TY  - JOUR
A1  - Malinova, Irina
A1  - Mahlow, Sebastian
A1  - Alseekh, Saleh
A1  - Orawetz, Tom
A1  - Fernie, Alisdair R.
A1  - Baumann, Otto
A1  - Steup, Martin
A1  - Fettke, Jörg
T1  - Double knockout mutants of arabidopsis grown under normal conditions reveal that the plastidial phosphorylase isozyme participates in transitory starch metabolism
JF  - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants
N2  - 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.
Y1  - 2014
U6  - https://doi.org/10.1104/pp.113.227843
SN  - 0032-0889
SN  - 1532-2548
VL  - 164
IS  - 2
SP  - 907
EP  - 921
PB  - American Society of Plant Physiologists
CY  - Rockville
ER  - 
TY  - JOUR
A1  - Balazadeh, Salma
A1  - Schildhauer, Joerg
A1  - Araujo, Wagner L.
A1  - Munne-Bosch, Sergi
A1  - Fernie, Alisdair R.
A1  - Proost, Sebastian
A1  - Humbeck, Klaus
A1  - Müller-Röber, Bernd
T1  - Reversal of senescence by N resupply to N-starved Arabidopsis thaliana: transcriptomic and metabolomic consequences
JF  - Journal of experimental botany
N2  - Leaf senescence is a developmentally controlled process, which is additionally modulated by a number of adverse environmental conditions. Nitrogen shortage is a well-known trigger of precocious senescence in many plant species including crops, generally limiting biomass and seed yield. However, leaf senescence induced by nitrogen starvation may be reversed when nitrogen is resupplied at the onset of senescence. Here, the transcriptomic, hormonal, and global metabolic rearrangements occurring during nitrogen resupply-induced reversal of senescence in Arabidopsis thaliana were analysed. The changes induced by senescence were essentially in keeping with those previously described; however, these could, by and large, be reversed. The data thus indicate that plants undergoing senescence retain the capacity to sense and respond to the availability of nitrogen nutrition. The combined data are discussed in the context of the reversibility of the senescence programme and the evolutionary benefit afforded thereby. Future prospects for understanding and manipulating this process in both Arabidopsis and crop plants are postulated.
KW  - Arabidopsis
KW  - gene expression
KW  - metabolomics
KW  - nitrogen limitation
KW  - senescence
KW  - transcriptome
Y1  - 2014
U6  - https://doi.org/10.1093/jxb/eru119
SN  - 0022-0957
SN  - 1460-2431
VL  - 65
IS  - 14
SP  - 3975
EP  - 3992
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Wang, Ting
A1  - Tohge, Takayuki
A1  - Ivakov, Alexander
A1  - Müller-Röber, Bernd
A1  - Fernie, Alisdair R.
A1  - Mutwil, Marek
A1  - Schippers, Jos H. M.
A1  - Persson, Staffan
T1  - Salt-Related MYB1 Coordinates Abscisic Acid Biosynthesis and Signaling during Salt Stress in Arabidopsis
JF  - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants
N2  - 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.
Y1  - 2015
U6  - https://doi.org/10.1104/pp.15.00962
SN  - 0032-0889
SN  - 1532-2548
VL  - 169
IS  - 2
SP  - 1027
EP  - +
PB  - American Society of Plant Physiologists
CY  - Rockville
ER  - 
TY  - JOUR
A1  - Zhang, Youjun
A1  - Sun, Feng
A1  - Fettke, Jörg
A1  - Schoettler, Mark Aurel
A1  - Ramsden, Lawrence
A1  - Fernie, Alisdair R.
A1  - Lim, Boon Leong
T1  - Heterologous expression of AtPAP2 in transgenic potato influences carbon metabolism and tuber development
JF  - FEBS letters : the journal for rapid publication of short reports in molecular biosciences
N2  - 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.
KW  - Potato
KW  - AtPAP2
KW  - Photosynthesis
KW  - Tuber yield
KW  - Sugar efflux
Y1  - 2014
U6  - https://doi.org/10.1016/j.febslet.2014.08.019
SN  - 0014-5793
SN  - 1873-3468
VL  - 588
IS  - 20
SP  - 3726
EP  - 3731
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Fettke, Jörg
A1  - Fernie, Alisdair R.
T1  - Intracellular and cell-to-apoplast compartmentation of carbohydrate metabolism
JF  - Trends in plant science
N2  - 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.
Y1  - 2015
U6  - https://doi.org/10.1016/j.tplants.2015.04.012
SN  - 1360-1385
VL  - 20
IS  - 8
SP  - 490
EP  - 497
PB  - Elsevier
CY  - London
ER  - 
TY  - JOUR
A1  - Smirnova, Julia
A1  - Fernie, Alisdair R.
A1  - Spahn, Christian M. T.
A1  - Steup, Martin
T1  - Photometric assay of maltose and maltose-forming enzyme activity by using 4-alpha-glucanotransferase (DPE2) from higher plants
JF  - Analytical biochemistry : methods in the biological sciences
N2  - 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.
KW  - Arabidopsis thaliana
KW  - beta-amylase assay
KW  - Disproportionating isozyme 2 (DPE2) dpe2-deficient plants
KW  - Maltose assay
KW  - Leaf maltose content
Y1  - 2017
U6  - https://doi.org/10.1016/j.ab.2017.05.026
SN  - 0003-2697
SN  - 1096-0309
VL  - 532
SP  - 72
EP  - 82
PB  - Elsevier
CY  - San Diego
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  - Apriyanto, Ardha
A1  - Compart, Julia
A1  - Zimmermann, Vincent
A1  - Alseekh, Saleh
A1  - Fernie, Alisdair R.
A1  - Fettke, Jörg
T1  - Indication that starch and sucrose are biomarkers for oil yield in oil palm (Elaeis guineensis Jacq.)
JF  - Food chemistry
N2  - Oil palm (Elaeis guineensis Jacq.) is the most productive oil-producing crop per hectare of land. The oil that accumulates in the mesocarp tissue of the fruit is the highest observed among fruit-producing plants. A comparative analysis between high-, medium-, and low-yielding oil palms, particularly during fruit development, revealed unique characteristics. Metabolomics analysis was able to distinguish accumulation patterns defining of the various developmental stages and oil yield. Interestingly, high- and medium-yielding oil palms exhibited substantially increased sucrose levels compared to low-yielding palms. In addition, parameters such as starch granule morphology, granule size, total starch content, and starch chain length distribution (CLD) differed significantly among the oil yield categories with a clear correlation between oil yield and various starch parameters. These results provide new insights into carbohydrate and starch metabolism for biosynthesis of oil palm fruits, indicating that starch and sucrose can be used as novel, easy-to-analyze, and reliable biomarker for oil yield.
KW  - carbohydrate
KW  - mesocarp
KW  - metabolites
KW  - oil palm
KW  - oil yield
KW  - sucrose;
KW  - starch
Y1  - 2022
U6  - https://doi.org/10.1016/j.foodchem.2022.133361
SN  - 0308-8146
SN  - 1873-7072
VL  - 393
PB  - Elsevier
CY  - New York, NY [u.a.]
ER  - 
TY  - JOUR
A1  - Córdoba, Sandra Correa
A1  - Tong, Hao
A1  - Burgos, Asdrubal
A1  - Zhu, Feng
A1  - Alseekh, Saleh
A1  - Fernie, Alisdair R.
A1  - Nikoloski, Zoran
T1  - Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism
JF  - Nature Communications
N2  - The use of automated tools to reconstruct lipid metabolic pathways is not warranted in plants. Here, the authors construct Plant Lipid Module for Arabidopsis rosette using constraint-based modeling, demonstrate its integration in other plant metabolic models, and use it to dissect the genetic architecture of lipid metabolism. 
Lipids play fundamental roles in regulating agronomically important traits. Advances in plant lipid metabolism have until recently largely been based on reductionist approaches, although modulation of its components can have system-wide effects. However, existing models of plant lipid metabolism provide lumped representations, hindering detailed study of component modulation. Here, we present the Plant Lipid Module (PLM) which provides a mechanistic description of lipid metabolism in the Arabidopsis thaliana rosette. We demonstrate that the PLM can be readily integrated in models of A. thaliana Col-0 metabolism, yielding accurate predictions (83%) of single lethal knock-outs and 75% concordance between measured transcript and predicted flux changes under extended darkness. Genome-wide associations with fluxes obtained by integrating the PLM in diel condition- and accession-specific models identify up to 65 candidate genes modulating A. thaliana lipid metabolism. Using mutant lines, we validate up to 40% of the candidates, paving the way for identification of metabolic gene function based on models capturing natural variability in metabolism.
KW  - Biochemical networks
KW  - Biochemical reaction networks
KW  - Genetic models
KW  - Plant molecular biology
Y1  - 2023
U6  - https://doi.org/10.1038/s41467-023-40644-9
SN  - 2041-1723
VL  - 14
IS  - 1
PB  - Springer Nature
CY  - London
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  - 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  - 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  - 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  - Engqvist, Martin K. M.
A1  - Schmitz, Jessica
A1  - Gertzmann, Anke
A1  - Florian, Alexandra
A1  - Jaspert, Nils
A1  - Arif, Muhammad
A1  - Balazadeh, Salma
A1  - Müller-Röber, Bernd
A1  - Fernie, Alisdair R.
A1  - Maurino, Veronica G.
T1  - GLYCOLATE OXIDASE3, a Glycolate Oxidase Homolog of Yeast L-Lactate Cytochrome c Oxidoreductase, Supports L-Lactate Oxidation in Roots of Arabidopsis
JF  - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants
N2  - 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.
Y1  - 2015
U6  - https://doi.org/10.1104/pp.15.01003
SN  - 0032-0889
SN  - 1532-2548
VL  - 169
IS  - 2
SP  - 1042
EP  - 1061
PB  - American Society of Plant Physiologists
CY  - Rockville
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  - 
TY  - JOUR
A1  - Nietzsche, Madlen
A1  - Guerra, Tiziana
A1  - Alseekh, Saleh
A1  - Wiermer, Marcel
A1  - Sonnewald, Sophia
A1  - Fernie, Alisdair R.
A1  - Börnke, Frederik
T1  - STOREKEEPER RELATED1/G-Element Binding Protein (STKR1) Interacts with Protein Kinase SnRK1
JF  - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants
N2  - 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.
Y1  - 2017
U6  - https://doi.org/10.1104/pp.17.01461
SN  - 0032-0889
SN  - 1532-2548
VL  - 176
IS  - 2
SP  - 1773
EP  - 1792
PB  - American Society of Plant Physiologists
CY  - Rockville
ER  - 
TY  - JOUR
A1  - Oliver, Sandra N.
A1  - Lunn, John Edward
A1  - Urbanczyk-Wochniak, Ewa
A1  - Lytovchenko, Anna
A1  - van Dongen, Joost T.
A1  - Faix, Benjamin
A1  - Schmälzlin, Elmar
A1  - Fernie, Alisdair R.
A1  - Schmäelzlin, E.
A1  - Geigenberger, Peter
T1  - Decreased expression of cytosolic pyruvate kinase in potato tubers leads to a decline in pyruvate resulting in an in vivo repression of the alternative oxidase
N2  - The aim of this work was to investigate the effect of decreased cytosolic pyruvate kinase (PKc) on potato (Solanum tuberosum) tuber metabolism. Transgenic potato plants with strongly reduced levels of PKc were generated by RNA interference gene silencing under the control of a tuber-specific promoter. Metabolite profiling showed that decreased PKc activity led to a decrease in the levels of pyruvate and some other organic acids involved in the tricarboxylic acid cycle. Flux analysis showed that this was accompanied by changes in carbon partitioning, with carbon flux being diverted from glycolysis toward starch synthesis. However, this metabolic shift was relatively small and hence did not result in enhanced starch levels in the tubers. Although total respiration rates and the ATP to ADP ratio were largely unchanged, transgenic tubers showed a strong decrease in the levels of alternative oxidase (AOX) protein and a corresponding decrease in the capacity of the alternative pathway of respiration. External feeding of pyruvate to tuber tissue or isolated mitochondria resulted in activation of the AOX pathway, both in the wild type and the PKc transgenic lines, providing direct evidence for the regulation of AOX by changes in pyruvate levels. Overall, these results provide evidence for a crucial role of PKc in the regulation of pyruvate levels as well as the level of the AOX in heterotrophic plant tissue, and furthermore reveal that these parameters are interlinked in vivo.
Y1  - 2008
UR  - http://www.plantphysiol.org/content/148/3/1640.full
U6  - https://doi.org/10.1104/pp.108.126516
ER  - 
TY  - JOUR
A1  - Tabatabaei, Iman
A1  - Alseekh, Saleh
A1  - Shahid, Mohammad
A1  - Leniak, Ewa
A1  - Wagner, Mateusz
A1  - Mahmoudi, Henda
A1  - Thushar, Sumitha
A1  - Fernie, Alisdair R.
A1  - Murphy, Kevin M.
A1  - Schmöckel, Sandra M.
A1  - Tester, Mark
A1  - Müller-Röber, Bernd
A1  - Skirycz, Aleksandra
A1  - Balazadeh, Salma
T1  - The diversity of quinoa morphological traits and seed metabolic composition
JF  - Scientific data
N2  - Quinoa (Chenopodium quinoa Willd.) is an herbaceous annual crop of the amaranth family (Amaranthaceae). It is increasingly cultivated for its nutritious grains, which are rich in protein and essential amino acids, lipids, and minerals. Quinoa exhibits a high tolerance towards various abiotic stresses including drought and salinity, which supports its agricultural cultivation under climate change conditions. The use of quinoa grains is compromised by anti-nutritional saponins, a terpenoid class of secondary metabolites deposited in the seed coat; their removal before consumption requires extensive washing, an economically and environmentally unfavorable process; or their accumulation can be reduced through breeding. In this study, we analyzed the seed metabolomes, including amino acids, fatty acids, and saponins, from 471 quinoa cultivars, including two related species, by liquid chromatography - mass spectrometry. Additionally, we determined a large number of agronomic traits including biomass, flowering time, and seed yield. The results revealed considerable diversity between genotypes and provide a knowledge base for future breeding or genome editing of quinoa.
Y1  - 2022
U6  - https://doi.org/10.1038/s41597-022-01399-y
SN  - 2052-4463
VL  - 9
IS  - 1
PB  - Nature Research
CY  - Berlin
ER  -