TY - GEN A1 - Omidbakhshfard, Mohammad Amin A1 - Neerakkal, Sujeeth A1 - Gupta, Saurabh A1 - Omranian, Nooshin A1 - Guinan, Kieran J. A1 - Brotman, Yariv A1 - Nikoloski, Zoran A1 - Fernie, Alisdair R. A1 - Mueller-Roeber, Bernd A1 - Gechev, Tsanko S. T1 - A Biostimulant Obtained from the Seaweed Ascophyllum nodosum Protects Arabidopsis thaliana from Severe Oxidative Stress T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - Abiotic stresses cause oxidative damage in plants. Here, we demonstrate that foliar application of an extract from the seaweed Ascophyllum nodosum, SuperFifty (SF), largely prevents paraquat (PQ)-induced oxidative stress in Arabidopsis thaliana. While PQ-stressed plants develop necrotic lesions, plants pre-treated with SF (i.e., primed plants) were unaffected by PQ. Transcriptome analysis revealed induction of reactive oxygen species (ROS) marker genes, genes involved in ROS-induced programmed cell death, and autophagy-related genes after PQ treatment. These changes did not occur in PQ-stressed plants primed with SF. In contrast, upregulation of several carbohydrate metabolism genes, growth, and hormone signaling as well as antioxidant-related genes were specific to SF-primed plants. Metabolomic analyses revealed accumulation of the stress-protective metabolite maltose and the tricarboxylic acid cycle intermediates fumarate and malate in SF-primed plants. Lipidome analysis indicated that those lipids associated with oxidative stress-induced cell death and chloroplast degradation, such as triacylglycerols (TAGs), declined upon SF priming. Our study demonstrated that SF confers tolerance to PQ-induced oxidative stress in A. thaliana, an effect achieved by modulating a range of processes at the transcriptomic, metabolic, and lipid levels. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 823 KW - Ascophyllum nodosum KW - Arabidopsis thaliana KW - biostimulant KW - paraquat KW - priming KW - oxidative stress tolerance KW - reactive oxygen species Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-445093 SN - 1866-8372 IS - 823 ER - TY - JOUR A1 - Omidbakhshfard, Mohammad Amin A1 - Neerakkal, Sujeeth A1 - Gupta, Saurabh A1 - Omranian, Nooshin A1 - Guinan, Kieran J. A1 - Brotman, Yariv A1 - Nikoloski, Zoran A1 - Fernie, Alisdair R. A1 - Mueller-Roeber, Bernd A1 - Gechev, Tsanko S. T1 - A Biostimulant Obtained from the Seaweed Ascophyllum nodosum Protects Arabidopsis thaliana from Severe Oxidative Stress JF - International Journal of Molecular Sciences N2 - Abiotic stresses cause oxidative damage in plants. Here, we demonstrate that foliar application of an extract from the seaweed Ascophyllum nodosum, SuperFifty (SF), largely prevents paraquat (PQ)-induced oxidative stress in Arabidopsis thaliana. While PQ-stressed plants develop necrotic lesions, plants pre-treated with SF (i.e., primed plants) were unaffected by PQ. Transcriptome analysis revealed induction of reactive oxygen species (ROS) marker genes, genes involved in ROS-induced programmed cell death, and autophagy-related genes after PQ treatment. These changes did not occur in PQ-stressed plants primed with SF. In contrast, upregulation of several carbohydrate metabolism genes, growth, and hormone signaling as well as antioxidant-related genes were specific to SF-primed plants. Metabolomic analyses revealed accumulation of the stress-protective metabolite maltose and the tricarboxylic acid cycle intermediates fumarate and malate in SF-primed plants. Lipidome analysis indicated that those lipids associated with oxidative stress-induced cell death and chloroplast degradation, such as triacylglycerols (TAGs), declined upon SF priming. Our study demonstrated that SF confers tolerance to PQ-induced oxidative stress in A. thaliana, an effect achieved by modulating a range of processes at the transcriptomic, metabolic, and lipid levels. KW - Ascophyllum nodosum KW - Arabidopsis thaliana KW - biostimulant KW - paraquat KW - priming KW - oxidative stress tolerance KW - reactive oxygen species Y1 - 2019 U6 - https://doi.org/10.3390/ijms21020474 SN - 1422-0067 VL - 21 IS - 2 PB - Molecular Diversity Preservation International CY - Basel ER - TY - JOUR A1 - Zhang, Youjun A1 - Chen, Moxian A1 - Siemiatkowska, Beata A1 - Toleco, Mitchell Rey A1 - Jing, Yue A1 - Strotmann, Vivien A1 - Zhang, Jianghua A1 - Stahl, Yvonne A1 - Fernie, Alisdair R. T1 - A highly efficient agrobacterium-mediated method for transient gene expression and functional studies in multiple plant species JF - Plant Communications N2 - 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. KW - transient expression KW - agro-infiltration KW - subcellular localization KW - protein-protein interaction Y1 - 2019 SN - 2590-3462 VL - 1 IS - 5 PB - Science Direct CY - New York ER - TY - GEN A1 - Zhang, Youjun A1 - Chen, Moxian A1 - Siemiatkowska, Beata A1 - Toleco, Mitchell Rey A1 - Jing, Yue A1 - Strotmann, Vivien A1 - Zhang, Jianghua A1 - Stahl, Yvonne A1 - Fernie, Alisdair R. T1 - A highly efficient agrobacterium-mediated method for transient gene expression and functional studies in multiple plant species T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - 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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1189 KW - transient expression KW - agro-infiltration KW - subcellular localization KW - protein-protein interaction Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-524254 SN - 1866-8372 IS - 5 ER - TY - JOUR A1 - Ribeiro, Dimas M. A1 - Araujo, Wagner L. A1 - Fernie, Alisdair R. A1 - Schippers, Jos H. M. A1 - Müller-Röber, Bernd T1 - Action of Gibberellins on growth and metabolism of arabidopsis plants Associated with high concentration of carbon dioxide JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - Although the positive effect of elevated CO2 concentration [CO2] on plant growth is well known, it remains unclear whether global climate change will positively or negatively affect crop yields. In particular, relatively little is known about the role of hormone pathways in controlling the growth responses to elevated [CO2]. Here, we studied the impact of elevated [CO2] on plant biomass and metabolism in Arabidopsis (Arabidopsis thaliana) in relation to the availability of gibberellins (GAs). Inhibition of growth by the GA biosynthesis inhibitor paclobutrazol (PAC) at ambient [CO2] (350 mu mol CO2 mol(-1)) was reverted by elevated [CO2] (750 mu mol CO2 mol(-1)). Thus, we investigated the metabolic adjustment and modulation of gene expression in response to changes in growth of plants imposed by varying the GA regime in ambient and elevated [CO2]. In the presence of PAC (low-GA regime), the activities of enzymes involved in photosynthesis and inorganic nitrogen assimilation were markedly increased at elevated [CO2], whereas the activities of enzymes of organic acid metabolism were decreased. Under ambient [CO2], nitrate, amino acids, and protein accumulated upon PAC treatment; however, this was not the case when plants were grown at elevated [CO2]. These results suggest that only under ambient [CO2] is GA required for the integration of carbohydrate and nitrogen metabolism underlying optimal biomass determination. Our results have implications concerning the action of the Green Revolution genes in future environmental conditions. Y1 - 2012 U6 - https://doi.org/10.1104/pp.112.204842 SN - 0032-0889 VL - 160 IS - 4 SP - 1781 EP - 1794 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Basler, Georg A1 - Fernie, Alisdair R. A1 - Nikoloski, Zoran T1 - Advances in metabolic flux analysis toward genome-scale profiling of higher organisms JF - Bioscience reports : communications and reviews in molecular and cellular biology N2 - 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. Y1 - 2018 U6 - https://doi.org/10.1042/BSR20170224 SN - 0144-8463 SN - 1573-4935 VL - 38 PB - Portland Press (London) CY - London ER - TY - JOUR A1 - Depuydt, Stephen A1 - Trenkamp, Sandra A1 - Fernie, Alisdair R. A1 - Elftieh, Samira A1 - Renou, Jean-Pierre A1 - Vuylsteke, Marnik A1 - Holsters, Marcelle A1 - Vereecke, Danny T1 - An integrated genomics approach to define niche establishment by Rhodococcus fascians N2 - 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. Y1 - 2009 UR - http://www.plantphysiol.org/ U6 - https://doi.org/10.1104/pp.108.131805 SN - 0032-0889 ER - TY - JOUR A1 - Shahnejat-Bushehri, Sara A1 - Allu, Annapurna Devi A1 - Mehterov, Nikolay A1 - Thirumalaikumar, Venkatesh P. A1 - Alseekh, Saleh A1 - Fernie, Alisdair R. A1 - Mueller-Roeber, Bernd A1 - Balazadeh, Salma T1 - Arabidopsis NAC Transcription Factor JUNGBRUNNEN1 Exerts Conserved Control Over Gibberellin and Brassinosteroid Metabolism and Signaling Genes in Tomato JF - Frontiers in plant science N2 - 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. KW - Arabidopsis KW - tomato KW - fruit KW - growth KW - transcription factor KW - gibberellic acid KW - brassinosteroid KW - DELLA proteins Y1 - 2017 U6 - https://doi.org/10.3389/fpls.2017.00214 SN - 1664-462X VL - 8 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Rohrmann, Johannes A1 - Tohge, Takayuki A1 - Alba, Rob A1 - Osorio, Sonia A1 - Caldana, Camila A1 - McQuinn, Ryan A1 - Arvidsson, Samuel Janne A1 - van der Merwe, Margaretha J. A1 - Riano-Pachon, Diego Mauricio A1 - Müller-Röber, Bernd A1 - Fei, Zhangjun A1 - Nesi, Adriano Nunes A1 - Giovannoni, James J. A1 - Fernie, Alisdair R. T1 - Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development JF - The plant journal N2 - 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. KW - transcription factor KW - Solanum lycopersicum KW - quantitative RT-PCR KW - microarray KW - metabolomics KW - fleshy fruit ripening Y1 - 2011 U6 - https://doi.org/10.1111/j.1365-313X.2011.04750.x SN - 0960-7412 VL - 68 IS - 6 SP - 999 EP - 1013 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Benina, Maria A1 - Obata, Toshihiro A1 - Mehterov, Nikolay A1 - Ivanov, Ivan A1 - Petrov, Veselin A1 - Toneva, Valentina A1 - Fernie, Alisdair R. A1 - Gechev, Tsanko S. T1 - Comparative metabolic profiling of Haberlea rhodopensis, Thellungiella halophyla, and Arabidopsis thaliana exposed to low temperature JF - Frontiers in plant science N2 - 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. KW - Arabidopsis thaliana KW - Haberlea rhodopensis KW - low temperature stress KW - metabolite profiling KW - Thellungiella halophila Y1 - 2013 U6 - https://doi.org/10.3389/fpls.2013.00499 SN - 1664-462X VL - 4 IS - 1 PB - Frontiers Research Foundation CY - Lausanne ER -