TY - JOUR A1 - Kleessen, Sabrina A1 - Araujo, Wagner L. A1 - Fernie, Alisdair R. A1 - Nikoloski, Zoran T1 - Model-based Confirmation of Alternative Substrates of Mitochondrial Electron Transport Chain JF - The journal of biological chemistry N2 - Background: There are alternative substrates to the mitochondrial respiration. Results: Data-driven model-based analysis renders predictions of alternative substrates to the mitochondrial respiration. Conclusion: Metabolomics data in conjunction with flux-based models can discriminate among hypotheses based on enzymology alone. Significance: This analysis provides a basic framework for in silico studies of alternative pathways in metabolism. Y1 - 2012 U6 - https://doi.org/10.1074/jbc.M111.310383 SN - 0021-9258 VL - 287 IS - 14 SP - 11122 EP - 11131 PB - American Society for Biochemistry and Molecular Biology CY - Bethesda ER - TY - JOUR A1 - Lotkowska, Magda E. A1 - Tohge, Takayuki A1 - Fernie, Alisdair R. A1 - Xue, Gang-Ping A1 - Balazadeh, Salma A1 - Müller-Röber, Bernd T1 - The Arabidopsis Transcription Factor MYB112 Promotes Anthocyanin Formation during Salinity and under High Light Stress JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - MYB transcription factors (TFs) are important regulators of flavonoid biosynthesis in plants. Here, we report MYB112 as a formerly unknown regulator of anthocyanin accumulation in Arabidopsis (Arabidopsis thaliana). Expression profiling after chemically induced overexpression of MYB112 identified 28 up-and 28 down-regulated genes 5 h after inducer treatment, including MYB7 and MYB32, which are both induced. In addition, upon extended induction, MYB112 also positively affects the expression of PRODUCTION OF ANTHOCYANIN PIGMENT1, a key TF of anthocyanin biosynthesis, but acts negatively toward MYB12 and MYB111, which both control flavonol biosynthesis. MYB112 binds to an 8-bp DNA fragment containing the core sequence (A/T/G)(A/C) CC(A/T)(A/G/T)(A/C)(T/C). By electrophoretic mobility shift assay and chromatin immunoprecipitation coupled to quantitative polymerase chain reaction, we show that MYB112 binds in vitro and in vivo to MYB7 and MYB32 promoters, revealing them as direct downstream target genes. We further show that MYB112 expression is up-regulated by salinity and high light stress, environmental parameters that both require the MYB112 TF for anthocyanin accumulation under these stresses. In contrast to several other MYB TFs affecting anthocyanin biosynthesis, MYB112 expression is not controlled by nitrogen limitation or an excess of carbon. Thus, MYB112 constitutes a regulator that promotes anthocyanin accumulation under abiotic stress conditions. Y1 - 2015 U6 - https://doi.org/10.1104/pp.15.00605 SN - 0032-0889 SN - 1532-2548 VL - 169 IS - 3 SP - 1862 EP - 1880 PB - American Society of Plant Physiologists CY - Rockville ER - 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 - THES A1 - de Souza, Laise Rosado T1 - Metabolic signalling between organelles Y1 - 2017 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 - THES A1 - Pham, Phuong Anh T1 - The metabolic significance of the NAD+ salvage pathway and the alternative pathway of respiration in Arabidopsis thaliana Y1 - 2018 ER -