TY - JOUR A1 - Ribeiro, Dimas M. A1 - Araujo, Wagner L. A1 - Fernie, Alisdair R. A1 - Schippers, Jos H. M. A1 - Müller-Röber, Bernd T1 - Translatome and metabolome effects triggered by gibberellins during rosette growth in Arabidopsis JF - Journal of experimental botany N2 - Although gibberellins (GAs) are well known for their growth control function, little is known about their effects on primary metabolism. Here the modulation of gene expression and metabolic adjustment in response to changes in plant (Arabidopsis thaliana) growth imposed on varying the gibberellin regime were evaluated. Polysomal mRNA populations were profiled following treatment of plants with paclobutrazol (PAC), an inhibitor of GA biosynthesis, and gibberellic acid (GA(3)) to monitor translational regulation of mRNAs globally. Gibberellin levels did not affect levels of carbohydrates in plants treated with PAC and/or GA(3). However, the tricarboxylic acid cycle intermediates malate and fumarate, two alternative carbon storage molecules, accumulated upon PAC treatment. Moreover, an increase in nitrate and in the levels of the amino acids was observed in plants grown under a low GA regime. Only minor changes in amino acid levels were detected in plants treated with GA(3) alone, or PAC plus GA(3). Comparison of the molecular changes at the transcript and metabolite levels demonstrated that a low GA level mainly affects growth by uncoupling growth from carbon availability. These observations, together with the translatome changes, reveal an interaction between energy metabolism and GA-mediated control of growth to coordinate cell wall extension, secondary metabolism, and lipid metabolism. KW - Gibberellin KW - growth KW - paclobutrazol KW - primary metabolism KW - translatome Y1 - 2012 U6 - https://doi.org/10.1093/jxb/err463 SN - 0022-0957 VL - 63 IS - 7 SP - 2769 EP - 2786 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Balazadeh, Salma A1 - Schildhauer, Joerg A1 - Araujo, Wagner L. A1 - Munne-Bosch, Sergi A1 - Fernie, Alisdair R. A1 - Proost, Sebastian A1 - Humbeck, Klaus A1 - Müller-Röber, Bernd T1 - Reversal of senescence by N resupply to N-starved Arabidopsis thaliana: transcriptomic and metabolomic consequences JF - Journal of experimental botany N2 - Leaf senescence is a developmentally controlled process, which is additionally modulated by a number of adverse environmental conditions. Nitrogen shortage is a well-known trigger of precocious senescence in many plant species including crops, generally limiting biomass and seed yield. However, leaf senescence induced by nitrogen starvation may be reversed when nitrogen is resupplied at the onset of senescence. Here, the transcriptomic, hormonal, and global metabolic rearrangements occurring during nitrogen resupply-induced reversal of senescence in Arabidopsis thaliana were analysed. The changes induced by senescence were essentially in keeping with those previously described; however, these could, by and large, be reversed. The data thus indicate that plants undergoing senescence retain the capacity to sense and respond to the availability of nitrogen nutrition. The combined data are discussed in the context of the reversibility of the senescence programme and the evolutionary benefit afforded thereby. Future prospects for understanding and manipulating this process in both Arabidopsis and crop plants are postulated. KW - Arabidopsis KW - gene expression KW - metabolomics KW - nitrogen limitation KW - senescence KW - transcriptome Y1 - 2014 U6 - https://doi.org/10.1093/jxb/eru119 SN - 0022-0957 SN - 1460-2431 VL - 65 IS - 14 SP - 3975 EP - 3992 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Kleessen, Sabrina A1 - Araujo, Wagner L. A1 - Fernie, Alisdair R. A1 - Nikoloski, Zoran T1 - Model-based Confirmation of Alternative Substrates of Mitochondrial Electron Transport Chain JF - The journal of biological chemistry N2 - Background: There are alternative substrates to the mitochondrial respiration. Results: Data-driven model-based analysis renders predictions of alternative substrates to the mitochondrial respiration. Conclusion: Metabolomics data in conjunction with flux-based models can discriminate among hypotheses based on enzymology alone. Significance: This analysis provides a basic framework for in silico studies of alternative pathways in metabolism. Y1 - 2012 U6 - https://doi.org/10.1074/jbc.M111.310383 SN - 0021-9258 VL - 287 IS - 14 SP - 11122 EP - 11131 PB - American Society for Biochemistry and Molecular Biology CY - Bethesda ER - TY - JOUR A1 - Araujo, Wagner L. A1 - Nunes-Nesi, Adriano A1 - Nikoloski, Zoran A1 - Sweetlove, Lee J. A1 - Fernie, Alisdair R. T1 - Metabolic control and regulation of the tricarboxylic acid cycle in photosynthetic and heterotrophic plant tissues JF - Plant, cell & environment : cell physiology, whole-plant physiology, community physiology N2 - The tricarboxylic acid (TCA) cycle is a crucial component of respiratory metabolism in both photosynthetic and heterotrophic plant organs. All of the major genes of the tomato TCA cycle have been cloned recently, allowing the generation of a suite of transgenic plants in which the majority of the enzymes in the pathway are progressively decreased. Investigations of these plants have provided an almost complete view of the distribution of control in this important pathway. Our studies suggest that citrate synthase, aconitase, isocitrate dehydrogenase, succinyl CoA ligase, succinate dehydrogenase, fumarase and malate dehydrogenase have control coefficients flux for respiration of -0.4, 0.964, -0.123, 0.0008, 0.289, 0.601 and 1.76, respectively; while 2-oxoglutarate dehydrogenase is estimated to have a control coefficient of 0.786 in potato tubers. These results thus indicate that the control of this pathway is distributed among malate dehydrogenase, aconitase, fumarase, succinate dehydrogenase and 2-oxoglutarate dehydrogenase. The unusual distribution of control estimated here is consistent with specific non-cyclic flux mode and cytosolic bypasses that operate in illuminated leaves. These observations are discussed in the context of known regulatory properties of the enzymes and some illustrative examples of how the pathway responds to environmental change are given. KW - metabolic control analysis KW - metabolic regulation KW - respiration KW - Solanum lycopersicum (tomato) KW - TCA cycle Y1 - 2012 U6 - https://doi.org/10.1111/j.1365-3040.2011.02332.x SN - 0140-7791 VL - 35 IS - 1 SP - 1 EP - 21 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Smith, Sarah R. A1 - Dupont, Chris L. A1 - McCarthy, James K. A1 - Broddrick, Jared T. A1 - Obornik, Miroslav A1 - Horak, Ales A1 - Füssy, Zoltán A1 - Cihlar, Jaromir A1 - Kleessen, Sabrina A1 - Zheng, Hong A1 - McCrow, John P. A1 - Hixson, Kim K. A1 - Araujo, Wagner L. A1 - Nunes-Nesi, Adriano A1 - Fernie, Alisdair R. A1 - Nikoloski, Zoran A1 - Palsson, Bernhard O. A1 - Allen, Andrew E. T1 - Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom JF - Nature Communications N2 - Diatoms outcompete other phytoplankton for nitrate, yet little is known about the mechanisms underpinning this ability. Genomes and genome-enabled studies have shown that diatoms possess unique features of nitrogen metabolism however, the implications for nutrient utilization and growth are poorly understood. Using a combination of transcriptomics, proteomics, metabolomics, fluxomics, and flux balance analysis to examine short-term shifts in nitrogen utilization in the model pennate diatom in Phaeodactylum tricornutum, we obtained a systems-level understanding of assimilation and intracellular distribution of nitrogen. Chloroplasts and mitochondria are energetically integrated at the critical intersection of carbon and nitrogen metabolism in diatoms. Pathways involved in this integration are organelle-localized GS-GOGAT cycles, aspartate and alanine systems for amino moiety exchange, and a split-organelle arginine biosynthesis pathway that clarifies the role of the diatom urea cycle. This unique configuration allows diatoms to efficiently adjust to changing nitrogen status, conferring an ecological advantage over other phytoplankton taxa. KW - Biochemistry KW - Computational biology and bioinformatics KW - Evolution KW - Microbiology KW - Molecular biology Y1 - 2019 U6 - https://doi.org/10.1038/s41467-019-12407-y SN - 2041-1723 VL - 10 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Ribeiro, Dimas M. A1 - Araujo, Wagner L. A1 - Fernie, Alisdair R. A1 - Schippers, Jos H. M. A1 - Müller-Röber, Bernd T1 - Action of Gibberellins on growth and metabolism of arabidopsis plants Associated with high concentration of carbon dioxide JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - Although the positive effect of elevated CO2 concentration [CO2] on plant growth is well known, it remains unclear whether global climate change will positively or negatively affect crop yields. In particular, relatively little is known about the role of hormone pathways in controlling the growth responses to elevated [CO2]. Here, we studied the impact of elevated [CO2] on plant biomass and metabolism in Arabidopsis (Arabidopsis thaliana) in relation to the availability of gibberellins (GAs). Inhibition of growth by the GA biosynthesis inhibitor paclobutrazol (PAC) at ambient [CO2] (350 mu mol CO2 mol(-1)) was reverted by elevated [CO2] (750 mu mol CO2 mol(-1)). Thus, we investigated the metabolic adjustment and modulation of gene expression in response to changes in growth of plants imposed by varying the GA regime in ambient and elevated [CO2]. In the presence of PAC (low-GA regime), the activities of enzymes involved in photosynthesis and inorganic nitrogen assimilation were markedly increased at elevated [CO2], whereas the activities of enzymes of organic acid metabolism were decreased. Under ambient [CO2], nitrate, amino acids, and protein accumulated upon PAC treatment; however, this was not the case when plants were grown at elevated [CO2]. These results suggest that only under ambient [CO2] is GA required for the integration of carbohydrate and nitrogen metabolism underlying optimal biomass determination. Our results have implications concerning the action of the Green Revolution genes in future environmental conditions. Y1 - 2012 U6 - https://doi.org/10.1104/pp.112.204842 SN - 0032-0889 VL - 160 IS - 4 SP - 1781 EP - 1794 PB - American Society of Plant Physiologists CY - Rockville ER -