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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, isocitrate dehydrogenase

Abell LM, Schloss JV. Oxygenase side reactions of acetolactate synthase and other carbanion-forming enzymes. Biochemistry 30: 7883-7887 (1991).

Abiko T, Obara M, Ushioda A, Hayakawa T, Hodges M, Yamaya T. Localization of NAD-isocitrate dehydrogenase and glutamate dehydrogenase in rice roots: candidates for providing carbon skeletons to NADH-glutamate synthase. Plant Cell Physiol. 46: 1724-1734 (2005).

Anderson SL, Schirf V, McAlister-Henn L. Effect of AMP on mRNA binding by yeast NAD(+)-specific isocitrate dehydrogenase. Biochemistry 41: 7065-7073 (2002).

Anoop VM, Basu U, McCammon MT, McAlister-Henn L, Taylor GJ. Modulation of citrate metabolism alters aluminum tolerance in yeast and transgenic canola overexpressing a mitochondrial citrate synthase. Plant Physiol. 132: 2205-2217 (2003).

Appenroth KJ, Teller S. Are NADP-dependent isocitrate dehydrogenases and ferredoxin-dependent glutamate synthase co-regulated by the same photoreceptors? Planta 218: 775-783 (2004).

Baev MV, Kiriukhin MY, Tsygankov YD. Regulation of ammonia assimilation in an obligate methylotroph Methylobacillus flagellatum under steady-state and transient growth conditions. Antonie Van Leeuwenhoek 71: 353-361 (1997).

Barel I, MacDonald DW. Enzyme defects in glutamate-requiring strains of Schizosaccharomyces pombe. FEMS Microbiol. Lett. 113: 267-272 (1993).

Behal RH, Oliver DJ. NAD(+)-dependent isocitrate dehydrogenase from Arabidopsis thaliana. Characterization of two closely related subunits. Plant Mol. Biol. 36: 691-698 (1998).

Bendt AK, Burkovski A, Schaffer S, Bott M, Farwick M, Hermann T. Towards a phosphoproteome map of Corynebacterium glutamicum. Proteomics 3: 1637-1646 (2003).

Boiffin V, Hodges M, Galvez S, Balestrini R, Bonfante P, Gadal P, Martin F. Eucalypt NADP-dependent isocitrate dehydrogenase. cDNA cloning and expression in ectomycorrhizae. Plant Physiol. 117: 939-948 (1998).

Bykova NV, Keerberg O, Parnik T, Bauwe H, Gardestrom P. Interaction between photorespiration and respiration in transgenic potato plants with antisense reduction in glycine decarboxylase. Planta 222: 130-140 (2005).

Canas RA, Villalobos DP, Diaz-Moreno SM, Canovas FM, Canton FR. Molecular and functional analyses support a role of ornithine-delta-aminotransferase in the provision of glutamate for glutamine biosynthesis during pine germination. Plant Physiol. 148: 77-88 (2008).

Canovas M, Bernal V, Sevilla A, Iborra JL. Salt stress effects on the central and carnitine metabolisms of Escherichia coli. Biotechnol. Bioeng. 96: 722-737 (2007).

Canovas M, Bernal V, Torroglosa T, Ramirez JL, Iborra JL. Link between primary and secondary metabolism in the biotransformation of trimethylammonium compounds by Escherichia coli. Biotechnol. Bioeng. 84: 686-699 (2003).

Canovas M, Sevilla A, Bernal V, Leal R, Iborra JL. Role of energetic coenzyme pools in the production of L-carnitine by Escherichia coli. Metab. Eng. 8: 603-618 (2006).

Cao B, Loh KC. Catabolic pathways and cellular responses of Pseudomonas putida P8 during growth on benzoate with a proteomics approach. Biotechnol. Bioeng. 101: 1297-1312 (2008).

Chaffei C, Suzuki A, Masclaux-Daubresse C, Ghorbel MH, Gouia H. Implication of glutamate, isocitrate and malate deshydrogenases in nitrogen assimilation in the cadmium-stressed tomato. C. R. Biol. 329: 790-803 (2006).

Chao G, Shen J, Tseng CP, Park SJ, Gunsalus RP. Aerobic regulation of isocitrate dehydrogenase gene (icd) expression in Escherichia coli by the arcA and fnr gene products. J. Bacteriol. 179: 4299-4304 (1997).

Chen R. Plant NADP-dependent isocitrate dehydrogenases are predominantly localized in the cytosol. Planta 207: 280-285(1998).

Corpas FJ, Barroso JB, Sandalio LM, Palma JM, Lupianez JA, del Rio LA. Peroxisomal NADP-dependent isocitrate dehydrogenase. Characterization and activity regulation during natural senescence. Plant Physiol. 121: 921-928 (1999).

Cvitkovitch DG, Gutierrez JA, Bleiweis AS. Role of the citrate pathway in glutamate biosynthesis by Streptococcus mutans. J. Bacteriol. 179: 650-655 (1997).

del Rio LA, Corpas FJ, Sandalio LM, Palma JM, Gomez M, Barroso JB. Reactive oxygen species, antioxidant systems and nitric oxide in peroxisomes. J. Exp. Bot. 53: 1255-1272 (2002).

Des Rosiers C, Di Donato L, Comte B, Laplante A, Marcoux C, David F, Fernandez CA, Brunengraber H. Isotopomer analysis of citric acid cycle and gluconeogenesis in rat liver. Reversibility of isocitrate dehydrogenase and involvement of ATP-citrate lyase in gluconeogenesis. J. Biol. Chem. 270: 10027-10036 (1995).

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).

Dominguez MJ, Gutierrez F, Leon R, Vilchez C, Vega JM, Vigara J. Cadmium increases the activity levels of glutamate dehydrogenase and cysteine synthase in Chlamydomonas reinhardtii. Plant Physiol. Biochem. 41: 828-832 (2003).

Dong DF, Peng XX, Yan XL. Organic acid exudation induced by phosphorus deficiency and/or aluminium toxicity in two contrasting soybean genotypes. Physiol. Plant. 122: 190-199 (2004).

Dubois F, Terce-Laforgue T, Gonzalez-Moro MB, Estavillo JM, Sangwan R, Gallais A, Hirel B. Glutamate dehydrogenase in plants: is there a new story for an old enzyme? Plant Physiol. Biochem. 41: 565-576 (2003).

Dutilleul C, Lelarge C, Prioul JL, De Paepe R, Foyer CH, Noctor G. Mitochondria-driven changes in leaf NAD status exert a crucial influence on the control of nitrate assimilation and the integration of carbon and nitrogen metabolism. Plant Physiol. 139: 64-78 (2005).

Eckardt NA. Peroxisomal citrate synthase provides exit route from fatty acid metabolism in oilseeds. Plant Cell 17: 1863-1865 (2005).

el-Mansi EM, Dawson GC, Bryce CF. Steady-state modelling of metabolic flux between the tricarboxylic acid cycle and the glyoxylate bypass in Escherichia coli. Comput. Appl. Biosci. 10: 295-299 (1994).

Falk KL, Behal RH, Xiang C, Oliver DJ. Metabolic bypass of the tricarboxylic acid cycle during lipid mobilization in germinating oilseeds. Regulation of NAD+-dependent isocitrate dehydrogenase versus fumarase. Plant Physiol. 117: 473-481 (1998).

Fernandez CA, Des Rosiers C. Modeling of liver citric acid cycle and gluconeogenesis based on 13C mass isotopomer distribution analysis of intermediates. J. Biol. Chem. 270: 10037-10042 (1995).

Ferrario-Mery S, Hodges M, Hirel B, Foyer CH. Photorespiration-dependent increases in phosphoenolpyruvate carboxylase, isocitrate dehydrogenase and glutamate dehydrogenase in transformed tobacco plants deficient in ferredoxin-dependent glutamine-alpha-ketoglutarate aminotransferase. Planta 214: 877-886 (2002).

Ferrario-Mery S, Hodges M, Hirel B, Foyer CH. Photorespiration-dependent increases in phosphoenolpyruvate carboxylase, isocitrate dehydrogenase and glutamate dehydrogenase in transformed tobacco plants deficient in ferredoxin-dependent glutamine-alpha-ketoglutarate aminotransferase. Planta 214: 974 (2002).

Fieuw S, Muller-Rober B, Galvez S, Willmitzer L. Cloning and expression analysis of the cytosolic NADP(+)-dependent isocitrate dehydrogenase from potato. Implications for nitrogen metabolism. Plant Physiol. 107: 905-913 (1995).

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

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).

Galvez S, Lancien M, Hodges M. Are isocitrate dehydrogenases and 2-oxoglutarate involved in the regulation of glutamate synthesis? Trends Plant Sci. 4: 484-490 (1999).

Glevarec G, Bouton S, Jaspard E, Riou MT, Cliquet JB, Suzuki A, Limami AM. Respective roles of the glutamine synthetase/glutamate synthase cycle and glutamate dehydrogenase in ammonium and amino acid metabolism during germination and post-germinative growth in the model legume Medicago truncatula. Planta 219: 286-297 (2004).

Gonzalez EM, Galvez L, Arrese-Igor C. Abscisic acid induces a decline in nitrogen fixation that involves leghaemoglobin, but is independent of sucrose synthase activity. J. Exp. Bot. 52: 285-293 (2001).

Hanning I, Heldt HW. On the function of mitochondrial metabolism during photosynthesis in spinach (Spinacia oleracea L.) leaves. Partitioning between respiration and export of redox equivalents and precursors for nitrate assimilation products. Plant Physiol. 103: 1147-1154 (1993).

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).

Hausler RE, Rademacher T, Li J, Lipka V, Fischer KL, Schubert S, Kreuzaler F, Hirsch HJ. Single and double overexpression of C4-cycle genes had differential effects on the pattern of endogenous enzymes, attenuation of photorespiration and on contents of UV protectants in transgenic potato and tobacco plants. J. Exp. Bot. 52: 1785-1803 (2001).

Hayakawa T, Yamaya T, Mae T, Ojima K. Changes in the content of two glutamate synthase proteins in spikelets of rice (Oryza sativa) plants during ripening. Plant Physiol. 101: 1257-1262 (1993).

Hayes JE, Ma JF. Al-induced efflux of organic acid anions is poorly associated with internal organic acid metabolism in triticale roots. J. Exp. Bot. 54: 1753-1759 (2003).

Hodges M. Enzyme redundancy and the importance of 2-oxoglutarate in plant ammonium assimilation. J. Exp. Bot. 53: 905-916 (2002).

Howell DM, Graupner M, Xu H, White RH. Identification of enzymes homologous to isocitrate dehydrogenase that are involved in coenzyme B and leucine biosynthesis in methanoarchaea. J. Bacteriol. 182: 5013-5016 (2000).

Hurley JH, Chen R, Dean AM. Determinants of cofactor specificity in isocitrate dehydrogenase: structure of an engineered NADP+ --> NAD+ specificity-reversal mutant. Biochemistry 35: 5670-5678 (1996).

Imada K, Inagaki K, Matsunami H, Kawaguchi H, Tanaka H, Tanaka N, Namba K. Structure of 3-isopropylmalate dehydrogenase in complex with 3-isopropylmalate at 2.0 A resolution: the role of Glu88 in the unique substrate-recognition mechanism. Structure 6: 971-982 (1998).

Jin T, Huppe HC, Turpin DH. In vitro reconstitution of electron transport from glucose-6-phosphate and NADPH to nitrite. Plant Physiol. 117: 303-309 (1998).

Kanao T, Kawamura M, Fukui T, Atomi H, Imanaka T. Characterization of isocitrate dehydrogenase from the green sulfur bacterium Chlorobium limicola. A carbon dioxide-fixing enzyme in the reductive tricarboxylic acid cycle. Eur. J. Biochem. 269: 1926-1931 (2002).

Karr DB, Emerich DW. Bradyrhizobium japonicum isocitrate dehydrogenase exhibits calcium-dependent hysteresis. Arch. Biochem. Biophys. 376: 101-108 (2000).

Lancien M, Ferrario-Mery S, Roux Y, Bismuth E, Masclaux C, Hirel B, Gadal P, Hodges M. Simultaneous expression of NAD-dependent isocitrate dehydrogenase and other Krebs cycle genes after nitrate resupply to short-term nitrogen-starved tobacco. Plant Physiol. 120: 717-726 (1999).

Lancien M, Gadal P, Hodges M. Molecular characterization of higher plant NAD-dependent isocitrate dehydrogenase: evidence for a heteromeric structure by the complementation of yeast mutants. Plant J. 16: 325-333 (1998).

Lemaitre T, Urbanczyk-Wochniak E, Flesch V, Bismuth E, Fernie AR, Hodges M. NAD-dependent isocitrate dehydrogenase mutants of Arabidopsis suggest the enzyme is not limiting for nitrogen assimilation. Plant Physiol. 144: 1546-1558 (2007).

Li XF, Ma JF, Matsumoto H. Pattern of aluminum-induced secretion of organic acids differs between rye and wheat. Plant Physiol. 123: 1537-1544 (2000).

Liang A, Houghton RL. Coregulation of oxidized nicotinamide adenine dinucleotide (phosphate) transhydrogenase and glutamate dehydrogenase activities in enteric bacteria during nitrogen limitation. J. Bacteriol. 146: 997-1002 (1981).

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 J, Qian J, Greenbaum D, Bertone P, Das R, Echols N, Senes A, Stenger B, Gerstein M. GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing. Nucleic Acids Res. 30: 4574-4582 (2002).

Lu BB, Yuan YZ, Zhang CF, Ou JQ, Zhou W, Lin QH. Modulation of key enzymes involved in ammonium assimilation and carbon metabolism by low temperature in rice (Oryza sativa L.) roots. Plant Sci. 169: 295-302 (2005).

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).

MacDonald RC, Kimmerer TW. Metabolism of transpired ethanol by eastern cottonwood (Populus deltoides Bartr.). Plant Physiol. 102: 173-179 (1993).

Marino D, Frendo P, Ladrera R, Zabalza A, Puppo A, Arrese-Igor C, Gonzalez EM. Nitrogen fixation control under drought stress. Localized or systemic? Plant Physiol. 143: 1968-1974 (2007).

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-Figueroa E, Navarro F, Florencio FJ. The GS-GOGAT pathway is not operative in the heterocysts. Cloning and expression of glsF gene from the cyanobacterium Anabaena sp. PCC 7120. FEBS Lett. 476: 282-286 (2000).

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

Mateos RM, Bonilla-Valverde D, del Río LA, Palma JM, Corpas FJ. NADP-dehydrogenases from pepper fruits: effect of maturation. Physiol. Plant. 135: 130-139 (2009).

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McCluskey J, Herdman L, Skene KR. Iron deficiency induces changes in metabolism of citrate in lateral roots and cluster roots of Lupinus albus. Physiol. Plant. 121: 586-594 (2004).

Meijer S, Otero J, Olivares R, Andersen MR, Olsson L, Nielsen J. Overexpression of isocitrate lyase-glyoxylate bypass influence on metabolism in Aspergillus niger. Metab. Eng. 11: 107-116 (2009).

Mittal M, Picossi S, Sonenshein AL. CcpC-dependent regulation of citrate synthase gene expression in Listeria monocytogenes. J. Bacteriol. 191: 862-872 (2009).

Miyazaki J, Asada K, Fushinobu S, Kuzuyama T, Nishiyama M. Crystal structure of tetrameric homoisocitrate dehydrogenase from an extreme thermophile, Thermus thermophilus: involvement of hydrophobic dimer-dimer interaction in extremely high thermotolerance. J. Bacteriol. 187: 6779-6788 (2005).

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Number of references = 120

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Last Update: 10/01/09