TY  - JOUR
A1  - Pries, Christopher
A1  - Razaghi-Moghadam, Zahra
A1  - Kopka, Joachim
A1  - Nikoloski, Zoran
T1  - Integration of relative metabolomics and transcriptomics time-course data in a metabolic model pinpoints effects of ribosome biogenesis defects on Arabidopsis thaliana metabolism
JF  - Scientific reports
N2  - Ribosome biogenesis is tightly associated to plant metabolism due to the usage of ribosomes in the synthesis of proteins necessary to drive metabolic pathways. Given the central role of ribosome biogenesis in cell physiology, it is important to characterize the impact of different components involved in this process on plant metabolism. Double mutants of the Arabidopsis thaliana cytosolic 60S maturation factors REIL1 and REIL2 do not resume growth after shift to moderate 10 degrees C chilling conditions. To gain mechanistic insights into the metabolic effects of this ribosome biogenesis defect on metabolism, we developed TC-iReMet2, a constraint-based modelling approach that integrates relative metabolomics and transcriptomics time-course data to predict differential fluxes on a genome-scale level. We employed TC-iReMet2 with metabolomics and transcriptomics data from the Arabidopsis Columbia 0 wild type and the reil1-1 reil2-1 double mutant before and after cold shift. We identified reactions and pathways that are highly altered in a mutant relative to the wild type. These pathways include the Calvin-Benson cycle, photorespiration, gluconeogenesis, and glycolysis. Our findings also indicated differential NAD(P)/NAD(P)H ratios after cold shift. TC-iReMet2 allows for mechanistic hypothesis generation and interpretation of system biology experiments related to metabolic fluxes on a genome-scale level.
Y1  - 2021
U6  - https://doi.org/10.1038/s41598-021-84114-y
SN  - 2045-2322
VL  - 11
IS  - 1
PB  - Macmillan Publishers Limited, part of Springer Nature
CY  - London
ER  - 
TY  - JOUR
A1  - Watanabe, Mutsumi
A1  - Tohge, Takayuki
A1  - Balazadeh, Salma
A1  - Erban, Alexander
A1  - Giavalisco, Patrick
A1  - Kopka, Joachim
A1  - Mueller-Roeber, Bernd
A1  - Fernie, Alisdair R.
A1  - Hoefgen, Rainer
T1  - Comprehensive Metabolomics Studies of Plant Developmental Senescence
JF  - Plant Senescence: Methods and Protocols
N2  - 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.
KW  - Senescence
KW  - Metabolomics
KW  - Arabidopsis
KW  - GC/MS
KW  - LC/MS
KW  - HPLC
KW  - IC
Y1  - 2018
SN  - 978-1-4939-7672-0
SN  - 978-1-4939-7670-6
U6  - https://doi.org/10.1007/978-1-4939-7672-0_28
SN  - 1064-3745
SN  - 1940-6029
VL  - 1744
SP  - 339
EP  - 358
PB  - Humana Press
CY  - Totowa
ER  - 
TY  - JOUR
A1  - Sprenger, Heike
A1  - Erban, Alexander
A1  - Seddig, Sylvia
A1  - Rudack, Katharina
A1  - Thalhammer, Anja
A1  - Le, Mai Q.
A1  - Walther, Dirk
A1  - Zuther, Ellen
A1  - Koehl, Karin I.
A1  - Kopka, Joachim
A1  - Hincha, Dirk K.
T1  - Metabolite and transcript markers for the prediction of potato drought tolerance
JF  - Plant Biotechnology Journal
N2  - Potato (Solanum tuberosum L.) is one of the most important food crops worldwide. Current potato varieties are highly susceptible to drought stress. In view of global climate change, selection of cultivars with improved drought tolerance and high yield potential is of paramount importance. Drought tolerance breeding of potato is currently based on direct selection according to yield and phenotypic traits and requires multiple trials under drought conditions. Marker-assisted selection (MAS) is cheaper, faster and reduces classification errors caused by noncontrolled environmental effects. We analysed 31 potato cultivars grown under optimal and reduced water supply in six independent field trials. Drought tolerance was determined as tuber starch yield. Leaf samples from young plants were screened for preselected transcript and nontargeted metabolite abundance using qRT-PCR and GC-MS profiling, respectively. Transcript marker candidates were selected from a published RNA-Seq data set. A Random Forest machine learning approach extracted metabolite and transcript markers for drought tolerance prediction with low error rates of 6% and 9%, respectively. Moreover, by combining transcript and metabolite markers, the prediction error was reduced to 4.3%. Feature selection from Random Forest models allowed model minimization, yielding a minimal combination of only 20 metabolite and transcript markers that were successfully tested for their reproducibility in 16 independent agronomic field trials. We demonstrate that a minimum combination of transcript and metabolite markers sampled at early cultivation stages predicts potato yield stability under drought largely independent of seasonal and regional agronomic conditions.
KW  - drought tolerance
KW  - machine learning
KW  - metabolite markers
KW  - potato (Solanum tuberosum)
KW  - prediction models
KW  - transcript markers
Y1  - 2017
U6  - https://doi.org/10.1111/pbi.12840
SN  - 1467-7644
SN  - 1467-7652
VL  - 16
IS  - 4
SP  - 939
EP  - 950
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Hilker, Monika
A1  - Schwachtje, Jens
A1  - Baier, Margarete
A1  - Balazadeh, Salma
A1  - Bäurle, Isabel
A1  - Geiselhardt, Sven
A1  - Hincha, Dirk K.
A1  - Kunze, Reinhard
A1  - Mueller-Roeber, Bernd
A1  - Rillig, Matthias G.
A1  - Rolff, Jens
A1  - Schmülling, Thomas
A1  - Steppuhn, Anke
A1  - van Dongen, Joost
A1  - Whitcomb, Sarah J.
A1  - Wurst, Susanne
A1  - Zuther, Ellen
A1  - Kopka, Joachim
T1  - Priming and memory of stress responses in organisms lacking a nervous system
JF  - Biological reviews
KW  - priming
KW  - stress signalling
KW  - epigenetics
KW  - memory
KW  - fitness
KW  - stress tolerance
KW  - defence
KW  - bet hedging
Y1  - 2016
U6  - https://doi.org/10.1111/brv.12215
SN  - 1464-7931
SN  - 1469-185X
VL  - 91
SP  - 1118
EP  - 1133
PB  - Wiley-Blackwell
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Sprenger, Heike
A1  - Rudack, Katharina
A1  - Schudoma, Christian
A1  - Neumann, Arne
A1  - Seddig, Sylvia
A1  - Peters, Rolf
A1  - Zuther, Ellen
A1  - Kopka, Joachim
A1  - Hincha, Dirk K.
A1  - Walther, Dirk
A1  - Koehl, Karin
T1  - Assessment of drought tolerance and its potential yield penalty in potato
JF  - Functional plant biology : an international journal of plant function
N2  - Climate models predict an increased likelihood of seasonal droughts for many areas of the world. Breeding for drought tolerance could be accelerated by marker-assisted selection. As a basis for marker identification, we studied the genetic variance, predictability of field performance and potential costs of tolerance in potato (Solanum tuberosum L.). Potato produces high calories per unit of water invested, but is drought-sensitive. In 14 independent pot or field trials, 34 potato cultivars were grown under optimal and reduced water supply to determine starch yield. In an artificial dataset, we tested several stress indices for their power to distinguish tolerant and sensitive genotypes independent of their yield potential. We identified the deviation of relative starch yield from the experimental median (DRYM) as the most efficient index. DRYM corresponded qualitatively to the partial least square model-based metric of drought stress tolerance in a stress effect model. The DRYM identified significant tolerance variation in the European potato cultivar population to allow tolerance breeding and marker identification. Tolerance results from pot trials correlated with those from field trials but predicted field performance worse than field growth parameters. Drought tolerance correlated negatively with yield under optimal conditions in the field. The distribution of yield data versus DRYM indicated that tolerance can be combined with average yield potentials, thus circumventing potential yield penalties in tolerance breeding.
KW  - performance prediction
KW  - Solanum tuberosum
KW  - tolerance index
KW  - target environment
Y1  - 2015
U6  - https://doi.org/10.1071/FP15013
SN  - 1445-4408
SN  - 1445-4416
VL  - 42
IS  - 7
SP  - 655
EP  - 667
PB  - CSIRO
CY  - Clayton
ER  - 
TY  - JOUR
A1  - Schroeder, Florian
A1  - Lisso, Janina
A1  - Obata, Toshihiro
A1  - Erban, Alexander
A1  - Maximova, Eugenia
A1  - Giavalisco, Patrick
A1  - Kopka, Joachim
A1  - Fernie, Alisdair R.
A1  - Willmitzer, Lothar
A1  - Muessig, Carsten
T1  - Consequences of induced brassinosteroid deficiency in Arabidopsis leaves
JF  - BMC plant biology
N2  - 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.
KW  - Brassinosteroids
KW  - Arabidopsis
KW  - Tricarboxylic acid cycle
KW  - Biomass
KW  - Cell expansion
KW  - Growth
Y1  - 2014
U6  - https://doi.org/10.1186/s12870-014-0309-0
SN  - 1471-2229
VL  - 14
PB  - BioMed Central
CY  - London
ER  - 
TY  - JOUR
A1  - Hemme, Dorothea
A1  - Veyel, Daniel
A1  - Muehlhaus, Timo
A1  - Sommer, Frederik
A1  - Jueppner, Jessica
A1  - Unger, Ann-Katrin
A1  - Sandmann, Michael
A1  - Fehrle, Ines
A1  - Schoenfelder, Stephanie
A1  - Steup, Martin
A1  - Geimer, Stefan
A1  - Kopka, Joachim
A1  - Giavalisco, Patrick
A1  - Schroda, Michael
T1  - Systems-wide analysis of acclimation responses to long-term heat stress and recovery in the photosynthetic model organism Chlamydomonas reinhardtii
JF  - The plant cell
N2  - We applied a top-down systems biology approach to understand how Chlamydomonas reinhardtii acclimates to long-term heat stress (HS) and recovers from it. For this, we shifted cells from 25 to 42 degrees C for 24 h and back to 25 degrees C for >= 8 h and monitored abundances of 1856 proteins/protein groups, 99 polar and 185 lipophilic metabolites, and cytological and photosynthesis parameters. Our data indicate that acclimation of Chlamydomonas to long-term HS consists of a temporally ordered, orchestrated implementation of response elements at various system levels. These comprise (1) cell cycle arrest; (2) catabolism of larger molecules to generate compounds with roles in stress protection; (3) accumulation of molecular chaperones to restore protein homeostasis together with compatible solutes; (4) redirection of photosynthetic energy and reducing power from the Calvin cycle to the de novo synthesis of saturated fatty acids to replace polyunsaturated ones in membrane lipids, which are deposited in lipid bodies; and (5) when sinks for photosynthetic energy and reducing power are depleted, resumption of Calvin cycle activity associated with increased photorespiration, accumulation of reactive oxygen species scavengers, and throttling of linear electron flow by antenna uncoupling. During recovery from HS, cells appear to focus on processes allowing rapid resumption of growth rather than restoring pre-HS conditions.
Y1  - 2014
U6  - https://doi.org/10.1105/tpc.114.130997
SN  - 1040-4651
SN  - 1532-298X
VL  - 26
IS  - 11
SP  - 4270
EP  - 4297
PB  - American Society of Plant Physiologists
CY  - Rockville
ER  - 
TY  - JOUR
A1  - Mettler, Tabea
A1  - Mühlhaus, Timo
A1  - Hemme, Dorothea
A1  - Schöttler, Mark Aurel
A1  - Rupprecht, Jens
A1  - Idoine, Adam
A1  - Veyel, Daniel
A1  - Pal, Sunil Kumar
A1  - Yaneva-Roder, Liliya
A1  - Winck, Flavia Vischi
A1  - Sommer, Frederik
A1  - Vosloh, Daniel
A1  - Seiwert, Bettina
A1  - Erban, Alexander
A1  - Burgos, Asdrubal
A1  - Arvidsson, Samuel Janne
A1  - Schoenfelder, Stephanie
A1  - Arnold, Anne
A1  - Guenther, Manuela
A1  - Krause, Ursula
A1  - Lohse, Marc
A1  - Kopka, Joachim
A1  - Nikoloski, Zoran
A1  - Müller-Röber, Bernd
A1  - Willmitzer, Lothar
A1  - Bock, Ralph
A1  - Schroda, Michael
A1  - Stitt, Mark
T1  - Systems analysis of the response of photosynthesis, metabolism, and growth to an increase in irradiance in the photosynthetic model organism chlamydomonas reinhardtii
JF  - The plant cell
N2  - We investigated the systems response of metabolism and growth after an increase in irradiance in the nonsaturating range in the algal model Chlamydomonas reinhardtii. In a three-step process, photosynthesis and the levels of metabolites increased immediately, growth increased after 10 to 15 min, and transcript and protein abundance responded by 40 and 120 to 240 min, respectively. In the first phase, starch and metabolites provided a transient buffer for carbon until growth increased. This uncouples photosynthesis from growth in a fluctuating light environment. In the first and second phases, rising metabolite levels and increased polysome loading drove an increase in fluxes. Most Calvin-Benson cycle (CBC) enzymes were substrate-limited in vivo, and strikingly, many were present at higher concentrations than their substrates, explaining how rising metabolite levels stimulate CBC flux. Rubisco, fructose-1,6-biosphosphatase, and seduheptulose-1,7-bisphosphatase were close to substrate saturation in vivo, and flux was increased by posttranslational activation. In the third phase, changes in abundance of particular proteins, including increases in plastidial ATP synthase and some CBC enzymes, relieved potential bottlenecks and readjusted protein allocation between different processes. Despite reasonable overall agreement between changes in transcript and protein abundance (R-2 = 0.24), many proteins, including those in photosynthesis, changed independently of transcript abundance.
Y1  - 2014
U6  - https://doi.org/10.1105/tpc.114.124537
SN  - 1040-4651
SN  - 1532-298X
VL  - 26
IS  - 6
SP  - 2310
EP  - 2350
PB  - American Society of Plant Physiologists
CY  - Rockville
ER  - 
TY  - JOUR
A1  - Watanabe, Mutsumi
A1  - Balazadeh, Salma
A1  - Tohge, Takayuki
A1  - Erban, Alexander
A1  - Giavalisco, Patrick
A1  - Kopka, Joachim
A1  - Müller-Röber, Bernd
A1  - Fernie, Alisdair R.
A1  - Höfgen, Rainer
T1  - Comprehensive dissection of spatiotemporal metabolic shifts in primary, secondary, and lipid metabolism during developmental senescence in arabidopsis
JF  - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants
N2  - 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.
Y1  - 2013
U6  - https://doi.org/10.1104/pp.113.217380
SN  - 0032-0889
VL  - 162
IS  - 3
SP  - 1290
EP  - 1310
PB  - American Society of Plant Physiologists
CY  - Rockville
ER  - 
TY  - JOUR
A1  - Huege, Jan
A1  - Goetze, Jan
A1  - Schwarz, Doreen
A1  - Bauwe, Hermann
A1  - Hagemann, Martin
A1  - Kopka, Joachim
T1  - Modulation of the major Paths of Carbon in photorespiratory mutants of synechocystis
JF  - PLoS one
N2  - Background: Recent studies using transcript and metabolite profiles of wild-type and gene deletion mutants revealed that photorespiratory pathways are essential for the growth of Synechocystis sp. PCC 6803 under atmospheric conditions. Pool size changes of primary metabolites, such as glycine and glycolate, indicated a link to photorespiration.
 Methodology/Principal Findings: The (13)C labelling kinetics of primary metabolites were analysed in photoautotrophically grown cultures of Synechocystis sp. PCC 6803 by gas chromatography-mass spectrometry (GC-MS) to demonstrate the link with photorespiration. Cells pre-acclimated to high CO(2) (5%, HC) or limited CO(2) (0.035%, LC) conditions were pulse-labelled under very high (2% w/w) (13)C-NaHCO(3) (VHC) conditions followed by treatment with ambient (12)C at HC and LC conditions, respectively. The (13)C enrichment, relative changes in pool size, and (13)C flux of selected metabolites were evaluated. We demonstrate two major paths of CO(2) assimilation via Rubisco in Synechocystis, i.e., from 3PGA via PEP to aspartate, malate and citrate or, to a lesser extent, from 3PGA via glucose-6-phosphate to sucrose. The results reveal evidence of carbon channelling from 3PGA to the PEP pool. Furthermore, (13)C labelling of glycolate was observed under conditions thought to suppress photorespiration. Using the glycolate-accumulating Delta glcD1 mutant, we demonstrate enhanced (13)C partitioning into the glycolate pool under conditions favouring photorespiration and enhanced (13)C partitioning into the glycine pool of the glycine-accumulating Delta gcvT mutant. Under LC conditions, the photorespiratory mutants Delta glcD1 and Delta gcvT showed enhanced activity of the additional carbon-fixing PEP carboxylase pathway.
 Conclusions/Significance: With our approach of non-steady-state (13)C labelling and analysis of metabolite pool sizes with respective (13)C enrichments, we identify the use and modulation of major pathways of carbon assimilation in Synechocystis in the presence of high and low inorganic carbon supplies.
Y1  - 2011
U6  - https://doi.org/10.1371/journal.pone.0016278
SN  - 1932-6203
VL  - 6
IS  - 1
PB  - PLoS
CY  - San Fransisco
ER  -