@article{AlseekhTohgeWendenbergetal.2015, author = {Alseekh, Saleh and Tohge, Takayuki and Wendenberg, Regina and Scossa, Federico and Omranian, Nooshin and Li, Jie and Kleessen, Sabrina and Giavalisco, Patrick and Pleban, Tzili and M{\"u}ller-R{\"o}ber, Bernd and Zamir, Dani and Nikoloski, Zoran and Fernie, Alisdair R.}, title = {Identification and Mode of Inheritance of Quantitative Trait Loci for Secondary Metabolite Abundance in Tomato}, series = {The plant cell}, volume = {27}, journal = {The plant cell}, number = {3}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {1040-4651}, doi = {10.1105/tpc.114.132266}, pages = {485 -- 512}, year = {2015}, abstract = {A large-scale metabolic quantitative trait loci (mQTL) analysis was performed on the well-characterized Solanum pennellii introgression lines to investigate the genomic regions associated with secondary metabolism in tomato fruit pericarp. In total, 679 mQTLs were detected across the 76 introgression lines. Heritability analyses revealed that mQTLs of secondary metabolism were less affected by environment than mQTLs of primary metabolism. Network analysis allowed us to assess the interconnectivity of primary and secondary metabolism as well as to compare and contrast their respective associations with morphological traits. Additionally, we applied a recently established real-time quantitative PCR platform to gain insight into transcriptional control mechanisms of a subset of the mQTLs, including those for hydroxycinnamates, acyl-sugar, naringenin chalcone, and a range of glycoalkaloids. Intriguingly, many of these compounds displayed a dominant-negative mode of inheritance, which is contrary to the conventional wisdom that secondary metabolite contents decreased on domestication. We additionally performed an exemplary evaluation of two candidate genes for glycolalkaloid mQTLs via the use of virus-induced gene silencing. The combined data of this study were compared with previous results on primary metabolism obtained from the same material and to other studies of natural variance of secondary metabolism.}, language = {en} } @article{AraujoNunesNesiNikoloskietal.2012, author = {Araujo, Wagner L. and Nunes-Nesi, Adriano and Nikoloski, Zoran and Sweetlove, Lee J. and Fernie, Alisdair R.}, title = {Metabolic control and regulation of the tricarboxylic acid cycle in photosynthetic and heterotrophic plant tissues}, series = {Plant, cell \& environment : cell physiology, whole-plant physiology, community physiology}, volume = {35}, journal = {Plant, cell \& environment : cell physiology, whole-plant physiology, community physiology}, number = {1}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0140-7791}, doi = {10.1111/j.1365-3040.2011.02332.x}, pages = {1 -- 21}, year = {2012}, abstract = {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.}, language = {en} } @article{BalazadehSchildhauerAraujoetal.2014, author = {Balazadeh, Salma and Schildhauer, Joerg and Araujo, Wagner L. and Munne-Bosch, Sergi and Fernie, Alisdair R. and Proost, Sebastian and Humbeck, Klaus and M{\"u}ller-R{\"o}ber, Bernd}, title = {Reversal of senescence by N resupply to N-starved Arabidopsis thaliana: transcriptomic and metabolomic consequences}, series = {Journal of experimental botany}, volume = {65}, journal = {Journal of experimental botany}, number = {14}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0022-0957}, doi = {10.1093/jxb/eru119}, pages = {3975 -- 3992}, year = {2014}, abstract = {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.}, language = {en} } @misc{BaslerFernieNikoloski2018, author = {Basler, Georg and Fernie, Alisdair R. and Nikoloski, Zoran}, title = {Advances in metabolic flux analysis toward genome-scale profiling of higher organisms}, series = {Bioscience reports : communications and reviews in molecular and cellular biology}, volume = {38}, journal = {Bioscience reports : communications and reviews in molecular and cellular biology}, publisher = {Portland Press (London)}, address = {London}, issn = {0144-8463}, doi = {10.1042/BSR20170224}, pages = {11}, year = {2018}, abstract = {Methodological and technological advances have recently paved the way for metabolic flux profiling in higher organisms, like plants. However, in comparison with omics technologies, flux profiling has yet to provide comprehensive differential flux maps at a genome-scale and in different cell types, tissues, and organs. Here we highlight the recent advances in technologies to gather metabolic labeling patterns and flux profiling approaches. We provide an opinion of how recent local flux profiling approaches can be used in conjunction with the constraint-based modeling framework to arrive at genome-scale flux maps. In addition, we point at approaches which use metabolomics data without introduction of label to predict either non-steady state fluxes in a time-series experiment or flux changes in different experimental scenarios. The combination of these developments allows an experimentally feasible approach for flux-based large-scale systems biology studies.}, language = {en} } @article{BeninaObataMehterovetal.2013, author = {Benina, Maria and Obata, Toshihiro and Mehterov, Nikolay and Ivanov, Ivan and Petrov, Veselin and Toneva, Valentina and Fernie, Alisdair R. and Gechev, Tsanko S.}, title = {Comparative metabolic profiling of Haberlea rhodopensis, Thellungiella halophyla, and Arabidopsis thaliana exposed to low temperature}, series = {Frontiers in plant science}, volume = {4}, journal = {Frontiers in plant science}, number = {1}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2013.00499}, pages = {11}, year = {2013}, abstract = {Haberlea rhodopensis is a resurrection species with extreme resistance to drought stress and desiccation but also with ability to withstand low temperatures and freezing stress. In order to identify biochemical strategies which contribute to Haberlea's remarkable stress tolerance, the metabolic reconfiguration of H. rhodopensis during low temperature (4 degrees C) and subsequent return to optimal temperatures (21 degrees C) was investigated and compared with that of the stress tolerant Thellungiella halophyla and the stress sensitive Arabidopsis thaliana. Metabolic analysis by GC-MS revealed intrinsic differences in the metabolite levels of the three species even at 21 degrees C. H. rhodopensis had significantly more raffinose, melibiose, trehalose, rhamnose, myo-inositol, sorbitol, galactinol, erythronate, threonate, 2-oxoglutarate, citrate, and glycerol than the other two species. A. thaliana had the highest levels of putrescine and fumarate, while T halophila had much higher levels of several amino acids, including alanine, asparagine, beta-alanine, histidine, isoleucine, phenylalanine, serine, threonine, and valine. In addition, the three species responded differently to the low temperature treatment and the subsequent recovery, especially with regard to the sugar metabolism. Chilling induced accumulation of maltose in H. rhodopensis and raffinose in A. thaliana but the raffinose levels in low temperature exposed Arabidopsis were still much lower than these in unstressed Haberlea. While all species accumulated sucrose during chilling, that accumulation was transient in H. rhodopensis and A. thaliana but sustained in T halophila after the return to optimal temperature. Thus, Haberlea's metabolome appeared primed for chilling stress but the low temperature acclimation induced additional stress-protective mechanisms. A diverse array of sugars, organic acids, and polyols constitute Haberlea's main metabolic defence mechanisms against chilling, while accumulation of amino acids and amino acid derivatives contribute to the low temperature acclimation in Arabidopsis and Thellungiella. Collectively, these results show inherent differences in the metabolomes under the ambient temperature and the strategies to respond to low temperature in the three species.}, language = {en} } @article{DepuydtTrenkampFernieetal.2009, author = {Depuydt, Stephen and Trenkamp, Sandra and Fernie, Alisdair R. and Elftieh, Samira and Renou, Jean-Pierre and Vuylsteke, Marnik and Holsters, Marcelle and Vereecke, Danny}, title = {An integrated genomics approach to define niche establishment by Rhodococcus fascians}, issn = {0032-0889}, doi = {10.1104/pp.108.131805}, year = {2009}, abstract = {Rhodococcus fascians is a Gram-positive phytopathogen that induces shooty hyperplasia on its hosts through the secretion of cytokinins. Global transcriptomics using microarrays combined with profiling of primary metabolites on infected Arabidopsis (Arabidopsis thaliana) plants revealed that this actinomycete modulated pathways to convert its host into a niche. The transcript data demonstrated that R. fascians leaves a very characteristic mark on Arabidopsis with a pronounced cytokinin response illustrated by the activation of cytokinin perception, signal transduction, and homeostasis. The microarray data further suggested active suppression of an oxidative burst during the R. fascians pathology, and comparison with publicly available transcript data sets implied a central role for auxin in the prevention of plant defense activation. Gene Ontology categorization of the differentially expressed genes hinted at a significant impact of infection on the primary metabolism of the host, which was confirmed by subsequent metabolite profiling. The much higher levels of sugars and amino acids in infected plants are presumably accessed by the bacteria as carbon and nitrogen sources to support epiphytic and endophytic colonization. Hexoses, accumulating from a significantly increased invertase activity, possibly inhibited the expression of photosynthesis genes and photosynthetic activity in infected leaves. Altogether, these changes are indicative of sink development in symptomatic tissues. The metabolomics data furthermore point to the possible occurrence of secondary signaling during the interaction, which might contribute to symptom development. These data are placed in the context of regulation of bacterial virulence gene expression, suppression of defense, infection phenotype, and niche establishment.}, language = {en} } @article{DevkarThirumalaikumarXueetal.2019, author = {Devkar, Vikas and Thirumalaikumar, Venkatesh P. and Xue, Gang-Ping and Vallarino, Jose G. and Tureckova, Veronika and Strnad, Miroslav and Fernie, Alisdair R. and Hoefgen, Rainer and Mueller-Roeber, Bernd and Balazadeh, Salma}, title = {Multifaceted regulatory function of tomato SlTAF1 in the response to salinity stress}, series = {New phytologist : international journal of plant science}, volume = {225}, journal = {New phytologist : international journal of plant science}, number = {4}, publisher = {Wiley}, address = {Hoboken}, issn = {0028-646X}, doi = {10.1111/nph.16247}, pages = {1681 -- 1698}, year = {2019}, abstract = {Salinity stress limits plant growth and has a major impact on agricultural productivity. Here, we identify NAC transcription factor SlTAF1 as a regulator of salt tolerance in cultivated tomato (Solanum lycopersicum). While overexpression of SlTAF1 improves salinity tolerance compared with wild-type, lowering SlTAF1 expression causes stronger salinity-induced damage. Under salt stress, shoots of SlTAF1 knockdown plants accumulate more toxic Na+ ions, while SlTAF1 overexpressors accumulate less ions, in accordance with an altered expression of the Na+ transporter genes SlHKT1;1 and SlHKT1;2. Furthermore, stomatal conductance and pore area are increased in SlTAF1 knockdown plants during salinity stress, but decreased in SlTAF1 overexpressors. We identified stress-related transcription factor, abscisic acid metabolism and defence-related genes as potential direct targets of SlTAF1, correlating it with reactive oxygen species scavenging capacity and changes in hormonal response. Salinity-induced changes in tricarboxylic acid cycle intermediates and amino acids are more pronounced in SlTAF1 knockdown than wild-type plants, but less so in SlTAF1 overexpressors. The osmoprotectant proline accumulates more in SlTAF1 overexpressors than knockdown plants. In summary, SlTAF1 controls the tomato's response to salinity stress by combating both osmotic stress and ion toxicity, highlighting this gene as a promising candidate for the future breeding of stress-tolerant crops.}, language = {en} } @article{DurgudGuptaIvanovetal.2018, author = {Durgud, Meriem and Gupta, Saurabh and Ivanov, Ivan and Omidbakhshfard, Mohammad Amin and Benina, Maria and Alseekh, Saleh and Staykov, Nikola and Hauenstein, Mareike and Dijkwel, Paul P. and Hortensteiner, Stefan and Toneva, Valentina and Brotman, Yariv and Fernie, Alisdair R. and M{\"u}ller-R{\"o}ber, Bernd and Gechev, Tsanko S.}, title = {Molecular Mechanisms Preventing Senescence in Response to Prolonged Darkness in a Desiccation-Tolerant Plant}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {177}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {3}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.18.00055}, pages = {1319 -- 1338}, year = {2018}, abstract = {The desiccation-tolerant plant Haberlea rhodopensis can withstand months of darkness without any visible senescence. Here, we investigated the molecular mechanisms of this adaptation to prolonged (30 d) darkness and subsequent return to light. H. rhodopensis plants remained green and viable throughout the dark treatment. Transcriptomic analysis revealed that darkness regulated several transcription factor (TF) genes. Stress-and autophagy-related TFs such as ERF8, HSFA2b, RD26, TGA1, and WRKY33 were up-regulated, while chloroplast-and flowering-related TFs such as ATH1, COL2, COL4, RL1, and PTAC7 were repressed. PHYTOCHROME INTERACTING FACTOR4, a negative regulator of photomorphogenesis and promoter of senescence, also was down-regulated. In response to darkness, most of the photosynthesis-and photorespiratory-related genes were strongly down-regulated, while genes related to autophagy were up-regulated. This occurred concomitant with the induction of SUCROSE NON-FERMENTING1-RELATED PROTEIN KINASES (SnRK1) signaling pathway genes, which regulate responses to stress-induced starvation and autophagy. Most of the genes associated with chlorophyll catabolism, which are induced by darkness in dark-senescing species, were either unregulated (PHEOPHORBIDE A OXYGENASE, PAO; RED CHLOROPHYLL CATABOLITE REDUCTASE, RCCR) or repressed (STAY GREEN-LIKE, PHEOPHYTINASE, and NON-YELLOW COLORING1). Metabolite profiling revealed increases in the levels of many amino acids in darkness, suggesting increased protein degradation. In darkness, levels of the chloroplastic lipids digalactosyldiacylglycerol, monogalactosyldiacylglycerol, phosphatidylglycerol, and sulfoquinovosyldiacylglycerol decreased, while those of storage triacylglycerols increased, suggesting degradation of chloroplast membrane lipids and their conversion to triacylglycerols for use as energy and carbon sources. Collectively, these data show a coordinated response to darkness, including repression of photosynthetic, photorespiratory, flowering, and chlorophyll catabolic genes, induction of autophagy and SnRK1 pathways, and metabolic reconfigurations that enable survival under prolonged darkness.}, language = {en} } @article{EngqvistSchmitzGertzmannetal.2015, author = {Engqvist, Martin K. M. and Schmitz, Jessica and Gertzmann, Anke and Florian, Alexandra and Jaspert, Nils and Arif, Muhammad and Balazadeh, Salma and M{\"u}ller-R{\"o}ber, Bernd and Fernie, Alisdair R. and Maurino, Veronica G.}, title = {GLYCOLATE OXIDASE3, a Glycolate Oxidase Homolog of Yeast L-Lactate Cytochrome c Oxidoreductase, Supports L-Lactate Oxidation in Roots of Arabidopsis}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {169}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {2}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.15.01003}, pages = {1042 -- 1061}, year = {2015}, abstract = {In roots of Arabidopsis (Arabidopsis thaliana), L-lactate is generated by the reduction of pyruvate via L-lactate dehydrogenase, but this enzyme does not efficiently catalyze the reverse reaction. Here, we identify the Arabidopsis glycolate oxidase (GOX) paralogs GOX1, GOX2, and GOX3 as putative L-lactate-metabolizing enzymes based on their homology to CYB2, the L-lactate cytochrome c oxidoreductase from the yeast Saccharomyces cerevisiae. We found that GOX3 uses L-lactate with a similar efficiency to glycolate; in contrast, the photorespiratory isoforms GOX1 and GOX2, which share similar enzymatic properties, use glycolate with much higher efficiencies than L-lactate. The key factor making GOX3 more efficient with L-lactate than GOX1 and GOX2 is a 5- to 10-fold lower Km for the substrate. Consequently, only GOX3 can efficiently metabolize L-lactate at low intracellular concentrations. Isotope tracer experiments as well as substrate toxicity tests using GOX3 loss-of-function and overexpressor plants indicate that L-lactate is metabolized in vivo by GOX3. Moreover, GOX3 rescues the lethal growth phenotype of a yeast strain lacking CYB2, which cannot grow on L-lactate as a sole carbon source. GOX3 is predominantly present in roots and mature to aging leaves but is largely absent from young photosynthetic leaves, indicating that it plays a role predominantly in heterotrophic rather than autotrophic tissues, at least under standard growth conditions. In roots of plants grown under normoxic conditions, loss of function of GOX3 induces metabolic rearrangements that mirror wild-type responses under hypoxia. Thus, we identified GOX3 as the enzyme that metabolizes L-lactate to pyruvate in vivo and hypothesize that it may ensure the sustainment of low levels of L-lactate after its formation under normoxia.}, language = {en} } @article{FerrariProostJanowskietal.2019, author = {Ferrari, Camilla and Proost, Sebastian and Janowski, Marcin Andrzej and Becker, J{\"o}rg and Nikoloski, Zoran and Bhattacharya, Debashish and Price, Dana and Tohge, Takayuki and Bar-Even, Arren and Fernie, Alisdair R. and Stitt, Mark and Mutwil, Marek}, title = {Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida}, series = {Nature Communications}, volume = {10}, journal = {Nature Communications}, publisher = {Nature Publ. Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/s41467-019-08703-2}, pages = {13}, year = {2019}, abstract = {Plants have adapted to the diurnal light-dark cycle by establishing elaborate transcriptional programs that coordinate many metabolic, physiological, and developmental responses to the external environment. These transcriptional programs have been studied in only a few species, and their function and conservation across algae and plants is currently unknown. We performed a comparative transcriptome analysis of the diurnal cycle of nine members of Archaeplastida, and we observed that, despite large phylogenetic distances and dramatic differences in morphology and lifestyle, diurnal transcriptional programs of these organisms are similar. Expression of genes related to cell division and the majority of biological pathways depends on the time of day in unicellular algae but we did not observe such patterns at the tissue level in multicellular land plants. Hence, our study provides evidence for the universality of diurnal gene expression and elucidates its evolutionary history among different photosynthetic eukaryotes.}, language = {en} } @misc{FettkeFernie2015, author = {Fettke, J{\"o}rg and Fernie, Alisdair R.}, title = {Intracellular and cell-to-apoplast compartmentation of carbohydrate metabolism}, series = {Trends in plant science}, volume = {20}, journal = {Trends in plant science}, number = {8}, publisher = {Elsevier}, address = {London}, issn = {1360-1385}, doi = {10.1016/j.tplants.2015.04.012}, pages = {490 -- 497}, year = {2015}, abstract = {In most plants, carbohydrates represent the major energy store as well as providing the building blocks for essential structural polymers. Although the major pathways for carbohydrate biosynthesis, degradation, and transport are well characterized, several key steps have only recently been discovered. In addition, several novel minor metabolic routes have been uncovered in the past few years. Here we review current studies of plant carbohydrate metabolism detailing the expanding compendium of functionally characterized transport proteins as well as our deeper comprehension of more minor and conditionally activated metabolic pathways. We additionally explore the pertinent questions that will allow us to enhance our understanding of the response of both major and minor carbohydrate fluxes to changing cellular circumstances.}, language = {en} } @article{FettkeNunesNesiFernieetal.2011, author = {Fettke, J{\"o}rg and Nunes-Nesi, Adriano and Fernie, Alisdair R. and Steup, Martin}, title = {Identification of a novel heteroglycan-interacting protein, HIP 1.3, from Arabidopsis thaliana}, series = {Journal of plant physiology : biochemistry, physiology, molecular biology and biotechnology of plants}, volume = {168}, journal = {Journal of plant physiology : biochemistry, physiology, molecular biology and biotechnology of plants}, number = {12}, publisher = {Elsevier}, address = {Jena}, issn = {0176-1617}, doi = {10.1016/j.jplph.2010.09.008}, pages = {1415 -- 1425}, year = {2011}, abstract = {Plastidial degradation of transitory starch yields mainly maltose and glucose. Following the export into the cytosol, maltose acts as donor for a glucosyl transfer to cytosolic heteroglycans as mediated by a cytosolic transglucosidase (DPE2; EC 2.4.1.25) and the second glucosyl residue is liberated as glucose. The cytosolic phosphorylase (Pho2/PHS2; EC 2.4.1.1) also interacts with heteroglycans using the same intramolecular sites as DPE2. Thus, the two glucosyl transferases interconnect the cytosolic pools of glucose and glucose 1-phosphate. Due to the complex monosaccharide pattern, other heteroglycan-interacting proteins (Hips) are expected to exist. Identification of those proteins was approached by using two types of affinity chromatography. Heteroglycans from leaves of Arabidopsis thaliana (Col-0) covalently bound to Sepharose served as ligands that were reacted with a complex mixture of buffer-soluble proteins from Arabidopsis leaves. Binding proteins were eluted by sodium chloride. For identification, SDS-PAGE, tryptic digestion and MALDI-TOF analyses were applied. A strongly interacting polypeptide (approximately 40 kDa; designated as HIP1.3) was observed as product of locus At1g09340. Arabidopsis mutants deficient in HIP1.3 were reduced in growth and contained heteroglycans displaying an altered monosaccharide pattern. Wild type plants express HIP1.3 most strongly in leaves. As revealed by immuno fluorescence, HIP1.3 is located in the cytosol of mesophyll cells but mostly associated with the cytosolic surface of the chloroplast envelope membranes. In an HIP1.3-deficient mutant the immunosignal was undetectable. Metabolic profiles from leaves of this mutant and wild type plants as well were determined by GC-MS. As compared to the wild type control, more than ten metabolites, such as ascorbic acid, fructose, fructose bisphosphate, glucose, glycine, were elevated in darkness but decreased in the light. Although the biochemical function of HIP1.3 has not yet been elucidated, it is likely to possess an important function in the central carbon metabolism of higher plants.}, language = {en} } @article{GechevBeninaObataetal.2013, author = {Gechev, Tsanko S. and Benina, Maria and Obata, Toshihiro and Tohge, Takayuki and Neerakkal, Sujeeth and Minkov, Ivan and Hille, Jacques and Temanni, Mohamed-Ramzi and Marriott, Andrew S. and Bergstr{\"o}m, Ed and Thomas-Oates, Jane and Antonio, Carla and M{\"u}ller-R{\"o}ber, Bernd and Schippers, Jos H. M. and Fernie, Alisdair R. and Toneva, Valentina}, title = {Molecular mechanisms of desiccation tolerance in the resurrection glacial relic Haberlea rhodopensis}, series = {Cellular and molecular life sciences}, volume = {70}, journal = {Cellular and molecular life sciences}, number = {4}, publisher = {Springer}, address = {Basel}, issn = {1420-682X}, doi = {10.1007/s00018-012-1155-6}, pages = {689 -- 709}, year = {2013}, abstract = {Haberlea rhodopensis is a resurrection plant with remarkable tolerance to desiccation. Haberlea exposed to drought stress, desiccation, and subsequent rehydration showed no signs of damage or severe oxidative stress compared to untreated control plants. Transcriptome analysis by next-generation sequencing revealed a drought-induced reprogramming, which redirected resources from growth towards cell protection. Repression of photosynthetic and growth-related genes during water deficiency was concomitant with induction of transcription factors (members of the NAC, NF-YA, MADS box, HSF, GRAS, and WRKY families) presumably acting as master switches of the genetic reprogramming, as well as with an upregulation of genes related to sugar metabolism, signaling, and genes encoding early light-inducible (ELIP), late embryogenesis abundant (LEA), and heat shock (HSP) proteins. At the same time, genes encoding other LEA, HSP, and stress protective proteins were constitutively expressed at high levels even in unstressed controls. Genes normally involved in tolerance to salinity, chilling, and pathogens were also highly induced, suggesting a possible cross-tolerance against a number of abiotic and biotic stress factors. A notable percentage of the genes highly regulated in dehydration and subsequent rehydration were novel, with no sequence homology to genes from other plant genomes. Additionally, an extensive antioxidant gene network was identified with several gene families possessing a greater number of antioxidant genes than most other species with sequenced genomes. Two of the transcripts most abundant during all conditions encoded catalases and five more catalases were induced in water-deficient samples. Using the pharmacological inhibitor 3-aminotriazole (AT) to compromise catalase activity resulted in increased sensitivity to desiccation. Metabolome analysis by GC or LC-MS revealed accumulation of sucrose, verbascose, spermidine, and gamma-aminobutyric acid during drought, as well as particular secondary metabolites accumulating during rehydration. This observation, together with the complex antioxidant system and the constitutive expression of stress protective genes suggests that both constitutive and inducible mechanisms contribute to the extreme desiccation tolerance of H. rhodopensis.}, language = {en} } @misc{GechevHilleWoerdenbagetal.2014, author = {Gechev, Tsanko S. and Hille, Jacques and Woerdenbag, Herman J. and Benina, Maria and Mehterov, Nikolay and Toneva, Valentina and Fernie, Alisdair R. and M{\"u}ller-R{\"o}ber, Bernd}, title = {Natural products from resurrection plants: Potential for medical applications}, series = {Biotechnology advances : an international review journal ; research reviews and patent abstracts}, volume = {32}, journal = {Biotechnology advances : an international review journal ; research reviews and patent abstracts}, number = {6}, publisher = {Elsevier}, address = {Oxford}, issn = {0734-9750}, doi = {10.1016/j.biotechadv.2014.03.005}, pages = {1091 -- 1101}, year = {2014}, abstract = {Resurrection species are a group of land plants that can tolerate extreme desiccation of their vegetative tissues during harsh drought stress, and still quickly often within hours regain normal physiological and metabolic functions following rehydration. At the molecular level, this desiccation tolerance is attributed to basal cellular mechanisms including the constitutive expression of stress-associated genes and high levels of protective metabolites present already in the absence of stress, as well as to transcriptome and metabolome reconfigurations rapidly occurring during the initial phases of drought stress. Parts of this response are conferred by unique metabolites, including a diverse array of sugars, phenolic compounds, and polyols, some of which accumulate to high concentrations within the plant cell. In addition to drought stress, these metabolites are proposed to contribute to the protection against other abiotic stresses and to an increased oxidative stress tolerance. Recently, extracts of resurrection species and particular secondary metabolites therein were reported to display biological activities of importance to medicine, with e.g. antibacterial, anticancer, antifungal, and antiviral activities, rendering them possible candidates for the development of novel drug substances as well as for cosmetics. Herein, we provide an overview of the metabolite composition of resurrection species, summarize the latest reports related to the use of natural products from resurrection plants, and outline their potential for medical applications. (C) 2014 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/3.0/).}, language = {en} } @article{JoseClementeMorenoOmranianSaezetal.2019, author = {Jose Clemente-Moreno, Maria and Omranian, Nooshin and Saez, Patricia and Maria Figueroa, Carlos and Del-Saz, Nestor and Elso, Mhartyn and Poblete, Leticia and Orf, Isabel and Cuadros-Inostroza, Alvaro and Cavieres, Lohengrin and Bravo, Leon and Fernie, Alisdair R. and Ribas-Carbo, Miquel and Flexas, Jaume and Nikoloski, Zoran and Brotman, Yariv and Gago, Jorge}, title = {Cytochrome respiration pathway and sulphur metabolism sustain stress tolerance to low temperature in the Antarctic species Colobanthus quitensis}, series = {New phytologist : international journal of plant science}, volume = {225}, journal = {New phytologist : international journal of plant science}, number = {2}, publisher = {Wiley}, address = {Hoboken}, issn = {0028-646X}, doi = {10.1111/nph.16167}, pages = {754 -- 768}, year = {2019}, abstract = {Understanding the strategies employed by plant species that live in extreme environments offers the possibility to discover stress tolerance mechanisms. We studied the physiological, antioxidant and metabolic responses to three temperature conditions (4, 15, and 23 degrees C) of Colobanthus quitensis (CQ), one of the only two native vascular species in Antarctica. We also employed Dianthus chinensis (DC), to assess the effects of the treatments in a non-Antarctic species from the same family. Using fused LASSO modelling, we associated physiological and biochemical antioxidant responses with primary metabolism. This approach allowed us to highlight the metabolic pathways driving the response specific to CQ. Low temperature imposed dramatic reductions in photosynthesis (up to 88\%) but not in respiration (sustaining rates of 3.0-4.2 mu mol CO2 m(-2) s(-1)) in CQ, and no change in the physiological stress parameters was found. Its notable antioxidant capacity and mitochondrial cytochrome respiratory activity (20 and two times higher than DC, respectively), which ensure ATP production even at low temperature, was significantly associated with sulphur-containing metabolites and polyamines. Our findings potentially open new biotechnological opportunities regarding the role of antioxidant compounds and respiratory mechanisms associated with sulphur metabolism in stress tolerance strategies to low temperature.}, language = {en} } @article{KamranfarXueTohgeetal.2018, author = {Kamranfar, Iman and Xue, Gang-Ping and Tohge, Takayuki and Sedaghatmehr, Mastoureh and Fernie, Alisdair R. and Balazadeh, Salma and Mueller-Roeber, Bernd}, title = {Transcription factor RD26 is a key regulator of metabolic reprogramming during dark-induced senescence}, series = {New phytologist : international journal of plant science}, volume = {218}, journal = {New phytologist : international journal of plant science}, number = {4}, publisher = {Wiley}, address = {Hoboken}, issn = {0028-646X}, doi = {10.1111/nph.15127}, pages = {1543 -- 1557}, year = {2018}, abstract = {Leaf senescence is a key process in plants that culminates in the degradation of cellular constituents and massive reprogramming of metabolism for the recovery of nutrients from aged leaves for their reuse in newly developing sinks. We used molecular-biological and metabolomics approaches to identify NAC transcription factor (TF) RD26 as an important regulator of metabolic reprogramming in Arabidopsis thaliana. RD26 directly activates CHLOROPLAST VESICULATION (CV), encoding a protein crucial for chloroplast protein degradation, concomitant with an enhanced protein loss in RD26 over-expressors during senescence, but a reduced decline of protein in rd26 knockout mutants. RD26 also directly activates LKR/SDH involved in lysine catabolism, and PES1 important for phytol degradation. Metabolic profiling revealed reduced c-aminobutyric acid (GABA) in RD26 overexpressors, accompanied by the induction of respective catabolic genes. Degradation of lysine, phytol and GABA is instrumental for maintaining mitochondrial respiration in carbon-limiting conditions during senescence. RD26 also supports the degradation of starch and the accumulation of mono-and disaccharides during senescence by directly enhancing the expression of AMY1, SFP1 and SWEET15 involved in carbohydrate metabolism and transport. Collectively, during senescence RD26 acts by controlling the expression of genes across the entire spectrum of the cellular degradation hierarchy.}, language = {en} } @article{KleessenAraujoFernieetal.2012, author = {Kleessen, Sabrina and Araujo, Wagner L. and Fernie, Alisdair R. and Nikoloski, Zoran}, title = {Model-based Confirmation of Alternative Substrates of Mitochondrial Electron Transport Chain}, series = {The journal of biological chemistry}, volume = {287}, journal = {The journal of biological chemistry}, number = {14}, publisher = {American Society for Biochemistry and Molecular Biology}, address = {Bethesda}, issn = {0021-9258}, doi = {10.1074/jbc.M111.310383}, pages = {11122 -- 11131}, year = {2012}, abstract = {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.}, language = {en} } @article{LotkowskaTohgeFernieetal.2015, author = {Lotkowska, Magda E. and Tohge, Takayuki and Fernie, Alisdair R. and Xue, Gang-Ping and Balazadeh, Salma and M{\"u}ller-R{\"o}ber, Bernd}, title = {The Arabidopsis Transcription Factor MYB112 Promotes Anthocyanin Formation during Salinity and under High Light Stress}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {169}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {3}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.15.00605}, pages = {1862 -- 1880}, year = {2015}, abstract = {MYB transcription factors (TFs) are important regulators of flavonoid biosynthesis in plants. Here, we report MYB112 as a formerly unknown regulator of anthocyanin accumulation in Arabidopsis (Arabidopsis thaliana). Expression profiling after chemically induced overexpression of MYB112 identified 28 up-and 28 down-regulated genes 5 h after inducer treatment, including MYB7 and MYB32, which are both induced. In addition, upon extended induction, MYB112 also positively affects the expression of PRODUCTION OF ANTHOCYANIN PIGMENT1, a key TF of anthocyanin biosynthesis, but acts negatively toward MYB12 and MYB111, which both control flavonol biosynthesis. MYB112 binds to an 8-bp DNA fragment containing the core sequence (A/T/G)(A/C) CC(A/T)(A/G/T)(A/C)(T/C). By electrophoretic mobility shift assay and chromatin immunoprecipitation coupled to quantitative polymerase chain reaction, we show that MYB112 binds in vitro and in vivo to MYB7 and MYB32 promoters, revealing them as direct downstream target genes. We further show that MYB112 expression is up-regulated by salinity and high light stress, environmental parameters that both require the MYB112 TF for anthocyanin accumulation under these stresses. In contrast to several other MYB TFs affecting anthocyanin biosynthesis, MYB112 expression is not controlled by nitrogen limitation or an excess of carbon. Thus, MYB112 constitutes a regulator that promotes anthocyanin accumulation under abiotic stress conditions.}, language = {en} } @article{MaZhangTureckovaetal.2018, author = {Ma, Xuemin and Zhang, Youjun and Tureckova, Veronika and Xue, Gang-Ping and Fernie, Alisdair R. and Mueller-R{\"o}ber, Bernd and Balazadeh, Salma}, title = {The NAC Transcription Factor SlNAP2 Regulates Leaf Senescence and Fruit Yield in Tomato}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {177}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {3}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.18.00292}, pages = {1286 -- 1302}, year = {2018}, abstract = {Leaf senescence is an essential physiological process in plants that supports the recycling of nitrogen and other nutrients to support the growth of developing organs, including young leaves, seeds, and fruits. Thus, the regulation of senescence is crucial for evolutionary success in wild populations and for increasing yield in crops. Here, we describe the influence of a NAC transcription factor, SlNAP2 (Solanum lycopersicum NAC-like, activated by Apetala3/Pistillata), that controls both leaf senescence and fruit yield in tomato (S. lycopersicum). SlNAP2 expression increases during age-dependent and dark-induced leaf senescence. We demonstrate that SlNAP2 activates SlSAG113 (S. lycopersicum SENESCENCE-ASSOCIATED GENE113), a homolog of Arabidopsis (Arabidopsis thaliana) SAG113, chlorophyll degradation genes such as SlSGR1 (S. lycopersicum senescence-inducible chloroplast stay-green protein 1) and SlPAO (S. lycopersicum pheide a oxygenase), and other downstream targets by directly binding to their promoters, thereby promoting leaf senescence. Furthermore, SlNAP2 directly controls the expression of genes important for abscisic acid (ABA) biosynthesis, S. lycopersicum 9-cis-epoxycarotenoid dioxygenase 1 (SlNCED1); transport, S. lycopersicum ABC transporter G family member 40 (SlABCG40); and degradation, S. lycopersicum ABA 8′-hydroxylase (SlCYP707A2), indicating that SlNAP2 has a complex role in establishing ABA homeostasis during leaf senescence. Inhibiting SlNAP2 expression in transgenic tomato plants impedes leaf senescence but enhances fruit yield and sugar content likely due to prolonged leaf photosynthesis in aging tomato plants. Our data indicate that SlNAP2 has a central role in controlling leaf senescence and fruit yield in tomato.}, language = {en} } @article{MalinovaAlseekhFeiletal.2017, author = {Malinova, Irina and Alseekh, Saleh and Feil, Regina and Fernie, Alisdair R. and Baumann, Otto and Schoettler, Mark Aurel and Lunn, John Edward and Fettke, J{\"o}rg}, title = {Starch Synthase 4 and Plastidal Phosphorylase Differentially Affect Starch Granule Number and Morphology}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {174}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.16.01859}, pages = {73 -- 85}, year = {2017}, abstract = {The process of starch granule formation in leaves of Arabidopsis ( Arabidopsis thaliana) is obscure. Besides STARCH SYNTHASE4 (SS4), the PLASTIDIAL PHOSPHORYLASE (PHS1) also seems to be involved, since dpe2-1/phs1a double mutants lacking both PHS1 and the cytosolic DISPROPORTIONATING ENZYME2 (DPE2) displayed only one starch granule per chloroplast under normal growth conditions. For further studies, a dpe2-1/phs1a/ss4 triple mutant and various combinations of double mutants were generated and metabolically analyzed with a focus on starch metabolism. The dpe2-1/phs1a/ ss4 mutant revealed a massive starch excess phenotype. Furthermore, these plants grown under 12 h of light/12 h of dark harbored a single large and spherical starch granule per plastid. The number of starch granules was constant when the light/dark regime was altered, but this was not observed in the parental lines. With regard to growth, photosynthetic parameters, and metabolic analyses, the triple mutant additionally displayed alterations in comparison with ss4 and dpe21/phs1a. The results clearly illustrate that PHS1 and SS4 are differently involved in starch granule formation and do not act in series. However, SS4 appears to exert a stronger influence. In connection with the characterized double mutants, we discuss the generation of starch granules and the observed formation of spherical starch granules.}, language = {en} } @article{MalinovaKunzAlseekhetal.2014, author = {Malinova, Irina and Kunz, Hans-Henning and Alseekh, Saleh and Herbst, Karoline and Fernie, Alisdair R. and Gierth, Markus and Fettke, J{\"o}rg}, title = {Reduction of the cytosolic phosphoglucomutase in arabidopsis reveals impact on plant growth, seed and root development, and carbohydrate partitioning}, series = {PLoS one}, volume = {9}, journal = {PLoS one}, number = {11}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0112468}, pages = {11}, year = {2014}, abstract = {Phosphoglucomutase (PGM) catalyses the interconversion of glucose 1-phosphate (G1P) and glucose 6-phosphate (G6P) and exists as plastidial (pPGM) and cytosolic (cPGM) isoforms. The plastidial isoform is essential for transitory starch synthesis in chloroplasts of leaves, whereas the cytosolic counterpart is essential for glucose phosphate partitioning and, therefore, for syntheses of sucrose and cell wall components. In Arabidopsis two cytosolic isoforms (PGM2 and PGM3) exist. Both PGM2 and PGM3 are redundant in function as single mutants reveal only small or no alterations compared to wild type with respect to plant primary metabolism. So far, there are no reports of Arabidopsis plants lacking the entire cPGM or total PGM activity, respectively. Therefore, amiRNA transgenic plants were generated and used for analyses of various parameters such as growth, development, and starch metabolism. The lack of the entire cPGM activity resulted in a strongly reduced growth revealed by decreased rosette fresh weight, shorter roots, and reduced seed production compared to wild type. By contrast content of starch, sucrose, maltose and cell wall components were significantly increased. The lack of both cPGM and pPGM activities in Arabidopsis resulted in dwarf growth, prematurely die off, and inability to develop a functional inflorescence. The combined results are discussed in comparison to potato, the only described mutant with lack of total PGM activity.}, language = {en} } @article{MalinovaMahlowAlseekhetal.2014, author = {Malinova, Irina and Mahlow, Sebastian and Alseekh, Saleh and Orawetz, Tom and Fernie, Alisdair R. and Baumann, Otto and Steup, Martin and Fettke, J{\"o}rg}, title = {Double knockout mutants of arabidopsis grown under normal conditions reveal that the plastidial phosphorylase isozyme participates in transitory starch metabolism}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {164}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {2}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.113.227843}, pages = {907 -- 921}, year = {2014}, abstract = {In leaves of two starch-related single-knockout lines lacking either the cytosolic transglucosidase (also designated as disproportionating enzyme 2, DPE2) or the maltose transporter (MEX1), the activity of the plastidial phosphorylase isozyme (PHS1) is increased. In both mutants, metabolism of starch-derived maltose is impaired but inhibition is effective at different subcellular sites. Two constitutive double knockout mutants were generated (designated as dpe2-1 x phs1a and mex1 x phs1b) both lacking functional PHS1. They reveal that in normally grown plants, the plastidial phosphorylase isozyme participates in transitory starch degradation and that the central carbon metabolism is closely integrated into the entire cell biology. All plants were grown either under continuous illumination or in a light-dark regime. Both double mutants were compromised in growth and, compared with the single knockout plants, possess less average leaf starch when grown in a light-dark regime. Starch and chlorophyll contents decline with leaf age. As revealed by transmission electron microscopy, mesophyll cells degrade chloroplasts, but degradation is not observed in plants grown under continuous illumination. The two double mutants possess similar but not identical phenotypes. When grown in a light-dark regime, mesophyll chloroplasts of dpe2-1 x phs1a contain a single starch granule but under continuous illumination more granules per chloroplast are formed. The other double mutant synthesizes more granules under either growth condition. In continuous light, growth of both double mutants is similar to that of the parental single knockout lines. Metabolite profiles and oligoglucan patterns differ largely in the two double mutants.}, language = {en} } @article{MathieuRivetGevaudantSicardetal.2010, author = {Mathieu-Rivet, Elodie and G{\´e}vaudant, Fr{\´e}d{\´e}ric and Sicard, Adrien and Salar, Sophie and Do, Phuc Thi and Mouras, Armand and Fernie, Alisdair R. and Gibon, Yves and Rothan, Christophe and Chevalier, Christian and Hernould, Michel}, title = {Functional analysis of the anaphase promoting complex activator CCS52A highlights the crucial role of endo- reduplication for fruit growth in tomato}, issn = {1365-313X}, year = {2010}, language = {en} } @article{NietzscheGuerraAlseekhetal.2017, author = {Nietzsche, Madlen and Guerra, Tiziana and Alseekh, Saleh and Wiermer, Marcel and Sonnewald, Sophia and Fernie, Alisdair R. and B{\"o}rnke, Frederik}, title = {STOREKEEPER RELATED1/G-Element Binding Protein (STKR1) Interacts with Protein Kinase SnRK1}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {176}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {2}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.17.01461}, pages = {1773 -- 1792}, year = {2017}, abstract = {Sucrose nonfermenting related kinase1 (SnRK1) is a conserved energy sensor kinase that regulates cellular adaptation to energy deficit in plants. Activation of SnRK1 leads to the down-regulation of ATP-consuming biosynthetic processes and the stimulation of energy-generating catabolic reactions by transcriptional reprogramming and posttranslational modifications. Although considerable progress has been made during the last years in understanding the SnRK1 signaling pathway, many of its components remain unidentified. Here, we show that the catalytic alpha-subunits KIN10 and KIN11 of the Arabidopsis (Arabidopsis thaliana) SnRK1 complex interact with the STOREKEEPER RELATED1/G-Element Binding Protein (STKR1) inside the plant cell nucleus. Overexpression of STKR1 in transgenic Arabidopsis plants led to reduced growth, a delay in flowering, and strongly attenuated senescence. Metabolite profiling revealed that the transgenic lines exhausted their carbohydrates during the dark period to a greater extent than the wild type and accumulated a range of amino acids. At the global transcriptome level, genes affected by STKR1 overexpression were broadly associated with systemic acquired resistance, and transgenic plants showed enhanced resistance toward a virulent strain of the biotrophic oomycete pathogen Hyaloperonospora arabidopsidis Noco2. We discuss a possible connection of STKR1 function, SnRK1 signaling, and plant immunity.}, language = {en} } @article{NunesNesiAlseekhdeOliveiraSilvaetal.2019, author = {Nunes-Nesi, Adriano and Alseekh, Saleh and de Oliveira Silva, Franklin Magnum and Omranian, Nooshin and Lichtenstein, Gabriel and Mirnezhad, Mohammad and Romero Gonzalez, Roman R. and Sabio y Garcia, Julia and Conte, Mariana and Leiss, Kirsten A. and Klinkhamer, Peter Gerardus Leonardus and Nikoloski, Zoran and Carrari, Fernando and Fernie, Alisdair R.}, title = {Identification and characterization of metabolite quantitative trait loci in tomato leaves and comparison with those reported for fruits and seeds}, series = {Metabolomics}, volume = {15}, journal = {Metabolomics}, number = {46}, publisher = {Springer}, address = {New York}, issn = {1573-3882}, doi = {10.1007/s11306-019-1503-8}, pages = {13}, year = {2019}, abstract = {IntroductionTo date, most studies of natural variation and metabolite quantitative trait loci (mQTL) in tomato have focused on fruit metabolism, leaving aside the identification of genomic regions involved in the regulation of leaf metabolism.ObjectiveThis study was conducted to identify leaf mQTL in tomato and to assess the association of leaf metabolites and physiological traits with the metabolite levels from other tissues.MethodsThe analysis of components of leaf metabolism was performed by phenotypying 76 tomato ILs with chromosome segments of the wild species Solanum pennellii in the genetic background of a cultivated tomato (S. lycopersicum) variety M82. The plants were cultivated in two different environments in independent years and samples were harvested from mature leaves of non-flowering plants at the middle of the light period. The non-targeted metabolite profiling was obtained by gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). With the data set obtained in this study and already published metabolomics data from seed and fruit, we performed QTL mapping, heritability and correlation analyses.ResultsChanges in metabolite contents were evident in the ILs that are potentially important with respect to stress responses and plant physiology. By analyzing the obtained data, we identified 42 positive and 76 negative mQTL involved in carbon and nitrogen metabolism.ConclusionsOverall, these findings allowed the identification of S. lycopersicum genome regions involved in the regulation of leaf primary carbon and nitrogen metabolism, as well as the association of leaf metabolites with metabolites from seeds and fruits.}, language = {en} } @misc{OmranianKleessenTohgeetal.2015, author = {Omranian, Nooshin and Kleessen, Sabrina and Tohge, Takayuki and Klie, Sebastian and Basler, Georg and M{\"u}ller-R{\"o}ber, Bernd and Fernie, Alisdair R. and Nikoloski, Zoran}, title = {Differential metabolic and coexpression networks of plant metabolism}, series = {Trends in plant science}, volume = {20}, journal = {Trends in plant science}, number = {5}, publisher = {Elsevier}, address = {London}, issn = {1360-1385}, doi = {10.1016/j.tplants.2015.02.002}, pages = {266 -- 268}, year = {2015}, abstract = {Recent analyses have demonstrated that plant metabolic networks do not differ in their structural properties and that genes involved in basic metabolic processes show smaller coexpression than genes involved in specialized metabolism. By contrast, our analysis reveals differences in the structure of plant metabolic networks and patterns of coexpression for genes in (non)specialized metabolism. Here we caution that conclusions concerning the organization of plant metabolism based on network-driven analyses strongly depend on the computational approaches used.}, language = {en} } @article{PandeyYuOmranianetal.2019, author = {Pandey, Prashant K. and Yu, Jing and Omranian, Nooshin and Alseekh, Saleh and Vaid, Neha and Fernie, Alisdair R. and Nikoloski, Zoran and Laitinen, Roosa A. E.}, title = {Plasticity in metabolism underpins local responses to nitrogen in Arabidopsis thaliana populations}, series = {Plant Direct}, volume = {3}, journal = {Plant Direct}, number = {11}, publisher = {John Wiley \& sonst LTD}, address = {Chichester}, issn = {2475-4455}, doi = {10.1002/pld3.186}, pages = {6}, year = {2019}, abstract = {Nitrogen (N) is central for plant growth, and metabolic plasticity can provide a strategy to respond to changing N availability. We showed that two local A. thaliana populations exhibited differential plasticity in the compounds of photorespiratory and starch degradation pathways in response to three N conditions. Association of metabolite levels with growth-related and fitness traits indicated that controlled plasticity in these pathways could contribute to local adaptation and play a role in plant evolution.}, language = {en} } @article{RibeiroAraujoFernieetal.2012, author = {Ribeiro, Dimas M. and Araujo, Wagner L. and Fernie, Alisdair R. and Schippers, Jos H. M. and M{\"u}ller-R{\"o}ber, Bernd}, title = {Action of Gibberellins on growth and metabolism of arabidopsis plants Associated with high concentration of carbon dioxide}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {160}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {4}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.112.204842}, pages = {1781 -- 1794}, year = {2012}, abstract = {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.}, language = {en} } @article{RibeiroAraujoFernieetal.2012, author = {Ribeiro, Dimas M. and Araujo, Wagner L. and Fernie, Alisdair R. and Schippers, Jos H. M. and M{\"u}ller-R{\"o}ber, Bernd}, title = {Translatome and metabolome effects triggered by gibberellins during rosette growth in Arabidopsis}, series = {Journal of experimental botany}, volume = {63}, journal = {Journal of experimental botany}, number = {7}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0022-0957}, doi = {10.1093/jxb/err463}, pages = {2769 -- 2786}, year = {2012}, abstract = {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.}, language = {en} } @article{RobainaEstevezDalosoZhangetal.2017, author = {Robaina-Estevez, Semidan and Daloso, Danilo M. and Zhang, Youjun and Fernie, Alisdair R. and Nikoloski, Zoran}, title = {Resolving the central metabolism of Arabidopsis guard cells}, series = {Scientific reports}, volume = {7}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-017-07132-9}, pages = {1913 -- 1932}, year = {2017}, abstract = {Photosynthesis and water use efficiency, key factors affecting plant growth, are directly controlled by microscopic and adjustable pores in the leaf-the stomata. The size of the pores is modulated by the guard cells, which rely on molecular mechanisms to sense and respond to environmental changes. It has been shown that the physiology of mesophyll and guard cells differs substantially. However, the implications of these differences to metabolism at a genome-scale level remain unclear. Here, we used constraint-based modeling to predict the differences in metabolic fluxes between the mesophyll and guard cells of Arabidopsis thaliana by exploring the space of fluxes that are most concordant to cell-type-specific transcript profiles. An independent C-13-labeling experiment using isolated mesophyll and guard cells was conducted and provided support for our predictions about the role of the Calvin-Benson cycle in sucrose synthesis in guard cells. The combination of in silico with in vivo analyses indicated that guard cells have higher anaplerotic CO2 fixation via phosphoenolpyruvate carboxylase, which was demonstrated to be an important source of malate. Beyond highlighting the metabolic differences between mesophyll and guard cells, our findings can be used in future integrated modeling of multicellular plant systems and their engineering towards improved growth.}, language = {en} } @article{RodriguezCubillosTongAlseekhetal.2018, author = {Rodriguez Cubillos, Andres Eduardo and Tong, Hao and Alseekh, Saleh and de Abreu e Lima, Francisco Anastacio and Yu, Jing and Fernie, Alisdair R. and Nikoloski, Zoran and Laitinen, Roosa A. E.}, title = {Inheritance patterns in metabolism and growth in diallel crosses of Arabidopsis thaliana from a single growth habitat}, series = {Heredity}, volume = {120}, journal = {Heredity}, number = {5}, publisher = {Nature Publ. Group}, address = {London}, issn = {0018-067X}, doi = {10.1038/s41437-017-0030-5}, pages = {463 -- 473}, year = {2018}, abstract = {Metabolism is a key determinant of plant growth and modulates plant adaptive responses. Increased metabolic variation due to heterozygosity may be beneficial for highly homozygous plants if their progeny is to respond to sudden changes in the habitat. Here, we investigate the extent to which heterozygosity contributes to the variation in metabolism and size of hybrids of Arabidopsis thaliana whose parents are from a single growth habitat. We created full diallel crosses among seven parents, originating from Southern Germany, and analysed the inheritance patterns in primary and secondary metabolism as well as in rosette size in situ. In comparison to primary metabolites, compounds from secondary metabolism were more variable and showed more pronounced non-additive inheritance patterns which could be attributed to epistasis. In addition, we showed that glucosinolates, among other secondary metabolites, were positively correlated with a proxy for plant size. Therefore, our study demonstrates that heterozygosity in local A. thaliana population generates metabolic variation and may impact several tasks directly linked to metabolism.}, language = {en} } @article{RohrmannTohgeAlbaetal.2011, author = {Rohrmann, Johannes and Tohge, Takayuki and Alba, Rob and Osorio, Sonia and Caldana, Camila and McQuinn, Ryan and Arvidsson, Samuel Janne and van der Merwe, Margaretha J. and Riano-Pachon, Diego Mauricio and M{\"u}ller-R{\"o}ber, Bernd and Fei, Zhangjun and Nesi, Adriano Nunes and Giovannoni, James J. and Fernie, Alisdair R.}, title = {Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development}, series = {The plant journal}, volume = {68}, journal = {The plant journal}, number = {6}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {0960-7412}, doi = {10.1111/j.1365-313X.2011.04750.x}, pages = {999 -- 1013}, year = {2011}, abstract = {Maturation of fleshy fruits such as tomato (Solanum lycopersicum) is subject to tight genetic control. Here we describe the development of a quantitative real-time PCR platform that allows accurate quantification of the expression level of approximately 1000 tomato transcription factors. In addition to utilizing this novel approach, we performed cDNA microarray analysis and metabolite profiling of primary and secondary metabolites using GC-MS and LC-MS, respectively. We applied these platforms to pericarp material harvested throughout fruit development, studying both wild-type Solanum lycopersicum cv. Ailsa Craig and the hp1 mutant. This mutant is functionally deficient in the tomato homologue of the negative regulator of the light signal transduction gene DDB1 from Arabidopsis, and is furthermore characterized by dramatically increased pigment and phenolic contents. We choose this particular mutant as it had previously been shown to have dramatic alterations in the content of several important fruit metabolites but relatively little impact on other ripening phenotypes. The combined dataset was mined in order to identify metabolites that were under the control of these transcription factors, and, where possible, the respective transcriptional regulation underlying this control. The results are discussed in terms of both programmed fruit ripening and development and the transcriptional and metabolic shifts that occur in parallel during these processes.}, language = {en} } @article{SchmidtMieuletHubbertenetal.2013, author = {Schmidt, Romy and Mieulet, Delphine and Hubberten, Hans-Michael and Obata, Toshihiro and H{\"o}fgen, Rainer and Fernie, Alisdair R. and Fisahn, Joachim and Segundo, Blanca San and Guiderdoni, Emmanuel and Schippers, Jos H. M. and M{\"u}ller-R{\"o}ber, Bernd}, title = {Salt-responsive ERF1 regulates reactive oxygen species-dependent signaling during the initial response to salt stress in rice}, series = {The plant cell}, volume = {25}, journal = {The plant cell}, number = {6}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {1040-4651}, doi = {10.1105/tpc.113.113068}, pages = {2115 -- 2131}, year = {2013}, abstract = {Early detection of salt stress is vital for plant survival and growth. Still, the molecular processes controlling early salt stress perception and signaling are not fully understood. Here, we identified SALT-RESPONSIVE ERF1 (SERF1), a rice (Oryza sativa) transcription factor (TF) gene that shows a root-specific induction upon salt and hydrogen peroxide (H2O2) treatment. Loss of SERF1 impairs the salt-inducible expression of genes encoding members of a mitogen-activated protein kinase (MAPK) cascade and salt tolerance-mediating TFs. Furthermore, we show that SERF1-dependent genes are H2O2 responsive and demonstrate that SERF1 binds to the promoters of MAPK KINASE KINASE6 (MAP3K6), MAPK5, DEHYDRATION-RESPONSIVE ELEMENT BINDING2A (DREB2A), and ZINC FINGER PROTEIN179 (ZFP179) in vitro and in vivo. SERF1 also directly induces its own gene expression. In addition, SERF1 is a phosphorylation target of MAPK5, resulting in enhanced transcriptional activity of SERF1 toward its direct target genes. In agreement, plants deficient for SERF1 are more sensitive to salt stress compared with the wild type, while constitutive overexpression of SERF1 improves salinity tolerance. We propose that SERF1 amplifies the reactive oxygen species-activated MAPK cascade signal during the initial phase of salt stress and translates the salt-induced signal into an appropriate expressional response resulting in salt tolerance.}, language = {en} } @article{SchmidtSchippersMieuletetal.2013, author = {Schmidt, Romy and Schippers, Jos H. M. and Mieulet, Delphine and Obata, Toshihiro and Fernie, Alisdair R. and Guiderdoni, Emmanuel and M{\"u}ller-R{\"o}ber, Bernd}, title = {Multipass, a rice R2R3-type MYB transcription factor, regulates adaptive growth by integrating multiple hormonal pathways}, series = {The plant journal}, volume = {76}, journal = {The plant journal}, number = {2}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0960-7412}, doi = {10.1111/tpj.12286}, pages = {258 -- 273}, year = {2013}, abstract = {Growth regulation is an important aspect of plant adaptation during environmental perturbations. Here, the role of MULTIPASS (OsMPS), an R2R3-type MYB transcription factor of rice, was explored. OsMPS is induced by salt stress and expressed in vegetative and reproductive tissues. Over-expression of OsMPS reduces growth under non-stress conditions, while knockdown plants display increased biomass. OsMPS expression is induced by abscisic acid and cytokinin, but is repressed by auxin, gibberellin and brassinolide. Growth retardation caused by OsMPS over-expression is partially restored by auxin application. Expression profiling revealed that OsMPS negatively regulates the expression of EXPANSIN (EXP) and cell-wall biosynthesis as well as phytohormone signaling genes. Furthermore, the expression of OsMPS-dependent genes is regulated by auxin, cytokinin and abscisic acid. Moreover, we show that OsMPS is a direct upstream regulator of OsEXPA4, OsEXPA8, OsEXPB2, OsEXPB3, OsEXPB6 and the endoglucanase genes OsGLU5 and OsGLU14. The multiple responses of OsMPS and its target genes to various hormones suggest an integrative function of OsMPS in the cross-talk between phytohormones and the environment to regulate adaptive growth.}, language = {en} } @article{SchroederLissoObataetal.2014, author = {Schroeder, Florian and Lisso, Janina and Obata, Toshihiro and Erban, Alexander and Maximova, Eugenia and Giavalisco, Patrick and Kopka, Joachim and Fernie, Alisdair R. and Willmitzer, Lothar and Muessig, Carsten}, title = {Consequences of induced brassinosteroid deficiency in Arabidopsis leaves}, series = {BMC plant biology}, volume = {14}, journal = {BMC plant biology}, publisher = {BioMed Central}, address = {London}, issn = {1471-2229}, doi = {10.1186/s12870-014-0309-0}, pages = {14}, year = {2014}, abstract = {Background: The identification of brassinosteroid (BR) deficient and BR insensitive mutants provided conclusive evidence that BR is a potent growth-promoting phytohormone. Arabidopsis mutants are characterized by a compact rosette structure, decreased plant height and reduced root system, delayed development, and reduced fertility. Cell expansion, cell division, and multiple developmental processes depend on BR. The molecular and physiological basis of BR action is diverse. The BR signalling pathway controls the activity of transcription factors, and numerous BR responsive genes have been identified. The analysis of dwarf mutants, however, may to some extent reveal phenotypic changes that are an effect of the altered morphology and physiology. This restriction holds particularly true for the analysis of established organs such as rosette leaves. Results: In this study, the mode of BR action was analysed in established leaves by means of two approaches. First, an inhibitor of BR biosynthesis (brassinazole) was applied to 21-day-old wild-type plants. Secondly, BR complementation of BR deficient plants, namely CPD (constitutive photomorphogenic dwarf)-antisense and cbb1 (cabbage1) mutant plants was stopped after 21 days. BR action in established leaves is associated with stimulated cell expansion, an increase in leaf index, starch accumulation, enhanced CO2 release by the tricarboxylic acid cycle, and increased biomass production. Cell number and protein content were barely affected. Conclusion: Previous analysis of BR promoted growth focused on genomic effects. However, the link between growth and changes in gene expression patterns barely provided clues to the physiological and metabolic basis of growth. Our study analysed comprehensive metabolic data sets of leaves with altered BR levels. The data suggest that BR promoted growth may depend on the increased provision and use of carbohydrates and energy. BR may stimulate both anabolic and catabolic pathways.}, language = {en} } @article{SchwahndeSouzaFernieetal.2014, author = {Schwahn, Kevin and de Souza, Leonardo Perez and Fernie, Alisdair R. and Tohge, Takayuki}, title = {Metabolomics-assisted refinement of the pathways of steroidal glycoalkaloid biosynthesis in the tomato clade}, series = {Journal of integrative plant biology}, volume = {56}, journal = {Journal of integrative plant biology}, number = {9}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1672-9072}, doi = {10.1111/jipb.12274}, pages = {864 -- 875}, year = {2014}, abstract = {Steroidal glycoalkaloids (SGAs) are nitrogen-containing secondary metabolites of the Solanum species, which are known to have large chemical and bioactive diversity in nature. While recent effort and development on LC/MS techniques for SGA profiling have elucidated the main pathways of SGA metabolism in tomato, the problem of peak annotation still remains due to the vast diversity of chemical structure and similar on overlapping of chemical formula. Here we provide a case study of peak classification and annotation approach by integration of species and tissue specificities of SGA accumulation for provision of comprehensive pathways of SGA biosynthesis. In order to elucidate natural diversity of SGA biosynthesis, a total of 169 putative SGAs found in eight tomato accessions (Solanum lycopersicum, S. pimpinellifolium, S. cheesmaniae, S. chmielewskii, S. neorickii, S. peruvianum, S. habrochaites, S. pennellii) and four tissue types were used for correlation analysis. The results obtained in this study contribute annotation and classification of SGAs as well as detecting putative novel biosynthetic branch points. As such this represents a novel strategy for peak annotation for plant secondary metabolites.}, language = {en} } @article{ShahnejatBushehriAlluMehterovetal.2017, author = {Shahnejat-Bushehri, Sara and Allu, Annapurna Devi and Mehterov, Nikolay and Thirumalaikumar, Venkatesh P. and Alseekh, Saleh and Fernie, Alisdair R. and Mueller-Roeber, Bernd and Balazadeh, Salma}, title = {Arabidopsis NAC Transcription Factor JUNGBRUNNEN1 Exerts Conserved Control Over Gibberellin and Brassinosteroid Metabolism and Signaling Genes in Tomato}, series = {Frontiers in plant science}, volume = {8}, journal = {Frontiers in plant science}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2017.00214}, pages = {13}, year = {2017}, abstract = {The Arabidopsis thaliana NAC transcription factor JUNGBRUNNEN1 (AtJUB1) regulates growth by directly repressing GA3ox1 and DWF4, two key genes involved in gibberellin (GA) and brassinosteroid (BR) biosynthesis, respectively, leading to GA and BR deficiency phenotypes. AtJUB1 also reduces the expression of PIF4, a bHLH transcription factor that positively controls cell elongation, while it stimulates the expression of DELLA genes, which are important repressors of growth. Here, we extend our previous findings by demonstrating that AtJUB1 induces similar GA and BR deficiency phenotypes and changes in gene expression when overexpressed in tomato (Solanum lycopersicum). Importantly, and in accordance with the growth phenotypes observed, AtJUB1 inhibits the expression of growth-supporting genes, namely the tomato orthologs of GA3ox1, DWF4 and PIF4, but activates the expression of DELLA orthologs, by directly binding to their promoters. Overexpression of AtJUB1 in tomato delays fruit ripening, which is accompanied by reduced expression of several ripeningrelated genes, and leads to an increase in the levels of various amino acids (mostly proline, beta-alanine, and phenylalanine), gamma-aminobutyric acid (GABA), and major organic acids including glutamic acid and aspartic acid. The fact that AtJUB1 exerts an inhibitory effect on the GA/BR biosynthesis and PIF4 genes but acts as a direct activator of DELLA genes in both, Arabidopsis and tomato, strongly supports the model that the molecular constituents of the JUNGBRUNNEN1 growth control module are considerably conserved across species.}, language = {en} } @article{SmirnovaFernieSpahnetal.2017, author = {Smirnova, Julia and Fernie, Alisdair R. and Spahn, Christian M. T. and Steup, Martin}, title = {Photometric assay of maltose and maltose-forming enzyme activity by using 4-alpha-glucanotransferase (DPE2) from higher plants}, series = {Analytical biochemistry : methods in the biological sciences}, volume = {532}, journal = {Analytical biochemistry : methods in the biological sciences}, publisher = {Elsevier}, address = {San Diego}, issn = {0003-2697}, doi = {10.1016/j.ab.2017.05.026}, pages = {72 -- 82}, year = {2017}, abstract = {Maltose frequently occurs as intermediate of the central carbon metabolism of prokaryotic and eukaryotic cells. Various mutants possess elevated maltose levels. Maltose exists as two anomers, (alpha- and beta-form) which are rapidly interconverted without requiring enzyme-mediated catalysis. As maltose is often abundant together with other oligoglucans, selective quantification is essential. In this communication, we present a photometric maltose assay using 4-alpha-glucanotransferase (AtDPE2) from Arabidopsis thaliana. Under in vitro conditions, AtDPE2 utilizes maltose as glucosyl donor and glycogen as acceptor releasing the other hexosyl unit as free glucose which is photometrically quantified following enzymatic phosphorylation and oxidation. Under the conditions used, DPE2 does not noticeably react with other di- or oligosaccharides. Selectivity compares favorably with that of maltase frequently used in maltose assays. Reducing end interconversion of the two maltose anomers is in rapid equilibrium and, therefore, the novel assay measures total maltose contents. Furthermore, an AtDPE2-based continuous photometric assay is presented which allows to quantify beta-amylase activity and was found to be superior to a conventional test. Finally, the AtDPE2-based maltose assay was used to quantify leaf maltose contents of both Arabidopsis wild type and AtDPE2-deficient plants throughout the light-dark cycle. These data are presented together with assimilatory starch levels. (C) 2017 Published by Elsevier Inc.}, language = {en} } @article{SmithDupontMcCarthyetal.2019, author = {Smith, Sarah R. and Dupont, Chris L. and McCarthy, James K. and Broddrick, Jared T. and Obornik, Miroslav and Horak, Ales and F{\"u}ssy, Zolt{\´a}n and Cihlar, Jaromir and Kleessen, Sabrina and Zheng, Hong and McCrow, John P. and Hixson, Kim K. and Araujo, Wagner L. and Nunes-Nesi, Adriano and Fernie, Alisdair R. and Nikoloski, Zoran and Palsson, Bernhard O. and Allen, Andrew E.}, title = {Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom}, series = {Nature Communications}, volume = {10}, journal = {Nature Communications}, publisher = {Nature Publ. Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/s41467-019-12407-y}, pages = {14}, year = {2019}, abstract = {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.}, language = {en} } @article{SulpiceNikoloskiTschoepetal.2013, author = {Sulpice, Ronan and Nikoloski, Zoran and Tschoep, Hendrik and Antonio, Carla and Kleessen, Sabrina and Larhlimi, Abdelhalim and Selbig, Joachim and Ishihara, Hirofumi and Gibon, Yves and Fernie, Alisdair R. and Stitt, Mark}, title = {Impact of the Carbon and Nitrogen Supply on Relationships and Connectivity between Metabolism and Biomass in a Broad Panel of Arabidopsis Accessions(1[W][OA])}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {162}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {1}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.112.210104}, pages = {347 -- 363}, year = {2013}, abstract = {Natural genetic diversity provides a powerful tool to study the complex interrelationship between metabolism and growth. Profiling of metabolic traits combined with network-based and statistical analyses allow the comparison of conditions and identification of sets of traits that predict biomass. However, it often remains unclear why a particular set of metabolites is linked with biomass and to what extent the predictive model is applicable beyond a particular growth condition. A panel of 97 genetically diverse Arabidopsis (Arabidopsis thaliana) accessions was grown in near-optimal carbon and nitrogen supply, restricted carbon supply, and restricted nitrogen supply and analyzed for biomass and 54 metabolic traits. Correlation-based metabolic networks were generated from the genotype-dependent variation in each condition to reveal sets of metabolites that show coordinated changes across accessions. The networks were largely specific for a single growth condition. Partial least squares regression from metabolic traits allowed prediction of biomass within and, slightly more weakly, across conditions (cross-validated Pearson correlations in the range of 0.27-0.58 and 0.21-0.51 and P values in the range of <0.001-<0.13 and <0.001-<0.023, respectively). Metabolic traits that correlate with growth or have a high weighting in the partial least squares regression were mainly condition specific and often related to the resource that restricts growth under that condition. Linear mixed-model analysis using the combined metabolic traits from all growth conditions as an input indicated that inclusion of random effects for the conditions improves predictions of biomass. Thus, robust prediction of biomass across a range of conditions requires condition-specific measurement of metabolic traits to take account of environment-dependent changes of the underlying networks.}, language = {en} } @article{SulpicePylIshiharaetal.2009, author = {Sulpice, Ronan and Pyl, Eva-Theresa and Ishihara, Hirofumi and Trenkamp, Sandra and Steinfath, Matthias and Witucka-Wall, Hanna and Gibon, Yves and Usadel, Bj{\"o}rn and Poree, Fabien and Piques, Maria Conceicao and von Korff, Maria and Steinhauser, Marie Caroline and Keurentjes, Joost J. B. and Guenther, Manuela and Hoehne, Melanie and Selbig, Joachim and Fernie, Alisdair R. and Altmann, Thomas and Stitt, Mark}, title = {Starch as a major integrator in the regulation of plant growth}, issn = {0027-8424}, doi = {10.1073/pnas.0903478106}, year = {2009}, abstract = {Rising demand for food and bioenergy makes it imperative to breed for increased crop yield. Vegetative plant growth could be driven by resource acquisition or developmental programs. Metabolite profiling in 94 Arabidopsis accessions revealed that biomass correlates negatively with many metabolites, especially starch. Starch accumulates in the light and is degraded at night to provide a sustained supply of carbon for growth. Multivariate analysis revealed that starch is an integrator of the overall metabolic response. We hypothesized that this reflects variation in a regulatory network that balances growth with the carbon supply. Transcript profiling in 21 accessions revealed coordinated changes of transcripts of more than 70 carbon-regulated genes and identified 2 genes (myo-inositol-1- phosphate synthase, a Kelch-domain protein) whose transcripts correlate with biomass. The impact of allelic variation at these 2 loci was shown by association mapping, identifying them as candidate lead genes with the potential to increase biomass production.}, language = {en} } @article{ToepferCaldanaGrimbsetal.2013, author = {T{\"o}pfer, Nadine and Caldana, Camila and Grimbs, Sergio and Willmitzer, Lothar and Fernie, Alisdair R. and Nikoloski, Zoran}, title = {Integration of genome-scale modeling and transcript profiling reveals metabolic pathways underlying light and temperature acclimation in arabidopsis}, series = {The plant cell}, volume = {25}, journal = {The plant cell}, number = {4}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {1040-4651}, doi = {10.1105/tpc.112.108852}, pages = {1197 -- 1211}, year = {2013}, abstract = {Understanding metabolic acclimation of plants to challenging environmental conditions is essential for dissecting the role of metabolic pathways in growth and survival. As stresses involve simultaneous physiological alterations across all levels of cellular organization, a comprehensive characterization of the role of metabolic pathways in acclimation necessitates integration of genome-scale models with high-throughput data. Here, we present an integrative optimization-based approach, which, by coupling a plant metabolic network model and transcriptomics data, can predict the metabolic pathways affected in a single, carefully controlled experiment. Moreover, we propose three optimization-based indices that characterize different aspects of metabolic pathway behavior in the context of the entire metabolic network. We demonstrate that the proposed approach and indices facilitate quantitative comparisons and characterization of the plant metabolic response under eight different light and/or temperature conditions. The predictions of the metabolic functions involved in metabolic acclimation of Arabidopsis thaliana to the changing conditions are in line with experimental evidence and result in a hypothesis about the role of homocysteine-to-Cys interconversion and Asn biosynthesis. The approach can also be used to reveal the role of particular metabolic pathways in other scenarios, while taking into consideration the entirety of characterized plant metabolism.}, language = {en} } @article{WangTohgeIvakovetal.2015, author = {Wang, Ting and Tohge, Takayuki and Ivakov, Alexander and M{\"u}ller-R{\"o}ber, Bernd and Fernie, Alisdair R. and Mutwil, Marek and Schippers, Jos H. M. and Persson, Staffan}, title = {Salt-Related MYB1 Coordinates Abscisic Acid Biosynthesis and Signaling during Salt Stress in Arabidopsis}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {169}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {2}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.15.00962}, pages = {1027 -- +}, year = {2015}, abstract = {Abiotic stresses, such as salinity, cause global yield loss of all major crop plants. Factors and mechanisms that can aid in plant breeding for salt stress tolerance are therefore of great importance for food and feed production. Here, we identified a MYB-like transcription factor, Salt-Related MYB1 (SRM1), that negatively affects Arabidopsis (Arabidopsis thaliana) seed germination under saline conditions by regulating the levels of the stress hormone abscisic acid (ABA). Accordingly, several ABA biosynthesis and signaling genes act directly downstream of SRM1, including SALT TOLERANT1/NINE-CIS-EPOXYCAROTENOID DIOXYGENASE3, RESPONSIVE TO DESICCATION26, and Arabidopsis NAC DOMAIN CONTAINING PROTEIN19. Furthermore, SRM1 impacts vegetative growth and leaf shape. We show that SRM1 is an important transcriptional regulator that directly targets ABA biosynthesis and signaling-related genes and therefore may be regarded as an important regulator of ABA-mediated salt stress tolerance.}, language = {en} } @article{WatanabeBalazadehTohgeetal.2013, author = {Watanabe, Mutsumi and Balazadeh, Salma and Tohge, Takayuki and Erban, Alexander and Giavalisco, Patrick and Kopka, Joachim and M{\"u}ller-R{\"o}ber, Bernd and Fernie, Alisdair R. and H{\"o}fgen, Rainer}, title = {Comprehensive dissection of spatiotemporal metabolic shifts in primary, secondary, and lipid metabolism during developmental senescence in arabidopsis}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {162}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {3}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.113.217380}, pages = {1290 -- 1310}, year = {2013}, abstract = {Developmental senescence is a coordinated physiological process in plants and is critical for nutrient redistribution from senescing leaves to newly formed sink organs, including young leaves and developing seeds. Progress has been made concerning the genes involved and the regulatory networks controlling senescence. The resulting complex metabolome changes during senescence have not been investigated in detail yet. Therefore, we conducted a comprehensive profiling of metabolites, including pigments, lipids, sugars, amino acids, organic acids, nutrient ions, and secondary metabolites, and determined approximately 260 metabolites at distinct stages in leaves and siliques during senescence in Arabidopsis (Arabidopsis thaliana). This provided an extensive catalog of metabolites and their spatiotemporal cobehavior with progressing senescence. Comparison with silique data provides clues to source-sink relations. Furthermore, we analyzed the metabolite distribution within single leaves along the basipetal sink-source transition trajectory during senescence. Ceramides, lysolipids, aromatic amino acids, branched chain amino acids, and stress-induced amino acids accumulated, and an imbalance of asparagine/aspartate, glutamate/glutamine, and nutrient ions in the tip region of leaves was detected. Furthermore, the spatiotemporal distribution of tricarboxylic acid cycle intermediates was already changed in the presenescent leaves, and glucosinolates, raffinose, and galactinol accumulated in the base region of leaves with preceding senescence. These results are discussed in the context of current models of the metabolic shifts occurring during developmental and environmentally induced senescence. As senescence processes are correlated to crop yield, the metabolome data and the approach provided here can serve as a blueprint for the analysis of traits and conditions linking crop yield and senescence.}, language = {en} } @article{WatanabeTohgeBalazadehetal.2018, author = {Watanabe, Mutsumi and Tohge, Takayuki and Balazadeh, Salma and Erban, Alexander and Giavalisco, Patrick and Kopka, Joachim and Mueller-Roeber, Bernd and Fernie, Alisdair R. and Hoefgen, Rainer}, title = {Comprehensive Metabolomics Studies of Plant Developmental Senescence}, series = {Plant Senescence: Methods and Protocols}, volume = {1744}, journal = {Plant Senescence: Methods and Protocols}, publisher = {Humana Press}, address = {Totowa}, isbn = {978-1-4939-7672-0}, issn = {1064-3745}, doi = {10.1007/978-1-4939-7672-0_28}, pages = {339 -- 358}, year = {2018}, abstract = {Leaf senescence is an essential developmental process that involves diverse metabolic changes associated with degradation of macromolecules allowing nutrient recycling and remobilization. In contrast to the significant progress in transcriptomic analysis of leaf senescence, metabolomics analyses have been relatively limited. A broad overview of metabolic changes during leaf senescence including the interactions between various metabolic pathways is required to gain a better understanding of the leaf senescence allowing to link transcriptomics with metabolomics and physiology. In this chapter, we describe how to obtain comprehensive metabolite profiles and how to dissect metabolic shifts during leaf senescence in the model plant Arabidopsis thaliana. Unlike nucleic acid analysis for transcriptomics, a comprehensive metabolite profile can only be achieved by combining a suite of analytic tools. Here, information is provided for measurements of the contents of chlorophyll, soluble proteins, and starch by spectrophotometric methods, ions by ion chromatography, thiols and amino acids by HPLC, primary metabolites by GC/TOF-MS, and secondary metabolites and lipophilic metabolites by LC/ESI-MS. These metabolite profiles provide a rich catalogue of metabolic changes during leaf senescence, which is a helpful database and blueprint to be correlated to future studies such as transcriptome and proteome analyses, forward and reverse genetic studies, or stress-induced senescence studies.}, language = {en} } @article{WuAlluGarapatietal.2012, author = {Wu, Anhui and Allu, Annapurna Devi and Garapati, Prashanth and Siddiqui, Hamad and Dortay, Hakan and Zanor, Maria-Ines and Asensi-Fabado, Maria Amparo and Munne-Bosch, Sergi and Antonio, Carla and Tohge, Takayuki and Fernie, Alisdair R. and Kaufmann, Kerstin and Xue, Gang-Ping and M{\"u}ller-R{\"o}ber, Bernd and Balazadeh, Salma}, title = {Jungbrunnen1, a reactive oxygen species-responsive NAC transcription factor, regulates longevity in arabidopsis}, series = {The plant cell}, volume = {24}, journal = {The plant cell}, number = {2}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {1040-4651}, doi = {10.1105/tpc.111.090894}, pages = {482 -- 506}, year = {2012}, abstract = {The transition from juvenility through maturation to senescence is a complex process that involves the regulation of longevity. Here, we identify JUNGBRUNNEN1 (JUB1), a hydrogen peroxide (H2O2)-induced NAC transcription factor, as a central longevity regulator in Arabidopsis thaliana. JUB1 overexpression strongly delays senescence, dampens intracellular H2O2 levels, and enhances tolerance to various abiotic stresses, whereas in jub1-1 knockdown plants, precocious senescence and lowered abiotic stress tolerance are observed. A JUB1 binding site containing a RRYGCCGT core sequence is present in the promoter of DREB2A, which plays an important role in abiotic stress responses. JUB1 transactivates DREB2A expression in mesophyll cell protoplasts and transgenic plants and binds directly to the DREB2A promoter. Transcriptome profiling of JUB1 overexpressors revealed elevated expression of several reactive oxygen species-responsive genes, including heat shock protein and glutathione S-transferase genes, whose expression is further induced by H2O2 treatment. Metabolite profiling identified elevated Pro and trehalose levels in JUB1 overexpressors, in accordance with their enhanced abiotic stress tolerance. We suggest that JUB1 constitutes a central regulator of a finely tuned control system that modulates cellular H2O2 level and primes the plants for upcoming stress through a gene regulatory network that involves DREB2A.}, language = {en} } @article{ZhangChenSiemiatkowskaetal.2020, author = {Zhang, Youjun and Chen, Moxian and Siemiatkowska, Beata and Toleco, Mitchell Rey and Jing, Yue and Strotmann, Vivien and Zhang, Jianghua and Stahl, Yvonne and Fernie, Alisdair R.}, title = {A highly efficient agrobacterium-mediated method for transient gene expression and functional studies in multiple plant species}, series = {Plant Communications}, volume = {1}, journal = {Plant Communications}, number = {5}, publisher = {Science Direct}, address = {New York}, issn = {2590-3462}, pages = {12}, year = {2020}, abstract = {Although the use of stable transformation technology has led to great insight into gene function, its application in high-throughput studies remains arduous. Agro-infiltration have been widely used in species such as Nicotiana benthamiana for the rapid detection of gene expression and protein interaction analysis, but this technique does not work efficiently in other plant species, including Arabidopsis thaliana. As an efficient high-throughput transient expression system is currently lacking in the model plant species A. thaliana, we developed a method that is characterized by high efficiency, reproducibility, and suitability for transient expression of a variety of functional proteins in A. thaliana and 7 other plant species, including Brassica oleracea, Capsella rubella, Thellungiella salsuginea, Thellungiella halophila, Solanum tuberosum, Capsicum annuum, and N. benthamiana. Efficiency of this method was independently verified in three independent research facilities, pointing to the robustness of this technique. Furthermore, in addition to demonstrating the utility of this technique in a range of species, we also present a case study employing this method to assess protein-protein interactions in the sucrose biosynthesis pathway in Arabidopsis.}, language = {en} } @misc{ZhangChenSiemiatkowskaetal.2020, author = {Zhang, Youjun and Chen, Moxian and Siemiatkowska, Beata and Toleco, Mitchell Rey and Jing, Yue and Strotmann, Vivien and Zhang, Jianghua and Stahl, Yvonne and Fernie, Alisdair R.}, title = {A highly efficient agrobacterium-mediated method for transient gene expression and functional studies in multiple plant species}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {5}, issn = {1866-8372}, doi = {10.25932/publishup-52425}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-524254}, pages = {14}, year = {2020}, abstract = {Although the use of stable transformation technology has led to great insight into gene function, its application in high-throughput studies remains arduous. Agro-infiltration have been widely used in species such as Nicotiana benthamiana for the rapid detection of gene expression and protein interaction analysis, but this technique does not work efficiently in other plant species, including Arabidopsis thaliana. As an efficient high-throughput transient expression system is currently lacking in the model plant species A. thaliana, we developed a method that is characterized by high efficiency, reproducibility, and suitability for transient expression of a variety of functional proteins in A. thaliana and 7 other plant species, including Brassica oleracea, Capsella rubella, Thellungiella salsuginea, Thellungiella halophila, Solanum tuberosum, Capsicum annuum, and N. benthamiana. Efficiency of this method was independently verified in three independent research facilities, pointing to the robustness of this technique. Furthermore, in addition to demonstrating the utility of this technique in a range of species, we also present a case study employing this method to assess protein-protein interactions in the sucrose biosynthesis pathway in Arabidopsis.}, language = {en} } @article{ZhangSunFettkeetal.2014, author = {Zhang, Youjun and Sun, Feng and Fettke, J{\"o}rg and Schoettler, Mark Aurel and Ramsden, Lawrence and Fernie, Alisdair R. and Lim, Boon Leong}, title = {Heterologous expression of AtPAP2 in transgenic potato influences carbon metabolism and tuber development}, series = {FEBS letters : the journal for rapid publication of short reports in molecular biosciences}, volume = {588}, journal = {FEBS letters : the journal for rapid publication of short reports in molecular biosciences}, number = {20}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0014-5793}, doi = {10.1016/j.febslet.2014.08.019}, pages = {3726 -- 3731}, year = {2014}, abstract = {Changes in carbon flow and sink/source activities can affect floral, architectural, and reproductive traits of plants. In potato, overexpression (OE) of the purple acid phosphatase 2 of Arabidopsis (AtPAP2) resulted in earlier flowering, faster growth rate, increased tubers and tuber starch content, and higher photosynthesis rate. There was a significant change in sucrose, glucose and fructose levels in leaves, phloem and sink biomass of the OE lines, consistent with an increased expression of sucrose transporter 1 (StSUT1). Furthermore, the expression levels and enzyme activity of sucrose-phosphate synthase (SPS) were also significantly increased in the OE lines. These findings strongly suggest that higher carbon supply from the source and improved sink strength can improve potato tuber yield. (C) 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.}, language = {en} }