TY - JOUR A1 - Janowski, Marcin Andrzej A1 - Zoschke, Reimo A1 - Scharff, Lars B. A1 - Jaime, Silvia Martinez A1 - Ferrari, Camilla A1 - Proost, Sebastian A1 - Xiong, Jonathan Ng Wei A1 - Omranian, Nooshin A1 - Musialak-Lange, Magdalena A1 - Nikoloski, Zoran A1 - Graf, Alexander A1 - Schoettler, Mark Aurel A1 - Sampathkumar, Arun A1 - Vaid, Neha A1 - Mutwil, Marek T1 - AtRsgA from Arabidopsis thaliana is important for maturation of the small subunit of the chloroplast ribosome JF - The plant journal N2 - Plastid ribosomes are very similar in structure and function to the ribosomes of their bacterial ancestors. Since ribosome biogenesis is not thermodynamically favorable under biological conditions it requires the activity of many assembly factors. Here we have characterized a homolog of bacterial RsgA in Arabidopsis thaliana and show that it can complement the bacterial homolog. Functional characterization of a strong mutant in Arabidopsis revealed that the protein is essential for plant viability, while a weak mutant produced dwarf, chlorotic plants that incorporated immature pre-16S ribosomal RNA into translating ribosomes. Physiological analysis of the mutant plants revealed smaller, but more numerous, chloroplasts in the mesophyll cells, reduction of chlorophyll a and b, depletion of proplastids from the rib meristem and decreased photosynthetic electron transport rate and efficiency. Comparative RNA sequencing and proteomic analysis of the weak mutant and wild-type plants revealed that various biotic stress-related, transcriptional regulation and post-transcriptional modification pathways were repressed in the mutant. Intriguingly, while nuclear- and chloroplast-encoded photosynthesis-related proteins were less abundant in the mutant, the corresponding transcripts were increased, suggesting an elaborate compensatory mechanism, potentially via differentially active retrograde signaling pathways. To conclude, this study reveals a chloroplast ribosome assembly factor and outlines the transcriptomic and proteomic responses of the compensatory mechanism activated during decreased chloroplast function. Significance Statement AtRsgA is an assembly factor necessary for maturation of the small subunit of the chloroplast ribosome. Depletion of AtRsgA leads to dwarfed, chlorotic plants, a decrease of mature 16S rRNA and smaller, but more numerous, chloroplasts. Large-scale transcriptomic and proteomic analysis revealed that chloroplast-encoded and -targeted proteins were less abundant, while the corresponding transcripts were increased in the mutant. We analyze the transcriptional responses of several retrograde signaling pathways to suggest the mechanism underlying this compensatory response. KW - ribosome assembly KW - chloroplast ribosome KW - assembly factor KW - 30S subunit KW - RsgA KW - Arabidopsis thaliana Y1 - 2018 U6 - https://doi.org/10.1111/tpj.14040 SN - 0960-7412 SN - 1365-313X VL - 96 IS - 2 SP - 404 EP - 420 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Jose Clemente-Moreno, Maria A1 - Omranian, Nooshin A1 - Saez, Patricia A1 - Maria Figueroa, Carlos A1 - Del-Saz, Nestor A1 - Elso, Mhartyn A1 - Poblete, Leticia A1 - Orf, Isabel A1 - Cuadros-Inostroza, Alvaro A1 - Cavieres, Lohengrin A1 - Bravo, Leon A1 - Fernie, Alisdair R. A1 - Ribas-Carbo, Miquel A1 - Flexas, Jaume A1 - Nikoloski, Zoran A1 - Brotman, Yariv A1 - Gago, Jorge T1 - Cytochrome respiration pathway and sulphur metabolism sustain stress tolerance to low temperature in the Antarctic species Colobanthus quitensis JF - New phytologist : international journal of plant science N2 - 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. KW - Antarctica KW - antioxidant capacity KW - low temperature KW - photosynthesis KW - respiration KW - stress tolerance KW - sulphur metabolism Y1 - 2019 U6 - https://doi.org/10.1111/nph.16167 SN - 0028-646X SN - 1469-8137 VL - 225 IS - 2 SP - 754 EP - 768 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Nunes-Nesi, Adriano A1 - Alseekh, Saleh A1 - de Oliveira Silva, Franklin Magnum A1 - Omranian, Nooshin A1 - Lichtenstein, Gabriel A1 - Mirnezhad, Mohammad A1 - Romero Gonzalez, Roman R. A1 - Sabio y Garcia, Julia A1 - Conte, Mariana A1 - Leiss, Kirsten A. A1 - Klinkhamer, Peter Gerardus Leonardus A1 - Nikoloski, Zoran A1 - Carrari, Fernando A1 - Fernie, Alisdair R. T1 - Identification and characterization of metabolite quantitative trait loci in tomato leaves and comparison with those reported for fruits and seeds JF - Metabolomics N2 - 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. KW - Metabolite QTL KW - Tomato KW - Leaf metabolism KW - Metabolite network Y1 - 2019 U6 - https://doi.org/10.1007/s11306-019-1503-8 SN - 1573-3882 SN - 1573-3890 VL - 15 IS - 46 PB - Springer CY - New York ER - TY - JOUR A1 - Pandey, Prashant K. A1 - Yu, Jing A1 - Omranian, Nooshin A1 - Alseekh, Saleh A1 - Vaid, Neha A1 - Fernie, Alisdair R. A1 - Nikoloski, Zoran A1 - Laitinen, Roosa A. E. T1 - Plasticity in metabolism underpins local responses to nitrogen in Arabidopsis thaliana populations JF - Plant Direct N2 - 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. KW - Arabidopsis thaliana KW - natural variation KW - nitrogen availability KW - photorespiration KW - plasticity Y1 - 2019 U6 - https://doi.org/10.1002/pld3.186 SN - 2475-4455 VL - 3 IS - 11 PB - John Wiley & sonst LTD CY - Chichester ER - TY - JOUR A1 - Schwahn, Kevin A1 - Beleggia, Romina A1 - Omranian, Nooshin A1 - Nikoloski, Zoran T1 - Stoichiometric Correlation Analysis: Principles of Metabolic Functionality from Metabolomics Data JF - Frontiers in plant science N2 - Recent advances in metabolomics technologies have resulted in high-quality (time-resolved) metabolic profiles with an increasing coverage of metabolic pathways. These data profiles represent read-outs from often non-linear dynamics of metabolic networks. Yet, metabolic profiles have largely been explored with regression-based approaches that only capture linear relationships, rendering it difficult to determine the extent to which the data reflect the underlying reaction rates and their couplings. Here we propose an approach termed Stoichiometric Correlation Analysis (SCA) based on correlation between positive linear combinations of log-transformed metabolic profiles. The log-transformation is due to the evidence that metabolic networks can be modeled by mass action law and kinetics derived from it. Unlike the existing approaches which establish a relation between pairs of metabolites, SCA facilitates the discovery of higherorder dependence between more than two metabolites. By using a paradigmatic model of the tricarboxylic acid cycle we show that the higher-order dependence reflects the coupling of concentration of reactant complexes, capturing the subtle difference between the employed enzyme kinetics. Using time-resolved metabolic profiles from Arabidopsis thaliana and Escherichia coli, we show that SCA can be used to quantify the difference in coupling of reactant complexes, and hence, reaction rates, underlying the stringent response in these model organisms. By using SCA with data from natural variation of wild and domesticated wheat and tomato accession, we demonstrate that the domestication is accompanied by loss of such couplings, in these species. Therefore, application of SCA to metabolomics data from natural variation in wild and domesticated populations provides a mechanistic way to understanding domestication and its relation to metabolic networks. KW - metabolism KW - systems biology KW - maximal correlation KW - correlation analysis KW - domestication Y1 - 2017 U6 - https://doi.org/10.3389/fpls.2017.02152 SN - 1664-462X VL - 8 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Omranian, Nooshin A1 - Eloundou-Mbebi, Jeanne Marie Onana A1 - Müller-Röber, Bernd A1 - Nikoloski, Zoran T1 - Gene regulatory network inference using fused LASSO on multiple data sets JF - Scientific reports N2 - Devising computational methods to accurately reconstruct gene regulatory networks given gene expression data is key to systems biology applications. Here we propose a method for reconstructing gene regulatory networks by simultaneous consideration of data sets from different perturbation experiments and corresponding controls. The method imposes three biologically meaningful constraints: (1) expression levels of each gene should be explained by the expression levels of a small number of transcription factor coding genes, (2) networks inferred from different data sets should be similar with respect to the type and number of regulatory interactions, and (3) relationships between genes which exhibit similar differential behavior over the considered perturbations should be favored. We demonstrate that these constraints can be transformed in a fused LASSO formulation for the proposed method. The comparative analysis on transcriptomics time-series data from prokaryotic species, Escherichia coli and Mycobacterium tuberculosis, as well as a eukaryotic species, mouse, demonstrated that the proposed method has the advantages of the most recent approaches for regulatory network inference, while obtaining better performance and assigning higher scores to the true regulatory links. The study indicates that the combination of sparse regression techniques with other biologically meaningful constraints is a promising framework for gene regulatory network reconstructions. Y1 - 2016 U6 - https://doi.org/10.1038/srep20533 SN - 2045-2322 VL - 6 PB - Nature Publ. Group CY - London ER - 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 - Alseekh, Saleh A1 - Tohge, Takayuki A1 - Wendenberg, Regina A1 - Scossa, Federico A1 - Omranian, Nooshin A1 - Li, Jie A1 - Kleessen, Sabrina A1 - Giavalisco, Patrick A1 - Pleban, Tzili A1 - Müller-Röber, Bernd A1 - Zamir, Dani A1 - Nikoloski, Zoran A1 - Fernie, Alisdair R. T1 - Identification and Mode of Inheritance of Quantitative Trait Loci for Secondary Metabolite Abundance in Tomato JF - The plant cell N2 - 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. Y1 - 2015 U6 - https://doi.org/10.1105/tpc.114.132266 SN - 1040-4651 SN - 1532-298X VL - 27 IS - 3 SP - 485 EP - 512 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Omranian, Nooshin A1 - Müller-Röber, Bernd A1 - Nikoloski, Zoran T1 - Segmentation of biological multivariate time-series data JF - Scientific reports N2 - Time-series data from multicomponent systems capture the dynamics of the ongoing processes and reflect the interactions between the components. The progression of processes in such systems usually involves check-points and events at which the relationships between the components are altered in response to stimuli. Detecting these events together with the implicated components can help understand the temporal aspects of complex biological systems. Here we propose a regularized regression-based approach for identifying breakpoints and corresponding segments from multivariate time-series data. In combination with techniques from clustering, the approach also allows estimating the significance of the determined breakpoints as well as the key components implicated in the emergence of the breakpoints. Comparative analysis with the existing alternatives demonstrates the power of the approach to identify biologically meaningful breakpoints in diverse time-resolved transcriptomics data sets from the yeast Saccharomyces cerevisiae and the diatom Thalassiosira pseudonana. Y1 - 2015 U6 - https://doi.org/10.1038/srep08937 SN - 2045-2322 VL - 5 PB - Nature Publ. Group CY - London ER -