis, the TCA cycle and mitochondrial electron transport. Curr. Opin. Plant Biol. 7: 254-261 (2004).

Fernie AR, Tiessen A, Stitt M, Willmitzer L, Geigenberger P. Altered metabolic fluxes result from shifts in metabolite levels in sucrose phosphorylase-expressing potato tubers. Plant Cell Environ. 25: 1219-1232 (2002).

Fischer E, Sauer U. Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS. Eur. J. Biochem. 270: 880-891 (2003).

Flores CL, Rodriguez C, Petit T, Gancedo C. Carbohydrate and energy-yielding metabolism in non-conventional yeasts. FEMS Microbiol. Rev. 24: 507-529 (2000).

Forbes NS, Meadows AL, Clark DS, Blanch HW. Estradiol stimulates the biosynthetic pathways of breast cancer cells: detection by metabolic flux analysis. Metab. Eng. 8: 639-652 (2006).

Forsthoefel NR, Cushman MA, Cushman JC. Posttranscriptional and posttranslational control of enolase expression in the facultative Crassulacean acid metabolism plant Mesembryanthemum crystallinum L. Plant Physiol. 108: 1185-1195 (1995).

Fox TC, Green BJ, Kennedy RA, Rumpho ME. Changes in hexokinase activity in Echinochloa phyllopogon and Echinochloa crus-pavonis in response to abiotic stress. Plant Physiol. 118: 1403-1409 (1998).

Frey AD, Fiaux J, Szyperski T, Wuthrich K, Bailey JE, Kallio PT. Dissection of central carbon metabolism of hemoglobin-expressing Escherichia coli by (13)C nuclear magnetic resonance flux distribution analysis in microaerobic bioprocesses. Appl. Environ. Microbiol. 67: 680-687 (2001).

Frick O, Wittmann C. Characterization of the metabolic shift between oxidative and fermentative growth in Saccharomyces cerevisiae by comparative 13C flux analysis. Microb. Cell. Fact. 4: 30 (2005).

Galperin MY, Koonin EV. Functional genomics and enzyme evolution. Homologous and analogous enzymes encoded in microbial genomes. Genetica 106: 159-170 (1999).

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).

Garrigues C, Goupil-Feuillerat N, Cocaign-Bousquet M, Renault P, Lindley ND, Loubiere P. Glucose metabolism and regulation of glycolysis in Lactococcus lactis strains with decreased lactate dehydrogenase activity. Metab. Eng. 3: 211-217 (2001).

Garrigues C, Mercade M, Cocaign-Bousquet M, Lindley ND, Loubiere P. Regulation of pyruvate metabolism in Lactococcus lactis depends on the imbalance between catabolism and anabolism. Biotechnol. Bioeng. 74: 108-115 (2001).

Gayen K, Venkatesh KV. Analysis of optimal phenotypic space using elementary modes as applied to Corynebacterium glutamicum. BMC Bioinformatics 7: 445 (2006).

Geigenberger P, Fernie AR, Gibon Y, Christ M, Stitt M. Metabolic activity decreases as an adaptive response to low internal oxygen in growing potato tubers. Biol. Chem. 381: 723-740 (2000).

Gibon Y, Pyl ET, Sulpice R, Lunn JE, Höhne M, Gunther M, Stitt M. Adjustment of growth, starch turnover, protein content and central metabolism to a decrease of the carbon supply when Arabidopsis is grown in very short photoperiods. Plant Cell Environ. 32: 859-874 (2009).

Giege P, Heazlewood JL, Roessner-Tunali U, Millar AH, Fernie AR, Leaver CJ, Sweetlove LJ. Enzymes of glycolysis are functionally associated with the mitochondrion in Arabidopsis cells. Plant Cell 15: 2140-2151 (2003).

Giersch C. Determining elasticities from multiple measurements of flux rates and metabolite concentrations. Application of the multiple modulation method to a reconstituted pathway. Eur. J. Biochem. 227: 194-201 (1995).

Givan CV. Evolving concepts in plant glycolysis: two centuries of progress. Biol. Rev. Camb. Phil. Soc. 74: 277-309 (1999).

Glass-Marmor L, Beitner R. Taxol (paclitaxel) induces a detachment of phosphofructokinase from cytoskeleton of melanoma cells and decreases the levels of glucose 1,6-bisphosphate, fructose 1,6-bisphosphate and ATP. Eur. J. Pharmacol. 370: 195-199 (1999).

Glawischnig E, Gierl A, Tomas A, Bacher A, Eisenreich W. Starch biosynthesis and intermediary metabolism in maize kernels. Quantitative analysis of metabolite flux by nuclear magnetic resonance. Plant Physiol. 130: 1717-1727 (2002).

Goes da Silva F, Iandolino A, Al-Kayal F, Bohlmann MC, Cushman MA, Lim H, Ergul A, Figueroa R, Kabuloglu EK, Osborne C, Rowe J, Tattersall E, Leslie A, Xu J, Baek J, Cramer GR, Cushman JC, Cook DR. Characterizing the grape transcriptome. Analysis of expressed sequence tags from multiple Vitis species and development of a compendium of gene expression during berry development. Plant Physiol. 139: 574-597 (2005).

Gomes RA, Miranda HV, Silva MS, Graca G, Coelho AV, Ferreira AE, Cordeiro C, Freire AP. Yeast protein glycation in vivo by methylglyoxal. FEBS J. 273: 5273-5287 (2006).

Goncalves P, Planta RJ. Starting up yeast glycolysis. Trends Microbiol. 6: 314-319 (1998).

Guedon E, Desvaux M, Petitdemange H. Kinetic analysis of Clostridium cellulolyticum carbohydrate metabolism: J. Bacteriol. 182: 2010-2017 (2000).

Gutierrez RA, Gifford ML, Poultney C, Wang R, Shasha DE, Coruzzi GM, Crawford NM. Insights into the genomic nitrate response using genetics and the Sungear Software System. J. Exp. Bot. 58: 2359-2367 (2007).

Hajirezaei MR, Takahata Y, Trethewey RN, Willmitzer L, Sonnewald U. Impact of elevated cytosolic and apoplastic invertase activity on carbon metabolism during potato tuber development. J. Exp. Bot. 51: 439-445 (2000).

Hampp R, Hoffmann E, Schonherr K, Johann P, De Filippis L. Fusion and metabolism of plant cells as affected by microgravity. Planta 203 Suppl.: 42S-53S (1997).

Hancock J, Desikan R, Harrison J, Bright J, Hooley R, Neill S. Doing the unexpected: proteins involved in hydrogen peroxide perception. J. Exp. Bot. 57: 1711-1718 (2006).

Hara KY, Shimodate N, Ito M, Baba T, Mori H, Mori H. Systematic genome-wide scanning for genes involved in ATP generation in Escherichia coli. Metab. Eng. 11: 1-7 (2009).

Harndahl L, Schmoll D, Herling AW, Agius L. The role of glucose 6-phosphate in mediating the effects of glucokinase overexpression on hepatic glucose metabolism. FEBS J. 273: 336-346 (2006).

Hartwell J. The co-ordination of central plant metabolism by the circadian clock. Biochem. Soc. Trans. 33: 945-948 (2005).

Hasemann CA, Istvan ES, Uyeda K, Deisenhofer J. The crystal structure of the bifunctional enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase reveals distinct domain homologies. Structure 4: 1017-1029 (1996).

Heinrich R. Mathematical models of metabolic systems: general principles and control of glycolysis and membrane transport in erythrocytes. Biomed. Biochim. Acta 44: 913-927 (1985).

Heinrich R, Rapoport TA. Mathematical analysis of multienzyme systems. II. Steady state and transient control. Biosystems 7: 130-136 (1975).

Heinrich R, Reder C. Metabolic control analysis of relaxation processes. J. Theor. Biol. 151: 343-350 (1991).

Heinrich R, Schuster S. The modelling of metabolic systems. Structure, control and optimality. Biosystems 47: 61-77 (1998).

Hers HG, Hue L. Gluconeogenesis and related aspects of glycolysis. Annu. Rev. Biochem. 52: 617-653 (1983).

Hochuli M, Szyperski T, Wuthrich K. Deuterium isotope effects on the central carbon metabolism of Escherichia coli cells grown on a D2O-containing minimal medium. J. Biomol. NMR 17: 33-42 (2000).

Hofer T, Heinrich R. A second-order approach to metabolic control analysis. J. Theor. Biol. 164: 85-102 (1993).

Holtgrawe D, Scholz A, Altmann B, Scheibe R. Cytoskeleton-associated, carbohydrate-metabolizing enzymes in maize identified by yeast two-hybrid screening. Physiol. Plant. 125: 141-156 (2005).

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).

Hourton-Cabassa C, Ambard-Bretteville F, Moreau F, Davy de Virville J, Remy R, Francs-Small CC. Stress induction of mitochondrial formate dehydrogenase in potato leaves. Plant Physiol. 116: 627-635 (1998).

Hua Q, Joyce AR, Fong SS, Palsson BO. Metabolic analysis of adaptive evolution for in silico designed lactate-producing strains. Biotechnol. Bioeng. 95: 992-1002 (2006).

Igamberdiev AU, Hill RD. Plant mitochondrial function during anaerobiosis. Ann. Bot. (Lond.) 103: 259-268 (2009).

Jamshidi N, Palsson BO. Top-down analysis of temporal hierarchy in biochemical reaction networks. PLoS Comput. Biol. 4: e1000177 (2008).

Jannaschk D, Burgos M, Centerlles JJ, Ovadi J, Cascante M. Application of metabolic control analysis to the study of toxic effects of copper in muscle glycolysis. FEBS Lett. 445: 144-148 (1999).

Joosen R, Cordewener J, Supena ED, Vorst O, Lammers M, Maliepaard C, Zeilmaker T, Miki B, America T, Custers J, Boutilier K. Combined transcriptome and proteome analysis identifies pathways and markers associated with the establishment of rapeseed microspore-derived embryo development. Plant Physiol. 144: 155-172 (2007).

Jung Y, Park J, Lee Y. Metabolic engineering of Alcaligenes eutrophus through the transformation of cloned phbCAB genes for the investigation of the regulatory mechanism of polyhydroxyalkanoate biosynthesis. Enzyme Microb. Technol. 26: 201-208 (2000).

Junker BH, Wuttke R, Tiessen A, Geigenberger P, Sonnewald U, Willmitzer L, Fernie AR. Temporally regulated expression of a yeast invertase in potato tubers allows dissection of the complex metabolic phenotype obtained following its constitutive expression. Plant Mol. Biol. 56: 91-110 (2004).

Karni L, Aloni B. Fructokinase and hexokinase from pollen grains of bell pepper (Capsicum annuum L.): possible role in pollen germination under conditions of high temperature and CO2 enrichment. Ann. Bot. (Lond.) 90: 607-612 (2002).

Katagiri M, Nakamura M. Reappraisal of the 20th-century version of amino acid metabolism. Biochem. Biophys. Res. Commun. 312: 205-208 (2003).

Kim C, Lemke C, Paterson AH. Functional dissection of drought-responsive gene expression patterns in Cynodon dactylon L. Plant Mol. Biol. 70: 1-16 (2009).

Kim JK, Bamba T, Harada K, Fukusaki E, Kobayashi A. Time-course metabolic profiling in Arabidopsis thaliana cell cultures after salt stress treatment. J. Exp. Bot. 58: 415-424 (2007).

Kinney AJ. Manipulating flux through plant metabolic pathways. Curr. Opin. Plant Biol. 1: 173-178 (1998).

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, Ras C, van Gulik WM, Schipper D, Heijnen JJ. 13C-Labeled gluconate tracing as a direct and accurate method for determining the pentose phosphate pathway split ratio in Penicillium chrysogenum. Appl. Environ. Microbiol. 72: 4743-4754 (2006).

Koebmann B, Solem C, Jensen PR. Control analysis as a tool to understand the formation of the las operon in Lactococcus lactis. FEBS J. 272: 2292-2303 (2005).

Koebmann B, Solem C, Jensen PR. Control analysis of the importance of phosphoglycerate enolase for metabolic fluxes in Lactococcus lactis subsp. lactis IL1403. Syst. Biol. (Stevenage) 153: 346-349 (2006).

Koebmann BJ, Andersen HW, Solem C, Jensen PR. Experimental determination of control of glycolysis in Lactococcus lactis. Antonie Van Leeuwenhoek 82: 237-248 (2002).

Kreuzwieser J, Hauberg J, Howell KA, Carroll A, Rennenberg H, Millar AH, Whelan J. Differential response of gray poplar leaves and roots underpins stress adaptation during hypoxia. Plant Physiol. 149: 461-473 (2009).

Kromer JO, Sorgenfrei O, Klopprogge K, Heinzle E, Wittmann C. In-depth profiling of lysine-producing Corynebacterium glutamicum by combined analysis of the transcriptome, metabolome, and fluxome. J. Bacteriol. 186: 1769-1784 (2004).

Kuchel PW, Philp DJ. Isotopomer subspaces as indicators of metabolic-pathway structure. J. Theor. Biol. 252: 391-401 (2008).

Kuznetsova E, Proudfoot M, Gonzalez CF, Brown G, Omelchenko MV, Borozan I, Carmel L, Wolf YI, Mori H, Savchenko AV, Arrowsmith CH, Koonin EV, Edwards AM, Yakunin AF. Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family. J. Biol. Chem. 281: 36149-36161 (2006).

L'Her E, Sebert P. Glycolysis in the human muscle: a new approach. J. Lab. Clin. Med. 136: 281-286 (2000).

LeClere S, Rampey RA, Bartel B. IAR4, a gene required for auxin conjugate sensitivity in Arabidopsis, encodes a pyruvate dehydrogenase E1alpha homolog. Plant Physiol. 135: 989-999 (2004).

Lee JM, Williams ME, Tingey SV, Rafalski JA. DNA array profiling of gene expression changes during maize embryo development. Funct. Integr. Genomics 2: 13-27 (2002).

Lee YY, Wong KT, Nissom PM, Wong DC, Yap MG. Transcriptional profiling of batch and fed-batch protein-free 293-HEK cultures. Metab. Eng. 9: 52-67 (2007).

Leppanen VM, Merckel MC, Ollis DL, Wong KK, Kozarich JW, Goldman A. Pyruvate formate lyase is structurally homologous to type I ribonucleotide reductase. Structure Fold. Des. 7: 733-744 (1999).

Li J, Wu XD, Hao ST, Wang XJ, Ling HQ. Proteomic response to iron deficiency in tomato root. Proteomics 8: 2299-2311 (2008).

Li M, Ho PY, Yao S, Shimizu K. Effect of lpdA gene knockout on the metabolism in Escherichia coli based on enzyme activities, intracellular metabolite concentrations and metabolic flux analysis by (13)C-labeling experiments. J. Biotechnol. 122: 254-266 (2006).

Liang Y, Chen H, Tang M, Shen S. Proteome analysis of an ectomycorrhizal fungus Boletus edulis under salt shock. Mycol. Res. 111: 939-946 (2007).

Liao JC, Lightfoot EN Jr. Extending the quasi-steady state concept to analysis of metabolic networks. J. Theor. Biol. 126: 253-273 (1987).

Liebermeister W. Response to temporal parameter fluctuations in biochemical networks. J. Theor. Biol. 234: 423-438 (2005).

Limami AM, Glevarec G, Ricoult C, Cliquet JB, Planchet E. Concerted modulation of alanine and glutamate metabolism in young Medicago truncatula seedlings under hypoxic stress. J. Exp. Bot. 59: 2325-2335 (2008).

Lin KC, Bushnell WR, Smith AG, Szabo LJ. Temporal accumulation patterns of defence response gene transcripts in relation to resistant reactions in oat inoculated with Puccinia graminis. Physiol. Mol. Plant Pathol. 52: 95-114 (1998).

Lin SS, Manchester JK, Gordon JI. Enhanced gluconeogenesis and increased energy storage as hallmarks of aging in Saccharomyces cerevisiae. J. Biol. Chem. 276: 36000-36007 (2001).

Lin Y, Ulanov AV, Lozovaya V, Widholm J, Zhang G, Guo J, Goodman HM. Genetic and transgenic perturbations of carbon reserve production in Arabidopsis seeds reveal metabolic interactions of biochemical pathways. Planta 225: 153-164 (2006).

Liu F, Vantoai T, Moy LP, Bock G, Linford LD, Quackenbush J. Global transcription profiling reveals comprehensive insights into hypoxic response in Arabidopsis. Plant Physiol. 137: 1115-1129 (2005).

Loreto F, Ciccioli P, Brancaleoni E, Frattoni M, Delfine S. Incomplete 13C labelling of a-pinene content of Quercus ilex leaves and appearance of unlabelled C in a-pinene emission in the dark. Plant Cell Environ. 23: 229-234 (2000).

Lu M, Zhou L, Stanley WC, Cabrera ME, Saidel GM, Yu X. Role of the malate-aspartate shuttle on the metabolic response to myocardial ischemia. J. Theor. Biol. 254: 466-475 (2008).

Lutz PL, Nilsson GE. Contrasting strategies for anoxic brain survival--glycolysis up or down. J. Exp. Biol. 200: 411-419 (1997).

Lytovchenko A, Sweetlove L, Pauly M, Fernie AR. The influence of cytosolic phosphoglucomutase on photosynthetic carbohydrate metabolism. Planta 215: 1013-1021 (2002).

Maaheimo H, Fiaux J, Cakar ZP, Bailey JE, Sauer U, Szyperski T. Central carbon metabolism of Saccharomyces cerevisiae explored by biosynthetic fractional C-13 labeling of common amino acids. Eur. J. Biochem. 268: 2464-2479 (2001).

Maier K, Hofmann U, Reuss M, Mauch K. Identification of metabolic fluxes in hepatic cells from transient 13C-labeling experiments: Part II. Flux estimation. Biotechnol. Bioeng. 100: 355-370 (2008).

Mancuso A, Sharfstein ST, Tucker SN, Clark DS, Blanch HW. Examination of primary metabolic pathways in a murine hybridoma with C-13 nuclear magnetic resonance spectroscopy. Biotechnol. Bioeng. 44: 563-585 (1994).

Manjunath S, Lee CH, VanWinkle P, Bailey-Serres J. Molecular and biochemical characterization of cytosolic phosphoglucomutase in maize. Expression during development and in response to oxygen deprivation. Plant Physiol. 117: 997-1006 (1998).

Martinez I, Zhu J, Lin H, Bennett GN, San KY. Replacing Escherichia coli NAD-dependent glyceraldehyde 3-phosphate dehydrogenase (GAPDH) with a NADP-dependent enzyme from Clostridium acetobutylicum facilitates NADPH dependent pathways. Metab. Eng. 10: 352-359 (2008).

Martinez-Rivas JM, Vega JM. Purification and characterization of NAD-isocitrate dehydrogenase from Chlamydomonas reinhardtii. Plant Physiol. 118: 249-255 (1998).

Martins AM, Cordeiro CA, Ponces Freire AM. In situ analysis of methylglyoxal metabolism in Saccharomyces cerevisiae. FEBS Lett. 499: 41-44 (2001).

Massonneau A, Langlade N, Leon S, Smutny J, Vogt E, Neumann G, Martinoia E. Metabolic changes associated with cluster root development in white lupin (Lupinus albus L.): relationship between organic acid excretion, sucrose metabolism and energy status. Planta 213: 534-542 (2001).

Matheron C, Delort AM, Gaudet G, Liptaj T, Forano E. Interactions between carbon and nitrogen metabolism in Fibrobacter succinogenes S85: a 1H and 13C nuclear magnetic resonance and enzymatic study. Appl. Environ. Microbiol. 65: 1941-1948 (1999).

Mazarei M, Lennon KA, Puthoff DP, Rodermel SR, Baum TJ. Expression of an Arabidopsis phosphoglycerate mutase homologue is localized to apical meristems, regulated by hormones, and induced by sedentary plant-parasitic nematodes. Plant Mol. Biol. 53: 513-530 (2003).

Melcher K, Rose M, Kunzler M, Braus GH, Entian KD. Molecular analysis of the yeast SER1 gene encoding 3-phosphoserine aminotransferase: regulation by general control and serine repression. Curr. Genet. 27: 501-508 (1995).

Mercade M, Cocaign-Bousquet M, Loubiere P. Glyceraldehyde-3-phosphate dehydrogenase regulation in Lactococcus lactis ssp. cremoris MG1363 or relA mutant at low pH. J. Appl. Microbiol. 100: 1364-1372 (2006).

Messana I, Misiti F, el-Sherbini S, Giardina B, Castagnola M. Quantitative determination of the main glucose metabolic fluxes in human erythrocytes by 13C- and 1H-MR spectroscopy. J. Biochem. Biophys. Methods 39: 63-84 (1999).

Meurice G, Bondon A, Deborde C, Boyaval P. Determination of metabolic fluxes during glucose catabolism in Propionibacterium freudenreichii subsp. shermanii. Meded. Rijksuniv. Gent. Fak. Landbouwkd. Toegep. Biol. Wet. 66: 219-225 (2001).

Miccheli A, Tomassini A, Puccetti C, Valerio M, Peluso G, Tuccillo F, Calvani M, Manetti C, Conti F. Metabolic profiling by 13C-NMR spectroscopy: [1,2-13C2]glucose reveals a heterogeneous metabolism in human leukemia T cells. Biochimie 88: 437-448 (2006).

Mieskes G, Kuduz J, Soling HD. Are calcium-dependent protein kinases involved in the regulation of glycolytic/gluconeogenetic enzymes? Studies with Ca2+/calmodulin-dependent protein kinase and protein kinase C. Eur. J. Biochem. 167: 383-389 (1987).

Miki R, Kadota K, Bono H, Mizuno Y, Tomaru Y, Carninci P, Itoh M, Shibata K, Kawai J, Konno H, Watanabe S, Sato K, Tokusumi Y, Kikuchi N, Ishii Y, Hamaguchi et al. Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays. Proc. Natl. Acad. Sci. U.S.A. 98: 2199-2204 (2001).

Moreno-Sanchez R, Encalada R, Marin-Hernandez A, Saavedra E. Experimental validation of metabolic pathway modeling. An illustration with glycotic segments from Entamoeba histolytica. FEBS J. 275: 3454-3469 (2008).

Mu J, Tan H, Zheng Q, Fu F, Liang Y, Zhang J, Yang X, Wang T, Chong K, Wang XJ, Zuo J. LEAFY COTYLEDON1 is a key regulator of fatty acid biosynthesis in Arabidopsis thaliana. Plant Physiol. 148: 1042-1054 (2008).

Mulquiney PJ, Bubb WA, Kuchel PW. Model of 2,3-bisphosphoglycerate metabolism in the human erythrocyte based on detailed enzyme kinetic equations in vivo kinetic characterization of 2,3-bisphosphoglycerate synthase/phosphatase using C-13 and P-31 NMR. Biochem. J. 342: 567-580 (1999).

Mulquiney PJ, Kuchel PW. Model of 2,3-bisphosphoglycerate metabolism in the human erythrocyte based on detailed enzyme kinetic equations: computer simulation and Metabolic Control Analysis. Biochem. J. 342: 597-604 (1999).

Mulquiney PJ, Kuchel PW. Model of 2,3-bisphosphoglycerate metabolism in the human erythrocyte based on detailed enzyme kinetic equations: equations and parameter refinement. Biochem. J. 342: 581-596 (1999).

Mulquiney PJ, Kuchel PW. Model of the pH-dependence of the concentrations of complexes involving metabolites, haemoglobin and magnesium ions in the human erythrocyte. Eur. J. Biochem. 245: 71-83 (1997).

Mustroph A, Boamfa EI, Laarhoven LJ, Harren FJ, Albrecht G, Grimm B. Organ-specific analysis of the anaerobic primary metabolism in rice and wheat seedlings. I: Dark ethanol production is dominated by the shoots. Planta 225: 103-114 (2006).

Mustroph A, Boamfa EI, Laarhoven LJ, Harren FJ, Pors Y, Grimm B. Organ specific analysis of the anaerobic primary metabolism in rice and wheat seedlings II: Light exposure reduces needs for fermentation and extends survival during anaerobiosis. Planta 225: 139-152 (2006).

Nadeau I, Jacob D, Perrier M, Kamen A. 293SF metabolic flux analysis during cell growth and infection with an adenoviral vector. Biotechnol. Prog. 16: 872-884 (2000).

Naito Y, Ohno H, Seno S, Oguchi Y, Sano A, Nakajima H, Tomita M. A simulation model of diabetes using E-Cell system. Genome Informatics 12: 310-311 (2001).

Nakayama Y, Matsushima R, Tomita M. Computer simulation of human erythrocyte using the E-cell system. Genome Informatics 10: 364-365 (1999).

Nasution U, van Gulik WM, Proell A, van Winden WA, Heijnen JJ. Generating short-term kinetic responses of primary metabolism of Penicillium chrysogenum through glucose perturbation in the bioscope mini reactor. Metab. Eng. 8: 395-405 (2006).

Neves AR, Ramos A, Nunes MC, Kleerebezem M, Hugenholtz J, de Vos WM, Almeida J, Santos H. In vivo nuclear magnetic resonance studies of glycolytic kinetics in Lactococcus lactis. Biotechnol. Bioeng. 64: 200-212 (1999).

Ngai SM, Way MM, Chan H, Tsui SK, Lee CY, Fung KP. In silico studies of energy metabolism of normal and diseased heart. Mol. Biol. Rep. 27: 123-128 (2000).

Nielsen TH, Stitt M. Tobacco transformants with strongly decreased expression of pyrophosphate:fructose-6-phosphate expression in the base of their young growing leaves contain much higher levels of fructose-2,6-bisphosphate but no major changes in fluxes. Planta 214: 106-116 (2001).

Nikerel IE, van Winden WA, Verheijen PJ, Heijnen JJ. Model reduction and a priori kinetic parameter identifiability analysis using metabolome time series for metabolic reaction networks with linlog kinetics. Metab. Eng. 11: 20-30 (2009).

Obiadalla-Ali H, Fernie AR, Kossmann J, Lloyd JR. Developmental analysis of carbohydrate metabolism in tomato (Lycopersicon esculentum cv. Micro-Tom) fruits. Physiol. Plant. 120: 196-204 (2004).

Oehrle NW, Sarma AD, Waters JK, Emerich DW. Proteomic analysis of soybean nodule cytosol. Phytochemistry 69: 2426-2438 (2008).

Oh IJ, Lee HW, Park CH, Lee SY, Lee J. Succinic acid production from continuous fermentation process using Mannheimia succiniciproducens LPK7. J. Microbiol. Biotechnol. 18: 908-912 (2008).

Olah J, Orosz F, Puskas LG, Hackler L Jr, Horanyi M, Polgar L, Hollan S, Ovadi J. Triosephosphate isomerase deficiency: consequences of an inherited mutation at mRNA, protein and metabolic levels. Biochem J. 392: 675-683 (2005).

Osuna D, Usadel B, Morcuende R, Gibon Y, Blasing OE, Hohne M, Gunter M, Kamlage B, Trethewey R, Scheible WR, Stitt M. Temporal responses of transcripts, enzyme activities and metabolites after adding sucrose to carbon-deprived Arabidopsis seedlings. Plant J. 49: 463-491 (2007).

Ovadi J, Srere PA. Metabolic consequences of enzyme interactions. Cell Biochem. Funct. 14: 249-258 (1996).

Panagiotou G, Andersen MR, Grotkjaer T, Regueira TB, Nielsen J, Olsson L. Studies of the production of fungal polyketides in Aspergillus nidulans by using systems biology tools. Appl. Environ. Microbiol. 75: 2212-2220 (2009).

Parsons HL, Yip JY, Vanlerberghe GC. Increased respiratory restriction during phosphate-limited growth in transgenic tobacco cells lacking alternative oxidase. Plant Physiol. 121: 1309-1320 (1999).

Pearce AK, Crimmins K, Groussac E, Hewlins MJ, Dickinson JR, Francois J, Booth IR, Brown AJ. Pyruvate kinase (Pyk1) levels influence both the rate and direction of carbon flux in yeast under fermentative conditions. Microbiology 147: 391-401 (2001).

Perez JX, Roig T, Manzano A, Dalmau M, Boada J, Ventura F, Rosa JL, Bermudez J, Bartrons R. Overexpression of fructose 2,6-bisphosphatase decreases glycolysis and delays cell cycle progression. Am. J. Physiol. Cell Physiol. 279: C1359-C1365 (2000).

Pfefferle W, Mockel B, Bathe B, Marx A. Biotechnological manufacture of lysine. Adv. Biochem. Eng. Biotechnol. 79: 59-112 (2003).

Phillips JW, Jones ME, Berry MN. Implications of the simultaneous occurrence of hepatic glycolysis from glucose and gluconeogenesis from glycerol. Eur. J. Biochem. 269: 792-797 (2002).

Plaxton WC. The organization and regulation of plant glycolysis. Annu. Rev. Plant Physiol. Plant Mol. Biol. 47: 185-214 (1996).

Poitry S, Poitry-Yamate C, Ueberfeld J, MacLeish PR, Tsacopoulos M. Mechanisms of glutamate metabolic signaling in retinal glial (Muller) cells. J. Neurosci. 20: 1809-1821 (2000).

Preiss J. ADPglucose pyrophosphorylase: basic science and applications in biotechnology. Biotechnol. Annu. Rev. 2: 259-279 (1996).

Pritchard L, Kell DB. Schemes of flux control in a model of Saccharomyces cerevisiae glycolysis. Eur. J. Biochem. 269: 3894-3904 (2002).

Puigjaner J, Rais B, Burgos M, Comin B, Ovadi J, Cascante M. Comparison of control analysis data using different approaches: modelling and experiments with muscle extract. FEBS Lett. 418: 47-52 (1997).

Rapoport TA, Heinrich R. Mathematical analysis of multienzyme systems. I. Modelling of the glycolysis of human erythrocytes. Biosystems 7: 120-129 (1975).

Rapoport TA, Heinrich R, Rapoport SM. The regulatory principles of glycolysis in erythrocytes in vivo and in vitro. A minimal comprehensive model describing steady states, quasi-steady states and time-dependent processes. Biochem. J. 154: 449-469 (1976).

Reeds PJ, Berthold HK, Boza JJ, Burrin DG, Jahoor F, Jaksic T, Klein PD, Keshen T, Miller R, Stoll B, Wykes LJ. Integration of amino acid and carbon intermediary metabolism: studies with uniformly labeled tracers and mass isotopomer analysis. Eur. J. Pediatr. 156: S50-S58 (1997).

Reggiani R, Bertani A. Anaerobic amino acid metabolism. Russ. J. Plant Physiol. 50: 733-736 (2003).

Riccardi F, Gazeau P, de Vienne D, Zivy M. Protein changes in response to progressive water deficit in maize. Quantitative variation and polypeptide identification. Plant Physiol. 117: 1253-1263 (1998).

Ricci JCD. ADP modulates the dynamic behavior of the glycolytic pathway of Escherichia coli. Biochem. Biophys. Res. Comm. 271: 244-249 (2000).

Ricoult C, Cliquet JB, Limami AM. Stimulation of alanine amino transferase (AlaAT) gene expression and alanine accumulation in embryo axis of the model legume Medicago truncatula contribute to anoxia stress tolerance. Physiol. Plant. 123: 30-39 (2005).

Rijhwani SK, Ho CH, Shanks JV. In vivo 31P and multilabel 13C NMR measurements for evaluation of plant metabolic pathways. Metab. Eng. 1: 12-25 (1999).

Rius SP, Casati P, Iglesias AA, Gomez-Casati DF. Characterization of Arabidopsis thaliana lines deficient in GAPC-1, a cytosolic NAD-dependent glyceraldehyde 3-phosphate dehydrogenase. Plant Physiol. 148: 1655-1667 (2008).

Rivoal J, Hanson AD. Metabolic control of anaerobic glycolysis. Overexpression of lactate dehydrogenase in transgenic tomato roots supports the Davies-Roberts hypothesis and points to a critical role for lactate secretion. Plant Physiol. 106: 1179-1185 (1994).

Rizhsky L, Liang H, Mittler R. The combined effect of drought stress and heat shock on gene expression in tobacco. Plant Physiol. 130: 1143-1151 (2002).

Rizzi M, Baltes M, Theobald U, Reuss M. In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae. 2. Mathematical model. Biotechnol. Bioeng. 55: 592-608 (1997).

Robert L. Management of time by the cell and by the organism. J. Soc. Biol. 193: 401-410 (1999).

Roberts JK, Hooks MA, Miaullis AP, Edwards S, Webster C. Contribution of malate and amino acid metabolism to cytoplasmic pH regulation in hypoxic maize root tips studied using nuclear magnetic resonance spectroscopy. Plant Physiol. 98: 480-487 (1992).

Rolletschek H, Hosein F, Miranda M, Heim U, Gotz KP, Schlereth A, Borisjuk L, Saalbach I, Wobus U, Weber H. Ectopic expression of an amino acid transporter (VfAAP1) in seeds of Vicia narbonensis and pea increases storage proteins. Plant Physiol. 137: 1236-1249 (2005).

Romisch-Margl W, Schramek N, Radykewicz T, Ettenhuber C, Eylert E, Huber C, Romisch-Margl L, Schwarz C, Dobner M, Demmel N, Winzenhorlein B, Bacher A, Eisenreich W. (13)CO(2) as a universal metabolic tracer in isotopologue perturbation experiments. Phytochemistry 68: 2273-2289 (2007).

Rontein D, Dieuaide-Noubhani M, Dufourc EJ, Raymond P, Rolin D. The metabolic architecture of plant cells: stability of central metabolism and flexibility of anabolic pathways during the growth cycle of tomato cells. J. Biol. Chem. 277: 43948-43960 (2002).

Roscher A, Emsley L, Raymond P, Roby C. Unidirectional steady state rates of central metabolism enzymes measured simultaneously in a living plant tissue. J. Biol. Chem. 273: 25053-25061 (1998).

Ross BD, Kingsley PB, Benyoseph O. Measurement of pentose phosphate pathway activity in a single incubation with [1,6-C-13(2),6,6-H-2(2)]glucose. Biochem. J. 302: 31-38 (1994).

Rossa CA, White J, Kuiper A, Postma PW, Bibb M, Teixeira de Mattos MJ. Carbon flux distribution in antibiotic-producing chemostat cultures of Streptomyces lividans. Metab. Eng. 4: 138-150 (2002).

Ruelland E, Miginiac-Maslow M. Regulation of chloroplast enzyme activities by thioredoxins: activation or relief from inhibition? Trends Plant Sci. 4: 136-141 (1999).

Sacktor B. Biochemical adaptations for flight in the insect. Biochem. Soc. Symp. 41: 111-131 (1976).

Sahm H, Eggeling L, de Graaf AA. Pathway analysis and metabolic engineering in Corynebacterium glutamicum. Biol. Chem. 381: 899-910 (2000).

Sakagishi Y. Alanine aminotransferase. Nippon Rinsho 53: 1146-1150 (1995).

Salusjarvi L, Kankainen M, Soliymani R, Pitkanen JP, Penttila M, Ruohonen L. Regulation of xylose metabolism in recombinant Saccharomyces cerevisiae. Microb. Cell Fact. 7: 18 (2008).

Sato S, Soga T, Nishioka T, Tomita M. Simultaneous determination of the main metabolites in rice leaves using capillary electrophoresis mass spectrometry and capillary electrophoresis diode array detection. Plant J. 40: 151-163 (2004).

Sato T, Harada T, Ishizawa K. Stimulation of glycolysis in anaerobic elongation of pondweed (Potamogeton distinctus) turions. J. Exp. Bot. 53: 1847-1856 (2002).

Sauer U, Hatzimanikatis V, Bailey JE, Hochuli M, Szyperski T, Wuthrich K. Metabolic fluxes in riboflavin-producing Bacillus subtilis. Nat. Biotechnol. 15: 448-452 (1997).

Sauer U, Lasko DR, Fiaux J, Hochuli M, Glaser R, Szyperski T, Wuthrich K, Bailey JE. Metabolic flux ratio analysis of genetic and environmental modulations of Escherichia coli central carbon metabolism. J. Bacteriol. 181: 6679-6688 (1999).

Savitch LV, Pocock T, Krol M, Wilson KE, Greenberg BM, Huner NPA. Effects of growth under UVA radiation on CO2 assimilation, carbon partitioning, PSII photochemistry and resistance to UVB radiation in Brassica napus cv. Topas. Aust. J. Plant Physiol. 28: 203-212 (2001).

Schaub J, Reuss M. In vivo dynamics of glycolysis in Escherichia coli shows need for growth-rate dependent metabolome analysis. Biotechnol. Prog. 24: 1402-1407 (2008).

Scheibe R. Malate valves to balance cellular energy supply. Physiol. Plant. 120: 21-26 (2004).

Schlichting I, Yang XJ, Miles EW, Kim AY, Anderson KS. Structural and kinetic analysis of a channel-impaired mutant of tryptophan synthase. J. Biol. Chem. 269: 26591-26593 (1994).

Schneider K, Borchardt DC, Schafer-Pregl R, Nagl N, Glass C, Jeppsson A, Gebhardt C, Salamini F. PCR-based cloning and segregation analysis of functional gene homologues in Beta vulgaris. Mol. Gen. Genet. 262: 515-524 (1999).

Schoder H, Knight RJ, Kofoed KF, Schelbert HR, Buxton DB. Regulation of pyruvate dehydrogenase activity and glucose metabolism in post-ischaemic myocardium. Biochim. Biophys. Acta 1406: 62-72 (1998).

Schulz AR. Control analysis of muscle glycogen metabolism. Arch. Biochem. Biophys. 353: 172-180 (1998).

Schuster R, Schuster S. Refined algorithm and computer program for calculating all nonnegative fluxes admissible in steady-states of biochemical reaction systems with or without some flux rates fixed. Comp. Appl. Biosci. 9: 79-85 (1993).

Schuster S, Fell DA, Dandekar T. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat. Biotechnol. 18: 326-332 (2000).

Schuster S, Schuster R. Detecting strictly detailed balanced subnetworks in open chemical reaction networks. J. Math. Chem. 6: 17-40 (1991).

Schwartz JM, Kanehisa M. Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis. BMC Bioinformatics 7: 186 (2006).

Schwender J, Goffman F, Ohlrogge JB, Shachar-Hill Y. Rubisco without the Calvin cycle improves the carbon efficiency of developing green seeds. Nature 432: 779-782 (2004).

Schwender J, Ohlrogge JB. Probing in vivo metabolism by stable isotope labeling of storage lipids and proteins in developing Brassica napus embryos. Plant Physiol. 130: 347-361 (2002).

Schwender J, Ohlrogge JB, Shachar-Hill Y. A flux model of glycolysis and the oxidative pentosephosphate pathway in developing Brassica napus embryos. J. Biol. Chem. 278: 29442-29453 (2003).

Selivanov VA, Meshalkina LE, Solovjeva ON, Kuchel PW, Ramos-Montoya A, Kochetov GA, Lee PW, Cascante M. Rapid simulation and analysis of isotopomer distributions using constraints based on enzyme mechanisms: an example from HT29 cancer cells. Bioinformatics 21: 3558-3564 (2005).

Sevilla A, Schmid JW, Mauch K, Iborra JL, Reuss M, Canovas M. Model of central and trimethylammonium metabolism for optimizing l-carnitine production by E. coli. Metab. Eng. 7: 401-425 (2005).

Shi H, Shimizu K. On-line metabolic pathway analysis based on metabolic signal flow diagram. Biotechnol. Bioeng. 58: 139-148 (1998).

Shioya H, Mineura K, Kowada M, Iida H, Murakami M, Ogawa T, Hatazawa J, Uemura K. Hemocirculation and metabolism in intraventricular tumors: kinetic analysis of glucose metabolism. No Shinkei Geka 24: 211-219 (1996).

Simpson NE, Han Z, Berendzen KM, Sweeney CA, Oca-Cossio JA, Constantinidis I, Stacpoole PW. Magnetic resonance spectroscopic investigation of mitochondrial fuel metabolism and energetics in cultured human fibroblasts: effects of pyruvate dehydrogenase complex deficiency and dichloroacetate. Mol. Genet. Metab. 89: 97-105 (2006).

Snell K, Fell DA. Metabolic control analysis of mammalian serine metabolism. Adv. Enzyme Reg. 30: 13-32 (1990).

Soga T, Ueno Y, Naraoka H, Ohashi Y, Tomita M, Nishioka T. Simultaneous determination of anionic intermediates for Bacillus subtilis metabolic pathways by capillary electrophoresis electrospray ionization mass spectrometry. Anal. Chem. 74: 2233-2239 (2002).

Sreenivasulu N, Altschmied L, Radchuk V, Gubatz S, Wobus U, Weschke W. Transcript profiles and deduced changes of metabolic pathways in maternal and filial tissues of developing barley grains. Plant J. 37: 539-553 (2004).

Sriram G, Shanks JV. Improvements in metabolic flux analysis using carbon bond labeling experiments: bondomer balancing and Boolean function mapping. Metab. Eng. 6: 116-132 (2004).

Stephani A, Heinrich R. Kinetic and thermodynamic principles determining the structural design of ATP-producing systems. Bull. Math. Biol. 60: 505-543 (1998).

Stephani A, Nuno JC, Heinrich R. Optimal stoichiometric designs of ATP-producing systems as determined by an evolutionary algorithm. J. Theor. Biol. 199: 45-61 (1999).

Suarez RK. Energy metabolism during insect flight: biochemical design and physiological performance. Physiol. Biochem. Zool. 73: 765-771 (2000).

Subbaiah CC, Sachs MM. Molecular and cellular adaptations of maize to flooding stress. Ann. Bot. (Lond.) 91: 119-127 (2003).

Suzuki M, Hashioka A, Mimura T, Ashihara H. Salt stress and glycolytic regulation in suspension-cultured cells of the mangrove tree, Bruguiera sexangula. Physiol. Plant. 123: 246-253 (2005).

Sweetlove LJ, Kruger NJ, Hill SA. Starch synthesis in transgenic potato tubers with increased 3-phosphoglyceric acid content as a consequence of increased 6-phosphofructokinase activity. Planta 213: 478-482 (2001).

Sweetlove LJ, Tomlinson KL, Hill SA. The effect of exogenous sugars on the control of flux by adenosine 5'-diphosphoglucose pyrophosphorylase in potato tuber discs. Planta 214: 741-750 (2002).

Swiderek H, Logan A, Al-Rubeai M. Cellular and transcriptomic analysis of NS0 cell response during exposure to hypoxia. J. Biotechnol. 134: 103-111 (2008).

Szyperski T. Biosynthetically directed fractional 13C-labeling of proteinogenic amino acids. An efficient analytical tool to investigate intermediary metabolism. Eur. J. Biochem. 232: 433-448 (1995).

Tadege M, Dupuis I, Kuhlemeier C. Ethanolic fermentation: new functions for an old pathway. Trends Plant Sci. 4: 320-325 (1999).

Takahashi H, Hayashi M, Goto F, Sato S, Soga T, Nishioka T, Tomita M, Kawai-Yamada M, Uchimiya H. Evaluation of metabolic alteration in transgenic rice overexpressing dihydroflavonol-4-reductase. Ann. Bot. (Lond.) 98: 819-825 (2006).

Takahashi H, Uchimiya H, Hihara Y. Difference in metabolite levels between photoautotrophic and photomixotrophic cultures of Synechocystis sp. PCC 6803 examined by capillary electrophoresis electrospray ionization mass spectrometry. J. Exp. Bot. 59: 3009-3018 (2008).

Tambasco-Studart M, Titiz O, Raschle T, Forster G, Amrhein N, Fitzpatrick TB. Vitamin B6 biosynthesis in higher plants. Proc. Natl. Acad. Sci. U.S.A. 102: 13687-13692 (2005).

Tang YJ, Sapra R, Joyner D, Hazen TC, Myers S, Reichmuth D, Blanch H, Keasling JD. Analysis of metabolic pathways and fluxes in a newly discovered thermophilic and ethanol-tolerant Geobacillus strain. Biotechnol. Bioeng. 102: 1377-1386 (2009).

Tatarko M, Romeo T. Disruption of a global regulatory gene to enhance central carbon flux into phenylalanine biosynthesis in Escherichia coli. Curr. Microbiol. 43: 26-32 (2001).

Tcherkez G, Bligny R, Gout E, Mahe A, Hodges M, Cornic G. Respiratory metabolism of illuminated leaves depends on CO2 and O2 conditions. Proc. Natl. Acad. Sci. U.S.A. 105: 797-802 (2008).

Tcherkez G, Cornic G, Bligny R, Gout E, Ghashghaie J. In vivo respiratory metabolism of illuminated leaves. Plant Physiol. 138: 1596-1606 (2005).

Tecsi LI, Maule AJ, Smith AM, Leegood RC. Metabolic alterations in cotyledons of Cucurbita pepo infected by cucumber mosaic virus. J. Exp. Bot. 45: 1541-1551 (1994).

Temple SJ, Vance CP, Gantt JS. Glutamate synthase and nitrogen assimilation. Trends Plant Sci. 3: 51-56 (1998).

Tetlow IJ, Blissett KJ, Emes MJ. Metabolite pools during starch synthesis and carbohydrate oxidation in amyloplasts isolated from wheat endosperm. Planta 204: 100-108 (1998).

Theobald U, Mailinger W, Baltes M, Rizzi M, Reuss M. In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae. 1. Experimental observations. Biotechnol. Bioeng. 55: 305-316 (1997).

Theodorou ME, Plaxton WC. Metabolic adaptations of plant respiration to nutritional phosphate deprivation. Plant Physiol. 101: 339-344 (1993).

Thimm O, Essigmann B, Kloska S, Altmann T, Buckhout TJ. Response of Arabidopsis to iron deficiency stress as revealed by microarray analysis. Plant Physiol. 127: 1030-1043 (2001).

Thom E, Mohlmann T, Quick WP, Camara B, Neuhaus H-E. Sweet pepper plastids: enzymic equipment, characterisation of the plastidic oxidative pentose-phosphate pathway, and transport of phosphorylated intermediates across the envelope membrane. Planta 204: 226-233 (1998).

Thomas GH. Metabolomics breaks the silence. Trends Biotechnol. 19: 126-127 (2001).

Thomas S, Fell DA. A control analysis exploration of the role of ATP utilisation in glycolytic-flux control and glycolytic-metabolite-concentration regulation. Eur. J. Biochem. 258: 956-967 (1998).

Thomas S, Mooney PFJ, Burrell MM, Fell DA. Metabolic Control Analysis of glycolysis in tuber tissue of potato (Solanum tuberosum): Explanation for the low control coefficient of phosphofructokinase over respiratory flux. Biochem. J. 322: 119-127 (1997).

Thomas S, Mooney PJF, Burrell MM, Fell DA. Finite change analysis of glycolytic intermediates in tuber tissue of lines of transgenic potato (Solanum tuberosum) overexpressing phosphofructokinase. Biochem. J. 322: 111-117 (1997).

Thum KE, Shin MJ, Gutierrez RA, Mukherjee I, Katari MS, Nero D, Shasha D, Coruzzi GM. An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis. BMC Syst. Biol. 2: 31 (2008).

Toivari MH, Aristidou A, Ruohonen L, Penttila M. Conversion of xylose to ethanol by recombinant Saccharomyces cerevisiae: importance of xylulokinase (XKS1) and oxygen availability. Metab. Eng. 3: 236-249 (2001).

Trethewey RN, Fernie AR, Bachmann A, Fleischer-Notter H, Geigenberger P, Willmitzer L. Expression of a bacterial sucrose phosphorylase in potato tubers results in a glucose-independent induction of glycolysis. Plant Cell Environ. 24: 357-365 (2001).

Trethewey RN, Riesmeier JW, Willmitzer L, Stitt M, Geigenberger P. Tuber-specific expression of a yeast invertase and a bacterial glucokinase in potato leads to an activation of sucrose phosphate synthase and the creation of a sucrose futile cycle. Planta 208: 227-238 (1999).

Urbano AM, Gillham H, Groner Y, Brindle KM. Effects of overexpression of the liver subunit of 6-phosphofructo-1-kinase on the metabolism of a cultured mammalian cell line. Biochem. J. 352: 921-927 (2000).

Uzcategui NL, Szallies A, Pavlovic-Djuranovic S, Palmada M, Figarella K, Boehmer C, Lang F, Beitz E, Duszenko M. Cloning, heterologous expression, and characterization of three aquaglyceroporins from Trypanosoma brucei. J. Biol. Chem. 279: 42669-42676 (2004).

Valverde F, Losada M, Serrano A. Engineering a central metabolic pathway: glycolysis with no net phosphorylation in an Escherichia coli gap mutant complemented with a plant GapN gene. FEBS Lett. 449: 153-158 (1999).

Valverde F, Ortega JM, Losada M, Serrano A. Sugar-mediated transcriptional regulation of the Gap gene system and concerted photosystem II functional modulation in the microalga Scenedesmus vacuolatus. Planta 221: 937-952 (2005).

Van Winden WA, Van Gulik WM, Schipper D, Verheijen PJ, Krabben P, Vinke JL, Heijnen JJ. Metabolic flux and metabolic network analysis of Penicillium chrysogenum using 2D [13C, 1H] COSY NMR measurements and cumulative bondomer simulation. Biotechnol. Bioeng. 83: 75-92 (2003).

Vartapetian BB, Andreeva IN, Generozova IP, Polyakova LI, Maslova IP, Dolgikh YI, Stepanova AY. Functional electron microscopy in studies of plant response and adaptation to anaerobic stress. Ann. Bot. (Lond.) 91: 155-172 (2003).

Vaseghi S, Baumeister A, Rizzi M, Reuss M. In vivo dynamics of the pentose phosphate pathway in Saccharomyces cerevisiae. Metab. Eng. 1: 128-140 (1999).

Velasco R, Salamini F, Bartels D. Dehydration and ABA increase mRNA levels and enzyme activity of cytosolic GAPDH in the resurrection plant Craterostigma plantagineum. Plant Mol. Biol. 26: 541-546 (1994).

Vigeolas H, Mohlmann T, Martini N, Neuhaus HE, Geigenberger P. Embryo-specific reduction of ADP-Glc pyrophosphorylase leads to an inhibition of starch synthesis and a delay in oil accumulation in developing seeds of oilseed rape. Plant Physiol. 136: 2676-2686 (2004).

Vo TD, Palsson BO. Isotopomer analysis of myocardial substrate metabolism: a systems biology approach. Biotechnol. Bioeng. 95: 972-983 (2006).

Vogt AM, Nef H, Schaper J, Poolman M, Fell DA, Kubler W, Elsasser A. Metabolic control analysis of anaerobic glycolysis in human hibernating myocardium replaces traditional concepts of flux control. FEBS Lett. 517: 245-250 (2002).

Voit EO, Radivoyevitch T. Biochemical systems analysis of genome-wide expression data. Bioinformatics 16: 1023-1037 (2000).

Vojinovic V, von Stockar U. Influence of uncertainties in pH, pMg, activity coefficients, metabolite concentrations, and other factors on the analysis of the thermodynamic feasibility of metabolic pathways. Biotechnol. Bioeng. 103: 780-795 (2009).

Wahlbom CF, Eliasson A, Hahn-Hagerdal B. Intracellular fluxes in a recombinant xylose-utilizing Saccharomyces cerevisiae cultivated anaerobically at different dilution rates and feed concentrations. Biotechnol. Bioeng. 72: 289-296 (2001).

Wakisaka S, Ohshima Y, Ogawa M, Tochikura T, Tachiki T. Characteristics and efficiency of glutamine production by coupling of a bacterial glutamine synthetase reaction with the alcoholic fermentation system of baker's yeast. Appl. Environ. Microbiol. 64: 2952-2957 (1998).

Wang R, Okamoto M, Xing X, Crawford NM. Microarray analysis of the nitrate response in Arabidopsis roots and shoots reveals over 1,000 rapidly responding genes and new linkages to glucose, trehalose-6-phosphate, iron, and sulfate metabolism. Plant Physiol. 132: 556-567 (2003).

Wang R, Tischner R, Gutierrez RA, Hoffman M, Xing X, Chen M, Coruzzi G, Crawford NM. Genomic analysis of the nitrate response using a nitrate reductase-null mutant of Arabidopsis. Plant Physiol. 136: 2512-2522 (2004).

Wang X, Larkins BA. Genetic analysis of amino acid accumulation in opaque-2 maize endosperm. Plant Physiol. 125: 1766-1777 (2001).

Wang Z, Xiang L, Shao J, Wegrzyn A, Wegrzyn G. Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism. Microb. Cell Fact. 5: 34 (2006).

Wasaki J, Yonetani R, Kuroda S, Shinano T, Yazaki J, Fujii F, Shimbo K, Yamamoto K, Sakata K, Sasaki T, Kishimoto N, Kikuchi S, Yamagishi M, Osaki M. Transcriptomic analysis of metabolic changes by phosphorus stress in rice plant roots. Plant Cell Environ. 26: 1515-1523 (2003).

Wei B, Shin S, LaPorte D, Wolfe AJ, Romeo T. Global regulatory mutations in csrA and rpoS cause severe central carbon stress in Escherichia coli in the presence of acetate. J. Bacteriol. 182: 1632-1640 (2000).

Weigelt K, Kuster H, Radchuk R, Muller M, Weichert H, Fait A, Fernie AR, Saalbach I, Weber H. Increasing amino acid supply in pea embryos reveals specific interactions of N and C metabolism and highlights the importance of mitochondrial metabolism. Plant J. 55: 909-926 (2008).

Weigelt K, Kuster H, Rutten T, Fait A, Fernie AR, Miersch O, Wasternack C, Emery RJ, Desel C, Hosein F, Muller M, Saalbach I, Weber H. ADP-glucose pyrophosphorylase deficient pea embryos reveal specific transcriptional and metabolic changes of C:N metabolism and stress responses. Plant Physiol. 149: 395-411 (2009).

Wenzler M, Holscher D, Oerther T, Schneider B. Nectar formation and floral nectary anatomy of Anigozanthos flavidus: a combined magnetic resonance imaging and spectroscopy study. J. Exp. Bot. 59: 3425-3434 (2008).

Werle M, Kreuzer J, Hofele J, Elsasser A, Ackermann C, Katus HA, Vogt AM. Metabolic control analysis of the Warburg-effect in proliferating vascular smooth muscle cells. J. Biomed. Sci. 12: 827-834 (2005).

Werner T, Holst K, Pors Y, Guivarc'h A, Mustroph A, Chriqui D, Grimm B, Schmulling T. Cytokinin deficiency causes distinct changes of sink and source parameters in tobacco shoots and roots. J. Exp. Bot. 59: 2659-2672 (2008).

Westram A, Lloyd JR, Roessner U, Riesmeier JW, Kossmann J. Increases of 3-phosphoglyceric acid in potato plants through antisense reduction of cytoplasmic phosphoglycerate mutase impairs photosynthesis and growth, but does not increase starch contents. Plant Cell Environ. 25: 1133-1143 (2002).

Whittaker A, Martinelli T, Bochicchio A, Vazzana C, Farrant J. Comparison of sucrose metabolism during the rehydration of desiccation-tolerant and desiccation-sensitve leaf material of Sporobolus stapfianus. Physiol. Plant. 122: 11-20 (2004).

Whittaker A, Martinelli T, Farrant JM, Bochicchio A, Vazzana C. Sucrose phosphate synthase activity and the co-ordination of carbon partitioning during sucrose and amino acid accumulation in desiccation-tolerant leaf material of the C4 resurrection plant Sporobolus stapfianus during dehydration. J. Exp. Bot. 58: 3775-3787 (2007).

Wilkinson SJ, Benson N, Kell DB. Proximate parameter tuning for biochemical networks with uncertain kinetic parameters. Mol. Biosyst. 4: 74-97 (2007).

Winkelmann T, Heintz D, Van Dorsselaer A, Serek M, Braun HP. Proteomic analyses of somatic and zygotic embryos of Cyclamen persicum Mill. reveal new insights into seed and germination physiology. Planta 224: 508-519 (2006).

Wittmann C, Heinzle E. Modeling and experimental design for metabolic flux analysis of lysine-producing Corynebacteria by mass spectrometry. Metab. Eng. 3: 173-191 (2001).

Wittmann C, Kiefer P, Zelder O. Metabolic fluxes in Corynebacterium glutamicum during lysine production with sucrose as carbon source. Appl. Environ. Microbiol. 70: 7277-7287 (2004).

Wrenger C, Muller S. Isocitrate dehydrogenase of Plasmodium falciparum. Eur. J. Biochem. 270: 1775-1783 (2003).

Xiao J, Shi Z, Gao P, Feng H, Duan Z, Mao Z. On-line optimization of glutamate production based on balanced metabolic control by RQ. Bioprocess. Biosyst. Eng. 29: 109-117 (2006).

Xiao W, Sheen J, Jang JC. The role of hexokinase in plant sugar signal transduction and growth and development. Plant Mol. Biol. 44: 451-461 (2000).

Yang C, Hua Q, Shimizu K. Metabolic flux analysis in Synechocystis using isotope distribution from 13C-labeled glucose. Metab. Eng. 4: 202-216 (2002).

Yang TH, Heinzle E, Wittmann C. Theoretical aspects of 13C metabolic flux analysis with sole quantification of carbon dioxide labeling. Comput. Biol. Chem. 29: 121-133 (2005).

Yokoyama T, Banta S, Berthiaume F, Nagrath D, Tompkins RG, Yarmush ML. Evolution of intrahepatic carbon, nitrogen, and energy metabolism in a D-galactosamine-induced rat liver failure model. Metab. Eng. 7: 88-103 (2005).

Yoon SH, Han MJ, Lee SY, Jeong KJ, Yoo JS. Combined transcriptome and proteome analysis of Escherichia coli during high cell density culture. Biotechnol. Bioeng. 81: 753-767 (2003).

Yudkoff M, Daikhin Y, Nissim I, Nissim I. Acidosis and astrocyte amino acid metabolism. Neurochem. Int. 36: 329-339 (2000).

Zamboni N, Maaheimo H, Szyperski T, Hohmann HP, Sauer UU. The phosphoenolpyruvate carboxykinase also catalyzes C(3) carboxylation at the interface of glycolysis and the TCA cycle of Bacillus subtilis. Metab. Eng. 6: 277-284 (2004).

Zhang F, Yi XP, Sun XM, Zhang YX. Metabolism of recombinant CHO-GS cell reducing of toxic effect of ammonia. Sheng Wu Gong Cheng Xue Bao 22: 94-100 (2006).

Zhang H, Sreenivasulu N, Weschke W, Stein N, Rudd S, Radchuk V, Potokina E, Scholz U, Schweizer P, Zierold U, Langridge P, Varshney RK, Wobus U, Graner A. Large-scale analysis of the barley transcriptome based on expressed sequence tags. Plant J. 40: 276-290 (2004).

Zhang Y, Huang Z, Du C, Li Y, Cao Z. Introduction of an NADH regeneration system into Klebsiella oxytoca leads to an enhanced oxidative and reductive metabolism of glycerol. Metab. Eng. 11: 101-106 (2009).

Zhu J, Shalel-Levanon S, Bennett G, San KY. Effect of the global redox sensing/regulation networks on Escherichia coli and metabolic flux distribution based on C-13 labeling experiments. Metab. Eng. 8: 619-627 (2006).

Zhu J, Shimizu K. Effect of a single-gene knockout on the metabolic regulation in Escherichia coli for D-lactate production under microaerobic condition. Metab. Eng. 7: 104-115 (2005).

Ziegler A, Zaugg CE, Buser PT, Seelig J, Kunnecke B. Non-invasive measurements of myocardial carbon metabolism using in vivo C-13 NMR spectroscopy. NMR Biomed. 15: 222-234 (2002).

Zuin A, Vivancos AP, Sanso M, Takatsume Y, Ayte J, Inoue Y, Hidalgo E. The glycolytic metabolite methylglyoxal activates Pap1 and Sty1 stress responses in Schizosaccharomyces pombe. J. Biol. Chem. 280: 36708-36713 (2005).

Zwingmann C, Richter-Landsberg C, Leibfritz D. 13C isotopomer analysis of glucose and alanine metabolism reveals cytosolic pyruvate compartmentation as part of energy metabolism in astrocytes. Glia 34: 200-212 (2001).

Number of references = 359

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