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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, metabolic and profiling

Aharoni A, Vorst O. DNA microarrays for functional plant genomics. Plant Mol. Biol. 48: 99-118 (2002).

Anterola AM, Jeon JH, Davin LB, Lewis NG. Transcriptional control of monolignol biosynthesis in Pinus taeda - Factors affecting monolignol ratios and carbon allocation in phenylpropanoid metabolism. J. Biol. Chem. 277: 18272-18280 (2002).

Anterola AM, Lewis NG. Trends in lignin modification: a comprehensive analysis of the effects of genetic manipulations/mutations on lignification and vascular integrity. Phytochemistry 61: 221-294 (2002).

Aranibar N, Singh BK, Stockton GW, Ott KH. Automated mode-of-action detection by metabolic profiling. Biochem. Biophys. Res. Commun. 286: 150-155 (2001).

Barr J, White WS, Chen L, Bae H, Rodermel S. The GHOST terminal oxidase regulates developmental programming in tomato fruit. Plant Cell Environ. 27: 840-852 (2004).

Barsch A, Carvalho HG, Cullimore JV, Niehaus K. GC-MS based metabolite profiling implies three interdependent ways of ammonium assimilation in Medicago truncatula root nodules. J. Biotechnol. 127: 79-83 (2006).

Baxter CJ, Carrari F, Bauke A, Overy S, Hill SA, Quick PW, Fernie AR, Sweetlove LJ. Fruit carbohydrate metabolism in an introgression line of tomato with increased fruit soluble solids. Plant Cell Physiol. 46: 425-437 (2005).

Becker SA, Palsson BO. Context-specific metabolic networks are consistent with experiments. PLoS Comput. Biol. 4: e1000082 (2008).

Behrends V, Ebbels TM, Williams HD, Bundy JG. Time-resolved metabolic footprinting for nonlinear modeling of bacterial substrate utilization. Appl. Environ. Microbiol. 75: 2453-2463 (2009).

Bell CJ, Dixon RA, Farmer AD, Flores R, Inman J, Gonzales RA, Harrison MJ, Paiva NL, Scott AD, Weller JW, May GD. The Medicago Genome Initiative: a model legume database. Nuc. Acids Res. 29: 114-117 (2001).

Ben Zvi MM, Negre-Zakharov F, Masci T, Ovadis M, Shklarman E, Ben-Meir H, Tzfira T, Dudareva N, Vainstein A. Interlinking showy traits: co-engineering of scent and colour biosynthesis in flowers. Plant Biotechnol. J. 6: 403-415 (2008).

Bermudez L, Urias U, Milstein D, Kamenetzky L, Asis R, Fernie AR, Van Sluys MA, Carrari F, Rossi M. A candidate gene survey of quantitative trait loci affecting chemical composition in tomato fruit. J. Exp. Bot. 59: 2875-2890 (2008).

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).

Bligny R, Douce R. NMR and plant metabolism. Curr. Opin. Plant Biol. 4: 191-196 (2001).

Bollard ME, Xu J, Purcell W, Griffin JL, Quirk C, Holmes E, Nicholson JK. Metabolic profiling of the effects of D-galactosamine in liver spheroids using (1)H NMR and MAS-NMR spectroscopy. Chem. Res. Toxicol. 15: 1351-1359 (2002).

Bolling C, Fiehn O. Metabolite profiling of Chlamydomonas reinhardtii under nutrient deprivation. Plant Physiol. 139: 1995-2005 (2005).

Boros LG, Cascante M, Paul Lee WN. Metabolic profiling of cell growth and death in cancer: applications in drug discovery. Drug Discov. Today 7: 364-372 (2002).

Boudet AM. Evolution and current status of research in phenolic compounds. Phytochemistry 68: 2722-2735 (2007).

Boyer JS, Westgate ME. Grain yields with limited water. J. Exp. Bot. 55: 2385-2394 (2004).

Boyes DC, Zayed AM, Ascenzi R, McCaskill AJ, Hoffman NE, Davis KR, Gorlach J. Growth stage-based phenotypic analysis of Arabidopsis: a model for high throughput functional genomics in plants. Plant Cell 13: 1499-1510 (2001).

Branco-Price C, Kaiser KA, Jang CJ, Larive CK, Bailey-Serres J. Selective mRNA translation coordinates energetic and metabolic adjustments to cellular oxygen deprivation and reoxygenation in Arabidopsis thaliana. Plant J. 56: 743-755 (2008).

Brand MD, Curtis RK. Simplifying metabolic complexity. Biochem. Soc. Trans. 30: 25-30 (2002).

Brenner WG, Romanov GA, Kollmer I, Burkle L, Schmulling T. Immediate-early and delayed cytokinin response genes of Arabidopsis thaliana identified by genome-wide expression profiling reveal novel cytokinin-sensitive processes and suggest cytokinin action through transcriptional cascades. Plant J. 44: 314-333 (2005).

Bro C, Nielsen J. Impact of 'ome' analyses on inverse metabolic engineering. Metab. Eng. 6: 204-211 (2004).

Broeckling CD, Huhman DV, Farag MA, Smith JT, May GD, Mendes P, Dixon RA, Sumner LW. Metabolic profiling of Medicago truncatula cell cultures reveals the effects of biotic and abiotic elicitors on metabolism. J. Exp. Bot. 56: 323-336 (2005).

Bruce W, Folkerts O, Garnaat C, Crasta O, Roth B, Bowen B. Expression profiling of the maize flavonoid pathway genes controlled by estradiol-inducible transcription factors CRC and P. Plant Cell 12: 65-80 (2000).

Brusa T, Borin S, Ferrari F, Sorlini C, Corselli C, Daffonchio D. Aromatic hydrocarbon degradation patterns and catechol 2,3-dioxygenase genes in microbial cultures from deep anoxic hypersaline lakes in the eastern Mediterranean sea. Microbiol. Res. 156: 49-58 (2001).

Buitink J, Leger JJ, Guisle I, Vu BL, Wuilleme S, Lamirault G, Bars AL, Meur NL, Becker A, Kuster H, Leprince O. Transcriptome profiling uncovers metabolic and regulatory processes occurring during the transition from desiccation-sensitive to desiccation-tolerant stages in Medicago truncatula seeds. Plant J. 47: 735-750 (2006).

Bundy JG, Spurgeon DJ, Svendsen C, Hankard PK, Osborn D, Lindon JC, Nicholson JK. Earthworm species of the genus Eisenia can be phenotypically differentiated by metabolic profiling. FEBS Lett. 521: 115-120 (2002).

Burgess SC, Weis B, Jones JG, Smith E, Merritt ME, Margolis D, Dean Sherry A, Malloy CR. Noninvasive evaluation of liver metabolism by 2H and 13C NMR isotopomer analysis of human urine. Anal. Biochem. 312: 228-234 (2003).

Busov V, Meilan R, Pearce DW, Rood SB, Ma C, Tschaplinski TJ, Strauss SH. Transgenic modification of gai or rgl1 causes dwarfing and alters gibberellins, root growth, and metabolite profiles in Populus. Planta 224: 288-299 (2006).

Calderon-Vazquez C, Ibarra-Laclette E, Caballero-Perez J, Herrera-Estrella L. Transcript profiling of Zea mays roots reveals gene responses to phosphate deficiency at the plant- and species-specific levels. J. Exp. Bot. 59: 2479-2497 (2008).

Carrari F, Baxter C, Usadel B, Urbanczyk-Wochniak E, Zanor MI, Nunes-Nesi A, Nikiforova V, Centero D, Ratzka A, Pauly M, Sweetlove L, Fernie AR. Integrated analysis of metabolite and transcript levels reveals the metabolic shifts that underlie tomato fruit development and highlight regulatory aspects of metabolic network behavior. Plant Physiol. 142: 1380-1396 (2006).

Carrari F, Fernie AR. Metabolic regulation underlying tomato fruit development. J. Exp. Bot. 57: 1883-1897 (2006).

Chen S, Glawischnig E, Jorgensen K, Naur P, Jorgensen B, Olsen CE, Hansen CH, Rasmussen H, Pickett JA, Halkier BA. CYP79F1 and CYP79F2 have distinct functions in the biosynthesis of aliphatic glucosinolates in Arabidopsis. Plant J. 33: 923-937 (2003).

Choi YH, Tapias EC, Kim HK, Lefeber AW, Erkelens C, Verhoeven JT, Brzin J, Zel J, Verpoorte R. Metabolic discrimination of Catharanthus roseus leaves infected by phytoplasma using 1H-NMR spectroscopy and multivariate data analysis. Plant Physiol. 135: 2398-2410 (2004).

Clements LD, Streips UN, Miller BS. Differential proteomic analysis of Bacillus subtilis nitrate respiration and fermentation in defined medium. Proteomics 2: 1724-1734 (2002).

Cohen P, Miyazaki M, Socci ND, Hagge-Greenberg A, Liedtke W, Soukas AA, Sharma R, Hudgins LC, Ntambi JM, Friedman JM. Role for stearoyl-CoA desaturase-1 in leptin-mediated weight loss. Science 297: 240-243 (2002).

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).

Contento AL, Kim SJ, Bassham DC. Transcriptome profiling of the response of Arabidopsis suspension culture cells to Suc starvation. Plant Physiol. 135: 2330-2347 (2004).

Cramer GR, Ergul A, Grimplet J, Tillett RL, Tattersall EA, Bohlman MC, Vincent D, Sonderegger J, Evans J, Osborne C, Quilici D, Schlauch KA, Schooley DA, Cushman JC. Water and salinity stress in grapevines: early and late changes in transcript and metabolite profiles. Funct. Integr. Genomics 7: 111-134 (2007).

Dalgaard P, Vancanneyt M, Euras Vilalta N, Swings J, Fruekilde P, Leisner JJ. Identification of lactic acid bacteria from spoilage associations of cooked and brined shrimps stored under modified atmosphere between 0 degrees C and 25 degrees C. J. Appl. Microbiol. 94: 80-89 (2003).

Damiani I, Morreel K, Danoun S, Goeminne G, Yahiaoui N, Marque C, Kopka J, Messens E, Goffner D, Boerjan W, Boudet AM, Rochange S. Metabolite profiling reveals a role for atypical cinnamyl alcohol dehydrogenase CAD1 in the synthesis of coniferyl alcohol in tobacco xylem. Plant Mol. Biol. 59: 753-769 (2005).

Dan M, Su M, Gao X, Zhao T, Zhao A, Xie G, Qiu Y, Zhou M, Liu Z, Jia W. Metabolite profiling of Panax notoginseng using UPLC-ESI-MS. Phytochemistry 69: 2237-2244 (2008).

Dauwe R, Morreel K, Goeminne G, Gielen B, Rohde A, Van Beeumen J, Ralph J, Boudet AM, Kopka J, Rochange SF, Halpin C, Messens E, Boerjan W. Molecular phenotyping of lignin-modified tobacco reveals associated changes in cell-wall metabolism, primary metabolism, stress metabolism and photorespiration. Plant J. 52: 263-285 (2007).

Deavours BE, Dixon RA. Metabolic engineering of isoflavonoid biosynthesis in alfalfa. Plant Physiol. 138: 2245-2259 (2005).

Degenkolbe T, Do PT, Zuther E, Repsilber D, Walther D, Hincha DK, Kohl KI. Expression profiling of rice cultivars differing in their tolerance to long-term drought stress. Plant Mol. Biol. 69: 133-153 (2009).

Desbrosses GG, Kopka J, Udvardi MK. Lotus japonicus metabolic profiling. Development of gas chromatography-mass spectrometry resources for the study of plant-microbe interactions. Plant Physiol. 137: 1302-1318 (2005).

Deshpande R, Yang TH, Heinzle E. Towards a metabolic and isotopic steady state in CHO batch cultures for reliable isotope-based metabolic profiling. Biotechnol. J. 4: 247-263 (2009).

Devaiah SP, Roth MR, Baughman E, Li M, Tamura P, Jeannotte R, Welti R, Wang X. Quantitative profiling of polar glycerolipid species from organs of wild-type Arabidopsis and a phospholipase Dalpha1 knockout mutant. Phytochemistry 67: 1907-1924 (2006).

Diaz C, Purdy S, Christ A, Morot-Gaudry JF, Wingler A, Masclaux-Daubresse C. Characterization of markers to determine the extent and variability of leaf senescence in Arabidopsis. A metabolic profiling approach. Plant Physiol. 138: 898-908 (2005).

Doehlemann G, Wahl R, Horst RJ, Voll LM, Usadel B, Poree F, Stitt M, Pons-Kühnemann J, Sonnewald U, Kahmann R, Kämper J. Reprogramming a maize plant: transcriptional and metabolic changes induced by the fungal biotroph Ustilago maydis. Plant J. 56: 181-195 (2008).

Dong J, Keller WA, Yan W, Georges F. Gene expression at early stages of Brassica napus seed development as revealed by transcript profiling of seed-abundant cDNAs. Planta 218: 483-491 (2004).

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).

Dubouzet JG, Ishihara A, Matsuda F, Miyagawa H, Iwata H, Wakasa K. Integrated metabolomic and transcriptomic analyses of high-tryptophan rice expressing a mutant anthranilate synthase alpha subunit. J. Exp. Bot. 58: 3309-3321 (2007).

Dumas ME, Barton RH, Toye A, Cloarec O, Blancher C, Rothwell A, Fearnside J, Tatoud R, Blanc V, Lindon JC, Mitchell SC, Holmes E, McCarthy MI, Scott J, Gauguier D, Nicholson JK. Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant mice. Proc. Natl. Acad. Sci. U.S.A. 103: 12511-1256 (2006).

Durre P, Bohringer M, Nakotte S, Schaffer S, Thormann K, Zickner B. Transcriptional regulation of solventogenesis in Clostridium acetobutylicum. J. Mol. Microbiol. Biotechnol. 4: 295-300 (2002).

Ehlting J, Mattheus N, Aeschliman DS, Li E, Hamberger B, Cullis IF, Zhuang J, Kaneda M, Mansfield SD, Samuels L, Ritland K, Ellis BE, Bohlmann J, Douglas CJ. Global transcript profiling of primary stems from Arabidopsis thaliana identifies candidate genes for missing links in lignin biosynthesis and transcriptional regulators of fiber differentiation. Plant J. 42: 618-640 (2005).

Eisenhut M, Huege J, Schwarz D, Bauwe H, Kopka J, Hagemann M. Metabolome phenotyping of inorganic carbon limitation in cells of the wild type and photorespiratory mutants of the cyanobacterium Synechocystis sp. strain PCC 6803. Plant Physiol. 148: 2109-2120 (2008).

Ekman M, Tollback P, Bergman B. Proteomic analysis of the cyanobacterium of the Azolla symbiosis: identity, adaptation, and NifH modification. J. Exp. Bot. 59: 1023-1034 (2007).

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).

Fait A, Angelovici R, Less H, Ohad I, Urbanczyk-Wochniak E, Fernie AR, Galili G. Arabidopsis seed development and germination is associated with temporally distinct metabolic switches. Plant Physiol. 142: 839-854 (2006).

Famili I, Mahadevan R, Palsson BO. k-Cone analysis: determining all candidate values for kinetic parameters on a network scale. Biophys. J. 88: 1616-1625 (2005).

Fernandez-Murray JP, McMaster CR. Glycerophosphocholine catabolism as a new route for choline formation for phosphatidylcholine synthesis by the Kennedy pathway. J. Biol. Chem. 280: 38290-38296 (2005).

Fernie AR, Geigenberger P, Stitt M. Flux an important, but neglected, component of functional genomics. Curr. Opin. Plant Biol. 8: 174-182 (2005).

Feussner I, Wasternack C. The lipoxygenase pathway. Annu. Rev. Plant Biol. 53: 275-297 (2002).

Fiehn O. Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks. Comparative & Functional Genomics 2: 155-168 (2001).

Fiehn O. Metabolomics--the link between genotypes and phenotypes. Plant Mol. Biol. 48: 155-171 (2002).

Fiehn O. Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks. Comp. Funct. Genomics 2: 155-168 (2001).

Fiehn O, Kopka J, Dormann P, Altmann T, Trethewey RN, Willmitzer L. Metabolite profiling for plant functional genomics. Nat. Biotechnol. 18: 1157-1161 (2000).

Figueiredo A, Fortes AM, Ferreira S, Sebastiana M, Choi YH, Sousa L, Acioli-Santos B, Pessoa F, Verpoorte R, Pais MS. Transcriptional and metabolic profiling of grape (Vitis vinifera L.) leaves unravel possible innate resistance against pathogenic fungi. J. Exp. Bot. 59: 3371-3381 (2008).

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).

Fischer MD, Gorospe JR, Felder E, Bogdanovich S, Pedrosa-Domellof F, Ahima RS, Rubinstein NA, Hoffman EP, Khurana TS. Expression profiling reveals metabolic and structural components of extraocular muscles. Physiol. Genomics 9: 71-84 (2002).

Fraser PD, Pinto ME, Holloway DE, Bramley PM. Application of high-performance liquid chromatography with photodiode array detection to the metabolic profiling of plant isoprenoids. Plant J. 24: 551-558 (2000).

Frederich M, Choi YH, Angenot L, Harnischfeger G, Lefeber AW, Verpoorte R. Metabolomic analysis of Strychnos nux-vomica, Strychnos icaja and Strychnos ignatii extracts by (1)H nuclear magnetic resonance spectrometry and multivariate analysis techniques. Phytochemistry 65: 1993-2001 (2004).

Fridman E, Pichersky E. Metabolomics, genomics, proteomics, and the identification of enzymes and their substrates and products. Curr. Opin. Plant Biol. 8: 242-248 (2005).

Gao C, Wang Y, Liu G, Yang C, Jiang J, Li H. Expression profiling of salinity-alkali stress responses by large-scale expressed sequence tag analysis in Tamarix hispid. Plant Mol. Biol. 66: 245-258 (2008).

Ghassemian M, Lutes J, Chang HS, Lange I, Chen W, Zhu T, Wang X, Lange BM. Abscisic acid-induced modulation of metabolic and redox control pathways in Arabidopsis thaliana. Phytochemistry 69: 2899-2911 (2008).

Gibson KM, Schor DS, Gupta M, Guerand WS, Senephansiri H, Burlingame TG, Bartels H, Hogema BM, Bottiglieri T, Froestl W, Snead OC, Grompe M, Jakobs C. Focal neurometabolic alterations in mice deficient for succinate semialdehyde dehydrogenase. J. Neurochem. 81: 71-79 (2002).

Gipson GT, Tatsuoka KS, Ball RJ, Sokhansanj BA, Hansen MK, Ryan TE, Hodson MP, Sweatman BC, Connor SC. Multi-platform investigation of the metabolome in a leptin receptor defective murine model of type 2 diabetes. Mol. Biosyst. 4: 1015-1023 (2008).

Glassbrook G, Beecher C, Ryals J. Metabolic profiling on the right path. Nat. Biotechnol. 18: 1142-1143 (2000).

Glassbrook N, Ryals J. A systematic approach to biochemical profiling. Curr. Opin. Plant Biol. 4: 186-190 (2001).

Go VL, Nguyen CT, Harris DM, Paul Lee WN. Nutrient-gene interaction: metabolic genotype-phenotype relationship. J. Nutr. 135: 3016S-3020S (2005).

Goodacre R, Vaidyanathan S, Bianchi G, Kell DB. Metabolic profiling using direct infusion electrospray ionisation mass spectrometry for the characterisation of olive oils. Analyst 127: 1457-1462 (2002).

Grienenberger E, Besseau S, Geoffroy P, Debayle D, Heintz D, Lapierre C, Pollet B, Heitz T, Legrand M. A BAHD acyltransferase is expressed in tapetum of Arabidopsis anthers and is involved in the synthesis of hydroxycinnamoyl spermidines. Plant J. 58: 246-259 (2009).

Griffin JL, Bollard ME. Metabonomics: its potential as a tool in toxicology for safety assessment and data integration. Curr. Drug Metab. 5: 389-398 (2004).

Griffin JL, Nicholls AW, Keun HC, Mortishire-Smith RJ, Nicholson JK, Kuehn T. Metabolic profiling of rodent biological fluids via 1H NMR spectroscopy using a 1 mm microlitre probe. Analyst 127: 582-584 (2002).

Griffin JL, Williams HJ, Sang E, Clarke K, Rae C, Nicholson JK. Metabolic profiling of genetic disorders: a multitissue (1)H nuclear magnetic resonance spectroscopic and pattern recognition study into dystrophic tissue. Anal. Biochem. 293: 16-21 (2001).

Gu M, Lim HK. An intelligent data acquisition system for simultaneous screening of microsomal stability and metabolite profiling by liquid chromatography/mass spectrometry. J. Mass Spectrom. 36: 1053-1061 (2001).

Guy C, Kaplan F, Kopka J, Selbig J, Hincha DK. Metabolomics of temperature stress. Physiol. Plant. 132: 220-235 (2008).

Hagel JM, Weljie AM, Vogel HJ, Facchini PJ. Quantitative 1H NMR metabolite profiling as a functional genomics platform to investigate alkaloid biosynthesis in opium poppy. Plant Physiol. 147: 1805-1821 (2008).

Hakkinen ST, Tilleman S, Swiatek A, De Sutter V, Rischer H, Vanhoutte I, Van Onckelen H, Hilson P, Inze D, Oksman-Caldentey KM, Goossens A. Functional characterisation of genes involved in pyridine alkaloid biosynthesis in tobacco. Phytochemistry 68: 2773-2785 (2007).

Halket JM, Waterman D, Przyborowska AM, Patel RK, Fraser PD, Bramley PM. Chemical derivatization and mass spectral libraries in metabolic profiling by GC/MS and LC/MS/MS. J. Exp. Bot. 56: 219-243 (2005).

Harrigan G. Metabolic profiling: pathways in drug discovery. Drug Discov. Today 7: 351-352 (2002).

Haugen AC, Kelley R, Collins JB, Tucker CJ, Deng C, Afshari CA, Brown JM, Ideker T, Van Houten B. Integrating phenotypic and expression profiles to map arsenic-response networks. Genome Biol. 5: R95 (2004).

Hecker M, Volker U. Towards a comprehensive understanding of Bacillus subtilis cell physiology by physiological proteomics. Proteomics 4: 3727-3750 (2004).

Hellmold H, Nilsson CB, Schuppe-Koistinen I, Kenne K, Warngard L. Identification of end points relevant to detection of potentially adverse drug reactions. Toxicol. Lett. 127: 239-243 (2002).

Hendrickson EL, Lamont RJ, Hackett M. Tools for interpreting large-scale protein profiling in microbiology. J. Dent. Res. 87: 1004-1015 (2008).

Hernandez G, Ramirez M, Valdes-Lopez O, Tesfaye M, Graham MA, Czechowski T, Schlereth A, Wandrey M, Erban A, Cheung F, Wu HC, Lara M, Town CD, Kopka J, Udvardi MK, Vance CP. Phosphorus stress in common bean: root transcript and metabolic responses. Plant Physiol. 144: 752-767 (2007).

Hewezi T, Petitprez M, Gentzbittel L. Primary metabolic pathways and signal transduction in sunflower (Helianthus annuus L.): comparison of transcriptional profiling in leaves and immature embryos using cDNA microarrays. Planta 223: 948-964 (2006).

Holmes E, Nicholson JK. Human metabolic phenotyping and metabolome wide association studies. Ernst Schering Found. Symp. Proc. 4: 227-249 (2007).

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).

Hosp J, Tashpulatov A, Roessner U, Barsova E, Katholnigg H, Steinborn R, Melikant B, Lukyanov S, Heberle-Bors E, Touraev A. Transcriptional and metabolic profiles of stress-induced, embryogenic tobacco microspores. Plant Mol. Biol. 63: 137-149 (2007).

Howell KA, Narsai R, Carroll A, Ivanova A, Lohse M, Usadel B, Millar AH, Whelan J. Mapping metabolic and transcript temporal switches during germination in Oryza sativa highlights specific transcription factors and the role of RNA instability in the germination process. Plant Physiol. 149: 961-980 (2009).

Huang CY, Roessner U, Eickmeier I, Genc Y, Callahan DL, Shirley N, Langridge P, Bacic A. Metabolite profiling reveals distinct changes in carbon and nitrogen metabolism in phosphate-deficient barley plants (Hordeum vulgare L.). Plant Cell Physiol. 49: 691-703 (2008).

Huege J, Sulpice R, Gibon Y, Lisec J, Koehl K, Kopka J. GC-EI-TOF-MS analysis of in vivo carbon-partitioning into soluble metabolite pools of higher plants by monitoring isotope dilution after (13)CO(2) labelling. Phytochemistry 68: 2258-2272 (2007).

Huhman DV, Sumner LW. Metabolic profiling of saponins in Medicago sativa and Medicago truncatula using HPLC coupled to an electrospray ion-trap mass spectrometer. Phytochemistry 59: 347-360 (2002).

Huser AT, Chassagnole C, Lindley ND, Merkamm M, Guyonvarch A, Elisakova V, Patek M, Kalinowski J, Brune I, Puhler A, Tauch A. Rational design of a Corynebacterium glutamicum pantothenate production strain and its characterization by metabolic flux analysis and genome-wide transcriptional profiling. Appl. Environ. Microbiol. 71: 3255-3268 (2005).

Iles RA. Nuclear magnetic resonance spectroscopy and genetic disorders. Curr. Med. Chem. 15: 15-36 (2008).

Inaba Y, Brotherton JE, Ulanov A, Widholm JM. Expression of a feedback insensitive anthranilate synthase gene from tobacco increases free tryptophan in soybean plants. Plant Cell Rep. 26: 1763-1771 (2007).

Jalanko A, Tyynela J, Peltonen L. From genes to systems: new global strategies for the characterization of NCL biology. Biochim. Biophys. Acta 1762: 934-944 (2006).

Jansen RC, Nap JP. Genetical genomics: the added value from segregation. Trends Genet. 17: 388-391 (2001).

Jeong ML, Jiang H, Chen HS, Tsai CJ, Harding SA. Metabolic profiling of the sink-to-source transition in developing leaves of quaking aspen. Plant Physiol. 136: 3364-3375 (2004).

Joshi V, Laubengayer KM, Schauer N, Fernie AR, Jander G. Two Arabidopsis threonine aldolases are nonredundant and compete with threonine deaminase for a common substrate pool. Plant Cell 18: 3564-3575 (2006).

Jost R, Altschmied L, Bloem E, Bogs J, Gershenzon J, Hahnel U, Hansch R, Hartmann T, Kopriva S, Kruse C, Mendel RR, Papenbrock J, Reichelt M, Rennenberg H, Schnug E, Schmidt A, Textor S, Tokuhisa J, Wachter A, Wirtz M, Rausch T, Hell R. Expression profiling of metabolic genes in response to methyl jasmonate reveals regulation of genes of primary and secondary sulfur-related pathways in Arabidopsis thaliana. Photosynth Res. 86: 491-508 (2005).

Jumtee K, Bamba T, Okazawa A, Fukusaki E, Kobayashi A. Integrated metabolite and gene expression profiling revealing phytochrome A regulation of polyamine biosynthesis of Arabidopsis thaliana. J. Exp. Bot. 59: 1187-1200 (2008).

Kaan T, Homuth G, Mader U, Bandow J, Schweder T. Genome-wide transcriptional profiling of the Bacillus subtilis cold-shock response. Microbiology 148: 3441-3455 (2002).

Kaplan F, Kopka J, Haskell DW, Zhao W, Schiller KC, Gatzke N, Sung DY, Guy CL. Exploring the temperature-stress metabolome of Arabidopsis. Plant Physiol. 136: 4159-4168 (2004).

Kaplan F, Kopka J, Sung DY, Zhao W, Popp M, Porat R, Guy CL. Transcript and metabolite profiling during cold acclimation of Arabidopsis reveals an intricate relationship of cold-regulated gene expression with modifications in metabolite content. Plant J. 50: 967-981 (2007).

Kempa S, Rozhon W, Samaj J, Erban A, Baluska F, Becker T, Haselmayer J, Schleiff E, Kopka J, Hirt H, Jonak C. A plastid-localized glycogen synthase kinase 3 modulates stress tolerance and carbohydrate metabolism. Plant J. 49: 1076-1090 (2007).

Kharbanda KK, Vigneswara V, McVicker BL, Newlaczyl AU, Bailey K, Tuma D, Ray DE, Carter WG. Proteomics reveal a concerted upregulation of methionine metabolic pathway enzymes, and downregulation of carbonic anhydrase-III, in betaine supplemented ethanol-fed rats. Biochem. Biophys. Res. Commun. 381: 523-527 (2009).

Khoo SH, Al-Rubeai M. Metabolic characterization of a hyper-productive state in an antibody producing NS0 myeloma cell line. Metab. Eng. 11: 199-211 (2009).

Kim HU, Li Y, Huang AH. Ubiquitous and endoplasmic reticulum-located lysophosphatidyl acyltransferase, LPAT2, is essential for female but not male gametophyte development in Arabidopsis. Plant Cell 17: 1073-1089 (2005).

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David Rhodes
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Last Update: 10/01/09