|
HORT640 - Metabolic Plant Physiology
References, pentose phosphate
Altintas MM, Eddy CK, Zhang M, McMillan JD, Kompala DS. Kinetic modeling to optimize pentose fermentation in Zymomonas mobilis. Biotechnol. Bioeng. 94: 273-295 (2006).
Andersson-Gunneras S, Mellerowicz EJ, Love J, Segerman B, Ohmiya Y, Coutinho PM, Nilsson P, Henrissat B, Moritz T, Sundberg B. Biosynthesis of cellulose-enriched tension wood in Populus: global analysis of transcripts and metabolites identifies biochemical and developmental regulators in secondary wall biosynthesis. Plant J. 45: 144-165 (2006).
Antelmann H, Bernhardt J, Schmid R, Mach H, Volker U, Hecker M. First steps from a two-dimensional protein index towards a response-regulation map for Bacillus subtilis. Electrophoresis 18: 1451-1463 (1997).
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).
Ao P, Lee LW, Lidstrom ME, Yin L, Zhu X. Towards kinetic modeling of global metabolic networks: Methylobacterium extorquens AM1 growth as validation. Sheng Wu Gong Cheng Xue Bao 24: 980-994 (2008).
Aubert S, Juge C, Boisson AM, Gout E, Bligny R. Metabolic processes sustaining the reviviscence of lichen Xanthoria elegans (Link) in high mountain environments. Planta 226: 1287-1297 (2007).
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).
Babiak RM, Campello AP, Carnieri EG, Oliveira MB. Methotrexate: pentose cycle and oxidative stress. Cell Biochem. Funct. 16: 283-293 (1998).
Badger MR, Bek EJ. Multiple Rubisco forms in proteobacteria: their functional significance in relation to CO2 acquisition by the CBB cycle. J. Exp. Bot. 59: 1525-1541 (2008).
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).
Batz O, Logemann E, Reinold S, Hahlbrock K. Extensive reprogramming of primary and secondary metabolism by fungal elicitor or infection in parsley cells. Biol. Chem. 379: 1127-1135 (1998).
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).
Bender DA. Optimum nutrition: thiamin, biotin and pantothenate. Proc. Nutr. Soc. 58: 427-433 (1999).
Bengtsson O, Hahn-Hagerdal B, Gorwa-Grauslund MF. Xylose reductase from Pichia stipitis with altered coenzyme preference improves ethanolic xylose fermentation by recombinant Saccharomyces cerevisiae. Biotechnol. Biofuels 2: 9 (2009).
Bernacchia G, Schwall G, Lottspeich F, Salamini F, Bartels D. The transketolase gene family of the resurrection plant Craterostigma plantagineum: differential expression during the rehydration phase. EMBO J. 14: 610-618 (1995).
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).
Berthon HA, Bubb WA, Kuchel PW. 13C NMR isotopomer and computer-simulation studies of the nonoxidative pentose-phosphate pathway of human erythrocytes. Biochem. J. 296: 379-387 (1993).
Bi C, Rice JD, Preston JF. Complete fermentation of xylose and methylglucuronoxylose derived from methylglucuronoxylan by Enterobacter asburiae strain JDR-1. Appl. Environ. Microbiol. 75: 395-404 (2009).
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).
Blank LM, Lehmbeck F, Sauer U. Metabolic-flux and network analysis in fourteen hemiascomycetous yeasts. FEMS Yeast Res. 5: 545-558 (2005).
Blencke HM, Homuth G, Ludwig H, Mader U, Hecker M, Stulke J. Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab. Eng. 5: 133-149 (2003).
Boada J, Roig T, Perez X, Gamez A, Bartrons R, Cascante M, Bermudez J. Cells overexpressing fructose-2,6-bisphosphatase showed enhanced pentose phosphate pathway flux and resistance to oxidative stress. FEBS Lett. 480: 261-264 (2000).
Boer P, Sperling O. Stimulation of ribose-5-phosphate and 5-phosphoribosyl-1-pyrophosphate generation by pyrroline-5-carboxylate in mouse liver in vivo: evidence for a regulatory role of ribose-5-phosphate availability in nucleotide synthesis. Biochem. Med. Metab. Biol. 46: 28-32 (1991).
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).
Bongaerts J, Kramer M, Muller U, Raeven L, Wubbolts M. Metabolic engineering for microbial production of aromatic amino acids and derived compounds. Metab. Eng. 3: 289-300 (2001).
Borodina I, Scholler C, Eliasson A, Nielsen J. Metabolic network analysis of Streptomyces tenebrarius, a Streptomyces species with an active Entner-Doudoroff pathway. Appl. Environ. Microbiol. 71: 2294-2302 (2005).
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).
Bouvier F, d'Harlingue A, Suire C, Backhaus RA, Camara B. Dedicated roles of plastid transketolases during the early onset of isoprenoid biogenesis in pepper fruits. Plant Physiol. 117: 1423-1431 (1998).
Buchanan BB, Arnon DI. A reverse KREBS cycle in photosynthesis: consensus at last. Photosynth. Res. 24: 47-53 (1990).
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).
Bum Kim H, Smith CP, Micklefield J, Mavituna F. Metabolic flux analysis for calcium dependent antibiotic (CDA) production in Streptomyces coelicolor. Metab. Eng. 6: 313-325 (2004).
Caillau M, Paul Quick W. New insights into plant transaldolase. Plant J. 43: 1-16 (2005).
Cannizzaro C, Christensen B, Nielsen J, Stockar U. Metabolic network analysis on Phaffia rhodozyma yeast using (13)C-labeled glucose and gas chromatography-mass spectrometry. Metab. Eng. 6: 340-351 (2004).
Canonaco F, Hess TA, Heri S, Wang T, Szyperski T, Sauer U. Metabolic flux response to phosphoglucose isomerase knock-out in Escherichia coli and impact of overexpression of the soluble transhydrogenase UdhA. FEMS Microbiol. Lett. 204: 247-252 (2001).
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).
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).
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).
Chen L, Spiliotis ET, Roberts MF. Biosynthesis of di-myo-inositol-1,1'-phosphate, a novel osmolyte in hyperthermophilic archaea. J. Bacteriol. 180: 3785-3792 (1998).
Chong BF, Bonnett GD, Glassop D, O'Shea MG, Brumbley SM. Growth and metabolism in sugarcane are altered by the creation of a new hexose-phosphate sink. Plant Biotechnol. J. 5: 240-253 (2007).
Christensen B, Christiansen T, Gombert AK, Thykaer J, Nielsen J. Simple and robust method for estimation of the split between the oxidative pentose phosphate pathway and the Embden-Meyerhof-Parnas pathway in microorganisms. Biotechnol. Bioeng. 74: 517-523 (2001).
Christensen B, Gombert AK, Nielsen J. Analysis of flux estimates based on (13)C-labelling experiments. Eur. J. Biochem. 269: 2795-2800 (2002).
Christiansen T, Christensen B, Nielsen J. Metabolic network analysis of Bacillus clausii on minimal and semirich medium using 13C-labeled glucose. Metab. Eng. 4: 159-169 (2002).
Clayton H, Ap Rees T. Respiratory metabolism of the bundle sheath of maize leaves. J. Plant Physiol. 139: 350-354 (1992).
Cloutier M, Perrier M, Jolicoeur M. Dynamic flux cartography of hairy roots primary metabolism. Phytochemistry 68: 2393-2404 (2007).
Cordwell SJ. Microbial genomes and "missing" enzymes: redefining biochemical pathways. Arch. Microbiol. 172: 269-279 (1999).
Couee I, Sulmon C, Gouesbet G, El Amrani A. Involvement of soluble sugars in reactive oxygen species balance and responses to oxidative stress in plants. J. Exp. Bot. 57: 449-459 (2006).
Crecelius F, Streb P, Feierabend J. Malate metabolism and reactions of oxidoreduction in cold-hardened winter rye (Secale cereale L.) leaves. J. Exp. Bot. 54: 1075-1083 (2003).
Das R, Hegyi H, Gerstein M. Genome analyses of spirochetes: a study of the protein structures, functions and metabolic pathways in Treponema pallidum and Borrelia burgdorferi. J. Mol. Microbiol. Biotechnol. 2: 387-392 (2000).
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).
Davalos M, Fourment J, Lucas A, Berges H, Kahn D. Nitrogen regulation in Sinorhizobium meliloti probed with whole genome arrays. FEMS Microbiol. Lett. 241: 33-40 (2004).
David H, Krogh AM, Roca C, Akesson M, Nielsen J. CreA influences the metabolic fluxes of Aspergillus nidulans during growth on glucose and xylose. Microbiology 151: 2209-2221 (2005).
de Graaf AA, Striegel K, Wittig RM, Laufer B, Schmitz G, Wiechert W, Sprenger GA, Sahm H. Metabolic state of Zymomonas mobilis in glucose-, fructose-, and xylose-fed continuous cultures as analysed by 13C- and 31P-NMR spectroscopy. Arch. Microbiol. 171: 371-385 (1999).
De RK, Das M, Mukhopadhyay S. Incorporation of enzyme concentrations into FBA and identification of optimal metabolic pathways. BMC Syst. Biol. 2: 65 (2008).
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, 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).
Dolle A. Metabolism of D- and L-[13C]alanine in rat liver detected by 1H and 13C NMR spectroscopy in vivo and in vitro. NMR Biomed. 13: 72-81 (2000).
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).
Dragan CA, Blank LM, Bureik M. Increased TCA cycle activity and reduced oxygen consumption during cytochrome P450-dependent biotransformation in fission yeast. Yeast 23: 779-794 (2006).
Druart N, Johansson A, Baba K, Schrader J, Sjodin A, Bhalerao RR, Resman L, Trygg J, Moritz T, Bhalerao RP. Environmental and hormonal regulation of the activity-dormancy cycle in the cambial meristem involves stage-specific modulation of transcriptional and metabolic networks. Plant J. 50: 557-573 (2007).
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).
Eastmond PJ, Rawsthorne S. Coordinate changes in carbon partitioning and plastidial metabolism during the development of oilseed rape embryos. Plant Physiol. 122: 767-774 (2000).
Edwards JS, Palsson BO. Robustness analysis of the Escherichia coli metabolic network. Biotechnol. Prog. 16: 927-939 (2000).
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).
Eicks M, Maurino V, Knappe S, Flugge UI, Fischer K. The plastidic pentose phosphate translocator represents a link between the cytosolic and the plastidic pentose phosphate pathways in plants. Plant Physiol. 128: 512-522 (2002).
Eisenreich W, Slaghuis J, Laupitz R, Bussemer J, Stritzker J, Schwarz C, Schwarz R, Dandekar T, Goebel W, Bacher A. 13C Isotopologue perturbation studies of Listeria monocytogenes carbon metabolism and its modulation by the virulence regulator PrfA. Proc. Natl. Acad. Sci. U.S.A. 103: 2040-2045 (2006).
Emes MJ, Neuhaus HE. Metabolism and transport in non-photosynthetic plastids. J. Exp. Bot. 48: 1995-2005 (1997).
Emmerling M, Dauner M, Ponti A, Fiaux J, Hochuli M, Szyperski T, Wuthrich K, Bailey JE, Sauer U. Metabolic flux responses to pyruvate kinase knockout in Escherichia coli. J. Bacteriol. 184: 152-164 (2002).
Esposito S, Guerriero G, Vona V, Di Martino Rigano V, Carfagna S, Rigano C. Glutamate synthase activities and protein changes in relation to nitrogen nutrition in barley: the dependence on different plastidic glucose-6P dehydrogenase isoforms. J. Exp. Bot. 56: 55-64 (2005).
Esposito S, Massaro G, Vona V, Di Martino Rigano V, Carfagna S. Glutamate synthesis in barley roots: the role of the plastidic glucose-6-phosphate dehydrogenase. Planta 216: 639-647 (2003).
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).
Fahrendorf T, Ni W, Shorrosh BS, Dixon RA. Stress responses in alfalfa (Medicago sativa L.) XIX. Transcriptional activation of oxidative pentose phosphate pathway genes at the onset of the isoflavonoid phytoalexin response. Plant Mol. Biol. 28: 885-900 (1995).
Fleming GA, Steel G, Valle D, Granger AS, Phang JM. The aqueous humor of rabbit contains high concentrations of pyrroline-5-carboxylate. Metabolism 35: 933-937 (1986).
Flores CL, Rodriguez C, Petit T, Gancedo C. Carbohydrate and energy-yielding metabolism in non-conventional yeasts. FEMS Microbiol. Rev. 24: 507-529 (2000).
Flores S, Gosset G, Flores N, de Graaf AA, Bolivar F. Analysis of carbon metabolism in Escherichia coli strains with an inactive phosphotransferase system by (13)C labeling and NMR spectroscopy. Metab. Eng. 4: 124-137 (2002).
Follstad BD, Stephanopoulos G. Effect of reversible reactions on isotope label redistribution--analysis of the pentose phosphate pathway. Eur. J. Biochem. 252: 360-371 (1998).
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).
Fox SR, Rawsthorne S, Hills MJ. Fatty acid synthesis in pea root plastids is inhibited by the action of long-chain acyl-coenzyme As on metabolite transporters. Plant Physiol. 126: 1259-1265 (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).
Galvez L, Gonzalez EM, Arrese-Igor C. Evidence for carbon flux shortage and strong carbon/nitrogen interactions in pea nodules at early stages of water stress. J. Exp. Bot. 56: 2551-2561 (2005).
Garlick AP, Moore C, Kruger NJ. Monitoring flux through the oxidative pentose phosphate pathway using [1-(14)C]gluconate. Planta 216: 265-272 (2002).
Givan CV. Evolving concepts in plant glycolysis: two centuries of progress. Biol. Rev. Camb. Phil. Soc. 74: 277-309 (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).
Gombert AK, Moreira dos Santos M, Christensen B, Nielsen J. Network identification and flux quantification in the central metabolism of Saccharomyces cerevisiae under different conditions of glucose repression. J. Bacteriol. 183: 1441-1451 (2001).
Gonzalez R, Andrews BA, Molitor J, Asenjo JA. Metabolic analysis of the synthesis of high levels of intracellular human SOD in Saccharomyces cerevisiae rhSOD 2060 411 SGA122. Biotechnol. Bioeng. 82: 152-169 (2003).
Gonzalez R, Tao H, Shanmugam KT, York SW, Ingram LO. Global gene expression differences associated with changes in glycolytic flux and growth rate in Escherichia coli during the fermentation of glucose and xylose. Biotechnol. Prog. 18: 6-20 (2002).
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).
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).
Hagedorn CH, Phang JM. Catalytic transfer of hydride ions from NADPH to oxygen by the interconversions of proline and delta 1-pyrroline-5-carboxylate. Arch. Biochem. Biophys. 248: 166-174 (1986).
Hagedorn CH, Yeh GC, Phang JM. Transfer of 1-pyrroline-5-carboxylate as oxidizing potential from hepatocytes to erythrocytes. Biochem. J. 202: 31-39 (1982).
Hahn D, Kaltenbach C, Kuck U. The Calvin cycle enzyme sedoheptulose-1,7-bisphosphatase is encoded by a light-regulated gene in Chlamydomonas reinhardtii. Plant Mol. Biol. 36: 929-934 (1998).
Hare PD, Cress WA. Metabolic implications of stress-induced proline accumulation in plants. Plant Growth Regulation 21: 79-102 (1997).
Harris DM, Diderich JA, van der Krogt ZA, Luttik MA, Raamsdonk LM, Bovenberg RA, van Gulik WM, van Dijken JP, Pronk JT. Enzymic analysis of NADPH metabolism in beta-lactam-producing Penicillium chrysogenum: presence of a mitochondrial NADPH dehydrogenase. Metab. Eng. 8: 91-101 (2006).
Henkes S, Sonnewald U, Badur R, Flachmann R, Stitt M. A small decrease of plastid transketolase activity in antisense tobacco transformants has dramatic effects on photosynthesis and phenylpropanoid metabolism. Plant Cell 13: 535-551 (2001).
Hesse SJ, Ruijter GJ, Dijkema C, Visser J. Intracellular pH homeostasis in the filamentous fungus Aspergillus niger. Eur. J. Biochem. 269: 3485-3494 (2002).
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).
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).
Hu CA, Bart Williams D, Zhaorigetu S, Khalil S, Wan G, Valle D. Functional genomics and SNP analysis of human genes encoding proline metabolic enzymes. Amino Acids 35: 655-664 (2008).
Hutchings D, Rawsthorne S, Emes MJ. Fatty acid synthesis and the oxidative pentose phosphate pathway in developing embryos of oilseed rape (Brassica napus L.). J. Exp. Bot. 56: 577-585 (2005).
Iyer VV, Sriram G, Fulton DB, Zhou R, Westgate ME, Shanks JV. Metabolic flux maps comparing the effect of temperature on protein and oil biosynthesis in developing soybean cotyledons. Plant Cell Environ. 31: 506-517 (2008).
Jeppsson M, Johansson B, Hahn-Hagerdal B, Gorwa-Grauslund MF. Reduced oxidative pentose phosphate pathway flux in recombinant xylose-utilizing Saccharomyces cerevisiae strains improves the ethanol yield from xylose. Appl. Environ. Microbiol. 68: 1604-1609 (2002).
Jonsbu E, Christensen B, Nielsen J. Changes of in vivo fluxes through central metabolic pathways during the production of nystatin by Streptomyces noursei in batch culture. Appl. Microbiol. Biotechnol. 56: 93-100 (2001).
Joshi S, Singh AR, Kumar A, Misra PC, Siddiqi MI, Saxena JK. Molecular cloning and characterization of Plasmodium falciparum transketolase. Mol. Biochem. Parasitol. 160: 32-41 (2008).
Karl T, Fall R, Rosenstiel TN, Prazeller P, Larsen B, Seufert G, Lindinger W. On-line analysis of the 13CO2 labeling of leaf isoprene suggests multiple subcellular origins of isoprene precursors. Planta 215: 894-905 (2002).
Kayser A, Weber J, Hecht V, Rinas U. Metabolic flux analysis of Escherichia coli in glucose-limited continuous culture. I. Growth-rate-dependent metabolic efficiency at steady state. Microbiology 151: 693-706 (2005).
Kiefer P, Heinzle E, Wittmann C. Influence of glucose, fructose and sucrose as carbon sources on kinetics and stoichiometry of lysine production by Corynebacterium glutamicum. J. Ind. Microbiol. Biotechnol. 28: 338-343 (2002).
Kim BJ, Forbes NS. Flux analysis shows that hypoxia-inducible-factor-1-alpha minimally affects intracellular metabolism in tumor spheroids. Biotechnol. Bioeng. 96: 1167-1182 (2007).
Kleijn RJ, Geertman JM, Nfor BK, Ras C, Schipper D, Pronk JT, Heijnen JJ, van Maris AJ, van Winden WA. Metabolic flux analysis of a glycerol-overproducing Saccharomyces cerevisiae strain based on GC-MS, LC-MS and NMR-derived (13)C-labelling data. FEMS Yeast Res. 7: 216-231 (2007).
Kleijn RJ, Liu F, van Winden WA, van Gulik WM, Ras C, Heijnen JJ. Cytosolic NADPH metabolism in penicillin-G producing and non-producing chemostat cultures of Penicillium chrysogenum. Metab. Eng. 9: 112-123 (2007).
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).
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).
Kloosterman TG, Hendriksen WT, Bijlsma JJ, Bootsma HJ, van Hijum SA, Kok J, Hermans PW, Kuipers OP. Regulation of glutamine and glutamate metabolism by GlnR and GlnA in Streptococcus pneumoniae. J. Biol. Chem. 281: 25097-25109 (2006).
Kotakis C, Petropoulou Y, Stamatakis K, Yiotis C, Manetas Y. Evidence for active cyclic electron flow in twig chlorenchyma in the presence of an extremely deficient linear electron transport activity. Planta 225: 245-253 (2006).
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).
Kromer JO, Wittmann C, Schroder H, Heinzle E. Metabolic pathway analysis for rational design of L-methionine production by Escherichia coli and Corynebacterium glutamicum. Metab. Eng. 8: 353-369 (2006).
Krook J, Vreugdenhil D, Dijkema C, van der Plas LHW. Sucrose and starch metabolism in carrot (Daucus carota L.) cell suspensions analysed by C-13 labelling: indications for a cytosol and a plastid-localized oxidative pentose phosphate pathway. J. Exp. Bot. 49: 1917-1924 (1998).
Kruger NJ, von Schaewen A. The oxidative pentose phosphate pathway: structure and organisation. Curr. Opin. Plant Biol. 6: 236-246 (2003).
Kuchel PW, Philp DJ. Isotopomer subspaces as indicators of metabolic-pathway structure. J. Theor. Biol. 252: 391-401 (2008).
Kunnecke B, Seelig J. Glycogen-metabolism as detected by in vivo and in vitro C-13 NMR spectroscopy using [1,2-C-2(13)]glucose as substrate. Biochim. Biophys. Acta 1095: 103-113 (1991).
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).
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 K, Berthiaume F, Stephanopoulos GN, Yarmush DM, Yarmush ML. Metabolic flux analysis of postburn hepatic hypermetabolism. Metab. Eng. 2: 312-327 (2000).
Lee K, Berthiaume F, Stephanopoulos GN, Yarmush ML. Profiling of dynamic changes in hypermetabolic livers. Biotechnol. Bioeng. 83: 400-415 (2003).
Lee K, Berthiaume F, Stephanopoulos GN, Yarmush ML. Induction of a hypermetabolic state in cultured hepatocytes by glucagon and H2O2. Metab. Eng. 5: 221-229 (2003).
Lemuth K, Hardiman T, Winter S, Pfeiffer D, Keller MA, Lange S, Reuss M, Schmid RD, Siemann-Herzberg M. Global transcription and metabolic flux analysis of Escherichia coli in glucose-limited fed-batch cultivations. Appl. Environ. Microbiol. 74: 7002-7015 (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).
Lin YH, Bayrock D, Ingledew WM. Metabolic flux variation of Saccharomyces cerevisiae cultivated in a multistage continuous stirred tank reactor fermentation environment. Biotechnol. Prog. 17: 1055-1060 (2001).
Luo YE, Fan DD, Shang LA, Shi HJ, Ma XX, Mi Y, Zhao GF. Analysis of metabolic flux in Escherichia coli expressing human-like collagen in fed-batch culture. Biotechnol. Lett. 30: 637-643 (2008).
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).
Malaisse WJ. Modelling of isotopic discrimination in intact cells. Diabetes Res. 18: 31-43 (1991).
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).
Marino D, Gonzalez EM, Frendo P, Puppo A, Arrese-Igor C. NADPH recycling systems in oxidative stressed pea nodules: a key role for the NADP(+)-dependent isocitrate dehydrogenase. Planta 225: 413-421 (2007).
Martin F, Ramstedt M, Soderhall K. Carbon and nitrogen metabolism in ectomycorrhizal fungi and ectomycorrhizas. Biochimie 69: 569-581 (1987).
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).
Marx A, Eikmanns BJ, Sahm H, de Graaf AA, Eggeling L. Response of the central metabolism in Corynebacterium glutamicum to the use of an NADH-dependent glutamate dehydrogenase. Metab. Eng. 1: 35-48 (1999).
McKinlay JB, Shachar-Hill Y, Zeikus JG, Vieille C. Determining Actinobacillus succinogenes metabolic pathways and fluxes by NMR and GC-MS analyses of 13C-labeled metabolic product isotopomers. Metab. Eng. 9: 177-192 (2007).
Melendezhevia E, Waddell TG, Montero F. Optimization of metabolism: the evolution of metabolic pathways toward simplicity through the game of the pentose-phosphate cycle. J. Theor. Biol. 166: 201-219 (1994).
Menendez C, Bauer Z, Huber H, Gad'on N, Stetter KO, Fuchs G. Presence of acetyl coenzyme A (CoA) carboxylase and propionyl-CoA carboxylase in autotrophic Crenarchaeota and indication for operation of a 3-hydroxypropionate cycle in autotrophic carbon fixation. J. Bacteriol. 181: 1088-1098 (1999).
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).
Michels AK, Wedel N, Kroth PG. Diatom plastids possess a phosphoribulokinase with an altered regulation and no oxidative pentose phosphate pathway. Plant Physiol. 137: 911-920 (2005).
Mixson AJ, Phang JM. The uptake of pyrroline 5-carboxylate. Group translocation mediating the transfer of reducing-oxidizing potential. J. Biol. Chem. 263: 10720-10724 (1988).
Moller K, Christensen B, Forster J, Piskur J, Nielsen J, Olsson L. Aerobic glucose metabolism of Saccharomyces kluyveri: growth, metabolite production, and quantification of metabolic fluxes. Biotechnol. Bioeng. 77: 186-193 (2002).
Mollney M, Wiechert W, Kownatzki D, de Graaf AA. Bidirectional reaction steps in metabolic networks: IV. Optimal design of isotopomer labeling experiments. Biotechnol. Bioeng. 66: 86-103 (1999).
Moreira Dos Santos M, Raghevendran V, Kotter P, Olsson L, Nielsen J. Manipulation of malic enzyme in Saccharomyces cerevisiae for increasing NADPH production capacity aerobically in different cellular compartments. Metab. Eng. 6: 352-363 (2004).
Moritz B, Striegel K, de Graaf AA, Sahm H. Changes of pentose phosphate pathway flux in vivo in Corynebacterium glutamicum during leucine-limited batch cultivation as determined from intracellular metabolite concentration measurements. Metab. Eng. 4: 295-305 (2002).
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).
Nakayama Y, Matsushima R, Tomita M. Computer simulation of human erythrocyte using the E-cell system. Genome Informatics 10: 364-365 (1999).
Ni TC, Savageau MA. Application of biochemical systems theory to metabolism in human red blood cells. Signal propagation and accuracy of representation. J. Biol. Chem. 271: 7927-7941 (1996).
Niewiadomski P, Knappe S, Geimer S, Fischer K, Schulz B, Unte US, Rosso MG, Ache P, Flugge UI, Schneider A. The Arabidopsis plastidic glucose 6-phosphate/phosphate translocator GPT1 is essential for pollen maturation and embryo sac development. Plant Cell 17: 760-775 (2005).
Nissen TL, Schulze U, Nielsen J, Villadsen J. Flux distributions in anaerobic, glucose-limited continuous cultures of Saccharomyces cerevisiae. Microbiology 143: 203-218 (1997).
O'Fallon JV, Wright RW. Calculation of the pentose phosphate and Embden-Myerhoff pathways from a single incubation with [U-14C]- and [5-3H]glucose. Anal. Biochem. 162: 33-38 (1987).
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).
Oldiges M, Kunze M, Degenring D, Sprenger GA, Takors R. Stimulation, monitoring, and analysis of pathway dynamics by metabolic profiling in the aromatic amino acid pathway. Biotechnol. Prog. 20: 1623-1633 (2004).
Oracz K, El-Maarouf-Bouteau H, Bogatek R, Corbineau F, Bailly C. Release of sunflower seed dormancy by cyanide: cross-talk with ethylene signalling pathway. J. Exp. Bot. 59: 2241-2251 (2008).
Pandolfi PP, Sonati F, Rivi R, Mason P, Grosveld F, Luzzatto L. Targeted disruption of the housekeeping gene encoding glucose-6-phosphate-dehydrogenase (G6PD) - G6PD is dispensable for pentose synthesis but essential for defense against oxidative stress. EMBO J. 14: 5209-5215 (1995).
Park SM, Sinskey AJ, Stephanopoulos G. Metabolic and physiological studies of Corynebacterium glutamicum mutants. Biotechnol. Bioeng. 55: 864-879 (1997).
Pedersen H, Carlsen M, Nielsen J. Identification of enzymes and quantification of metabolic fluxes in the wild type and in a recombinant Aspergillus oryzae strain. Appl. Environ. Microbiol. 65: 11-19 (1999).
Pedersen H, Christensen B, Hjort C, Nielsen J. Construction and characterization of an oxalic acid nonproducing strain of Aspergillus niger. Metab. Eng. 2: 34-41 (2000).
Pereto JG, Velasco AM, Becerra A, Lazcano A. Comparative biochemistry of CO2 fixation and the evolution of autotrophy. Int. Microbiol. 2: 3-10 (1999).
Perez-Ruiz JM, Spinola MC, Kirchsteiger K, Moreno J, Sahrawy M, Cejudo FJ. Rice NTRC is a high-efficiency redox system for chloroplast protection against oxidative damage. Plant Cell 18: 2356-2368 (2006).
Peterhansel C, Niessen M, Kebeish RM. Metabolic engineering towards the enhancement of photosynthesis. Photochem. Photobiol. 84: 1317-1323 (2008).
Pfeffer PE, Douds Jr DD, Becard G, Shachar-Hill Y. Carbon uptake and the metabolism and transport of lipids in an arbuscular mycorrhiza. Plant Physiol. 120: 587-598 (1999).
Pfefferle W, Mockel B, Bathe B, Marx A. Biotechnological manufacture of lysine. Adv. Biochem. Eng. Biotechnol. 79: 59-112 (2003).
Phang JM, Downing SJ, Yeh GC, Smith RJ, Williams JA, Hagedorn CH. Stimulation of the hexosemonophosphate-pentose pathway by pyrroline-5-carboxylate in cultured cells. J. Cell Physiol. 110: 255-261 (1982).
Pleite R, Pike MJ, Garces R, Martinez-Force E, Rawsthorne S. The sources of carbon and reducing power for fatty acid synthesis in the heterotrophic plastids of developing sunflower (Helianthus annuus L.) embryos. J. Exp. Bot. 56: 1297-1303 (2005).
Ponce E, Martinez A, Bolivar F, Valle F. Stimulation of glucose catabolism through the pentose pathway by the absence of the two pyruvate kinase isoenzymes in Escherichia coli. Biotechnol. Bioeng. 58: 292-295 (1998).
Poolman MG, Fell DA, Raines CA. Elementary modes analysis of photosynthate metabolism in the chloroplast stroma. Eur. J. Biochem. 270: 430-439 (2003).
Portais JC, Tavernier P, Gosselin I, Barbotin JN. Cyclic organization of the carbohydrate metabolism in Sinorhizobium meliloti. Eur. J. Biochem. 265: 473-480 (1999).
R Poulsen B, Nohr J, Douthwaite S, Hansen LV, Iversen JJ, Visser J, Ruijter GJ. Increased NADPH concentration obtained by metabolic engineering of the pentose phosphate pathway in Aspergillus niger. FEBS J. 272: 1313-1325 (2005).
Rager MN, Binet MR, Bouvet OM. 31P and 13C nuclear magnetic resonance studies of metabolic pathways in Pasteurella multocida characterization of a new mannitol-producing metabolic pathway. Eur. J. Biochem. 263: 695-701 (1999).
Rahman M, Shimizu K. Altered acetate metabolism and biomass production in several Escherichia coli mutants lacking rpoS-dependent metabolic pathway genes. Mol. Biosyst. 4: 160-169 (2008).
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).
Rizhsky L, Hallak-Herr E, Van Breusegem F, Rachmilevitch S, Barr JE, Rodermel S, Inze D, Mittler R. Double antisense plants lacking ascorbate peroxidase and catalase are less sensitive to oxidative stress than single antisense plants lacking ascorbate peroxidase or catalase. Plant J. 32: 329-342 (2002).
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).
Roberts JKM. NMR adventures in the metabolic labyrinth within plants. Trends Plant Sci. 5: 30-34 (2000).
Roscher A, Kruger NJ, Ratcliffe RG. Strategies for metabolic flux analysis in plants using isotope labelling. J. Biotechnol. 77: 81-102 (2000).
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).
Sahm H, Eggeling L, de Graaf AA. Pathway analysis and metabolic engineering in Corynebacterium glutamicum. Biol. Chem. 381: 899-910 (2000).
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).
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).
Savitch LV, Barker-Astrom J, Ivanov AG, Hurry V, Oquist G, Huner NP, Gardestrom P. Cold acclimation of Arabidopsis thaliana results in incomplete recovery of photosynthetic capacity, associated with an increased reduction of the chloroplast stroma. Planta 214: 295-303 (2001).
Schaaff-Gerstenschlager I, Zimmermann FK. Pentose-phosphate pathway in Saccharomyces cerevisiae: analysis of deletion mutants for transketolase, transaldolase, and glucose 6-phosphate dehydrogenase. Curr. Genet. 24: 373-376 (1993).
Scharte J, SchonH, Weis E. Photosynthesis and carbohydrate metabolism in tobacco leaves during an incompatible interaction with Phytophthora nicotianae. Plant Cell Environ. 28: 1421-1435 (2005).
Scheibe R. Malate valves to balance cellular energy supply. Physiol. Plant. 120: 21-26 (2004).
Schmidt K, Carlsen M, Nielsen J, Villadsen J. Modeling isotopomer distributions in biochemical networks using isotopomer mapping matrices. Biotechnol. Bioeng. 55: 831-840 (1997).
Schmidt K, Carlsen M, Nielsen J, Villadsen J. Modeling isotopomer distributions in biochemical networks using isotopomer mapping matrices. Biotechnol. Bioeng. 55: 831-840 (1997).
Schmidt K, Marx A, de Graaf AA, Wiechert W, Sahm H, Nielsen J, Villadsen J. 13C tracer experiments and metabolite balancing for metabolic flux analysis: comparing two approaches. Biotechnol. Bioeng. 58: 254-257 (1998).
Schmidt K, Nielsen J, Villadsen J. Quantitative analysis of metabolic fluxes in Escherichia coli, using two-dimensional NMR spectroscopy and complete isotopomer models. J. Biotechnol. 71: 175-189 (1999).
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).
Schrader MC, Eskey CJ, Simplaceanu V, Ho C. A carbon-13 nuclear magnetic resonance investigation of the metabolic fluxes associated with glucose metabolism in human erythrocytes. Biochim. Biophys. Acta 1182: 162-178 (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).
Schwender J, Ohlrogge J, Shachar-Hill Y. Understanding flux in plant metabolic networks. Curr. Opin. Plant Biol. 7: 309-317 (2004).
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).
Shanmuganathan A, Avery SV, Willetts SA, Houghton JE. Copper-induced oxidative stress in Saccharomyces cerevisiae targets enzymes of the glycolytic pathway. FEBS Lett. 556: 253-259 (2004).
Sharples SC, Fry SC. Radioisotope ratios discriminate between competing pathways of cell wall polysaccharide and RNA biosynthesis in living plant cells. Plant J. 52: 252-262 (2007).
Shen ZW, Fisinger U, Poulev A, Eisenreich W, Werner I, Pleiner E, Bacher A, Zenk MH. Tracer studies with C-13-labeled carbohydrates in cultured plant cells. Retrobiosynthetic analysis of chelidonic acid biosynthesis. Phytochemistry 57: 33-42 (2001).
Shi H, Nikawa J, Shimizu K. Effect of modifying metabolic network on poly-3-hydroxybutyrate biosynthesis in recombinant Escherichia coli. J. Biosci. Bioeng. 87: 666-677 (1999).
Sprenger GA. Genetics of pentose-phosphate pathway enzymes of Escherichia coli K-12. Arch. Microbiol. 164: 324-330 (1995).
Sriram G, Fulton DB, Iyer VV, Peterson JM, Zhou R, Westgate ME, Spalding MH, Shanks JV. Quantification of compartmented metabolic fluxes in developing soybean embryos by employing biosynthetically directed fractional 13C labeling, two-dimensional [13C, 1H] nuclear magnetic resonance, and comprehensive isotopomer balancing. Plant Physiol. 136: 3043-3057 (2004).
Sriram G, Fulton DB, Shanks JV. Flux quantification in central carbon metabolism of Catharanthus roseus hairy roots by (13)C labeling and comprehensive bondomer balancing. Phytochemistry 68: 2243-2257 (2007).
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).
Stitt M, Krapp A. The interaction between elevated carbon dioxide and nitrogen nutrition: the physiological and molecular background. Plant Cell Environ. 22: 583-621 (1999).
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).
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).
Tamoi M, Miyazaki T, Fukamizo T, Shigeoka S. The Calvin cycle in cyanobacteria is regulated by CP12 via the NAD(H)/NADP(H) ratio under light/dark conditions. Plant J. 42: 504-513 (2005).
Tang Y, Pingitore F, Mukhopadhyay A, Phan R, Hazen TC, Keasling JD. Pathway confirmation and flux analysis of central metabolic pathways in Desulfovibrio vulgaris Hildenborough using GC-MS and FT-ICR mass spectrometry. J. Bacteriol. 189: 940-949 (2007).
Tang YJ, Hwang JS, Wemmer DE, Keasling JD. The Shewanella oneidensis MR-1 fluxome under various oxygen conditions. Appl. Environ. Microbiol. 73: 718-729 (2007).
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).
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).
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).
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).
Thom E, Neuhaus HE. Oxidation of imported or endogenous carbohydrates by isolated chloroplasts from green pepper fruits. Plant Physiol. 109: 1421-1426 (1995).
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).
Vallino JJ, Stephanopoulos G. Metabolic flux distributions in Corynebacterium glutamicum during growth and lysine overproduction. Biotechnol. Bioeng. 67: 872-885 (2000).
van Winden W, Verheijen P, Heijnen S. Possible pitfalls of flux calculations based on 13C-labeling. Metab. Eng. 3: 151-162 (2001).
Van Winden WA, Heijnen JJ, Verheijen PJ. Cumulative bondomers: A new concept in flux analysis from 2D [13C,1H] COSY NMR data. Biotechnol. Bioeng. 80: 731-745 (2002).
van Winden WA, van Dam JC, Ras C, Kleijn RJ, Vinke JL, van Gulik WM, Heijnen JJ. Metabolic-flux analysis of Saccharomyces cerevisiae CEN.PK113-7D based on mass isotopomer measurements of (13)C-labeled primary metabolites. FEMS Yeast Res. 5: 559-568 (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).
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).
Viola R, Davies HV, Chudeck AR. Pathways of starch and sucrose biosynthesis in developing tubers of potato (Solanum tuberosum L.) and seeds of faba bean (Vicia faba L.) : elucidation by C-13 nuclear magnetic resonance spectroscopy. Planta 183: 202-208 (1991).
Voss I, Koelmann M, Wojtera J, Holtgrefe S, Kitzmann C, Backhausen JE, Scheibe R. Knockout of major leaf ferredoxin reveals new redox-regulatory adaptations in Arabidopsis thaliana. Physiol. Plant. 133: 584-598 (2008).
Wahl SA, Takors R, Wiechert W. Interpretation of metabolic flux maps by limitation potentials and constrained limitation sensitivities. Biotechnol. Bioeng. 94: 263-272 (2006).
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).
Wahlbom CF, Hahn-Hagerdal B. Furfural, 5-hydroxymethyl furfural, and acetoin act as external electron acceptors during anaerobic fermentation of xylose in recombinant Saccharomyces cerevisiae. Biotechnol. Bioeng. 78: 172-178 (2002).
Wakao S, Benning C. Genome-wide analysis of glucose-6-phosphate dehydrogenases in Arabidopsis. Plant J. 41: 243-256 (2005).
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 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).
Weber A, Flugge UI. Interaction of cytosolic and plastidic nitrogen metabolism in plants. J. Exp. Bot. 53: 865-874 (2002).
Weber AP. Solute transporters as connecting elements between cytosol and plastid stroma. Curr. Opin. Plant Biol. 7: 247-253 (2004).
Weger HG, Espie GS. Ferric reduction by iron-limited Chlamydomonas cells interacts with both photosynthesis and respiration. Planta 210: 775-781 (2000).
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).
Wiechert W, de Graaf AA. Bidirectional reaction steps in metabolic networks. 1. Modeling and simulation of carbon isotope labeling experiments. Biotechnol. Bioeng. 55: 101-117 (1997).
Willige BC, Kutzer M, Tebartz F, Bartels D. Subcellular localization and enzymatic properties of differentially expressed transketolase genes isolated from the desiccation tolerant resurrection plant Craterostigma plantagineum. Planta 229: 659-666 (2009).
Wittmann C, Heinzle E. Application of MALDI-TOF MS to lysine-producing Corynebacterium glutamicum: a novel approach for metabolic flux analysis. Eur. J. Biochem. 268: 2441-2455 (2001).
Wittmann C, Heinzle E. Mass spectrometry for metabolic flux analysis. Biotechnol. Bioeng. 62: 739-750 (1999).
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, Heinzle E. Genealogy profiling through strain improvement by using metabolic network analysis: metabolic flux genealogy of several generations of lysine-producing Corynebacteria. Appl. Environ. Microbiol. 68: 5843-59 (2002).
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).
Woodrow IE, Murphy DJ, Walker DA. Regulation of photosynthetic carbon metabolism. The effect of inorganic phosphate on stromal sedoheptulose-1,7-bisphosphatase. Eur. J. Biochem. 132: 121-123 (1983).
Xiong Y, DeFraia C, Williams D, Zhang X, Mou Z. Characterization of Arabidopsis 6-phosphogluconolactonase T-DNA insertion mutants reveals an essential role for the oxidative section of the plastidic pentose phosphate pathway in plant growth and development. Plant Cell Physiol. 50: 1277-1291 (2009).
Yallop CA, Norby PL, Jensen R, Reinbach H, Svendsen I. Characterisation of G418-induced metabolic load in recombinant CHO and BHK cells: effect on the activity and expression of central metabolic enzymes. Cytotechnology 42: 87-99 (2003).
Yang C, Hua Q, Shimizu K. Energetics and carbon metabolism during growth of microalgal cells under photoautotrophic, mixotrophic and cyclic light-autotrophic/dark-heterotrophic conditions. Biochem. Eng. J. 6: 87-102 (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).
Yeh GC, Phang JM. Stimulation of phosphoribosyl pyrophosphate and purine nucleotide production by pyrroline 5-carboxylate in human erythrocytes. J. Biol. Chem. 263: 13083-13089 (1988).
Yeh GC, Phang JM. Pyrroline-5-carboxylate stimulates the conversion of purine antimetabolites to their nucleotide forms by a redox-dependent mechanism. J. Biol. Chem. 258: 9774-9779 (1983).
Yeh GC, Roth EF Jr, Phang JM, Harris SC, Nagel RL, Rinaldi A. The effect of pyrroline-5-carboxylic acid on nucleotide metabolism in erythrocytes from normal and glucose-6-phosphate dehydrogenase-deficient subjects. J. Biol. Chem. 259: 5454-5458 (1984).
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).
Zhao J, Baba T, Mori H, Shimizu K. Effect of zwf gene knockout on the metabolism of Escherichia coli grown on glucose or acetate. Metab. Eng. 6: 164-174 (2004).
Zhao Z, Kuijvenhoven K, Ras C, van Gulik WM, Heijnen JJ, Verheijen PJ, van Winden WA. Isotopic non-stationary 13C gluconate tracer method for accurate determination of the pentose phosphate pathway split-ratio in Penicillium chrysogenum. Metab. Eng. 10: 178-186 (2008).
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).
Number of references = 265
| PubMed Search | Entrez Protein Search | ISI Web of Knowledge Search | Scirus Search |
|