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Haberbosch L, Kierszniowska S, Willmitzer L, Mai K, Spranger J, Maurer L. 5-Aminovaleric acid betaine predicts impaired glucose metabolism and diabetes. Nutr Diabetes 2023; 13:17. [PMID: 37730732 PMCID: PMC10511423 DOI: 10.1038/s41387-023-00245-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 08/18/2023] [Accepted: 08/29/2023] [Indexed: 09/22/2023] Open
Abstract
BACKGROUND 5-Aminovaleric acid betaine (5-AVAB) has recently been identified as a diet and microbial-dependent factor inducing obesity and hepatic steatosis in mice fed a Western diet. Accumulating evidence suggests a role in metabolic dysfunction associated with obesity, diabetes, and fatty liver disease. However, whether 5-AVAB plays a role in human disease is unclear, and human data are sparse. METHODS We measured circulating 5-AVAB serum levels in 143 individuals with overweight or obesity participating in a randomized intervention study (NCT00850629) investigating the long-term effect of a weight maintenance strategy after diet-induced weight reduction. RESULTS Higher 5-AVAB serum levels correlate with worse estimates of obesity, glucose metabolism, and hepatic steatosis after weight loss. Furthermore, higher 5-AVAB levels after weight loss independently predict detrimental changes in glucose metabolism 18 months after the successful weight reduction. CONCLUSION Our human data supports previous findings in rodents indicating a relevant, potentially disadvantageous function of 5-AVAB in the context of metabolic dysbalance.
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Affiliation(s)
- Linus Haberbosch
- Department of Endocrinology and Metabolism, Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Junior Digital Clinician Scientist Program, Charitéplatz 1, 10117, Berlin, Germany
| | | | | | - Knut Mai
- Department of Endocrinology and Metabolism, Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Charité Center for Cardiovascular Research, 10117, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
| | - Joachim Spranger
- Department of Endocrinology and Metabolism, Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany.
- Charité - Universitätsmedizin Berlin, Charité Center for Cardiovascular Research, 10117, Berlin, Germany.
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany.
| | - Lukas Maurer
- Department of Endocrinology and Metabolism, Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Charité Center for Cardiovascular Research, 10117, Berlin, Germany
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2
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Almanza A, Mnich K, Blomme A, Robinson CM, Rodriguez-Blanco G, Kierszniowska S, McGrath EP, Le Gallo M, Pilalis E, Swinnen JV, Chatziioannou A, Chevet E, Gorman AM, Samali A. Regulated IRE1α-dependent decay (RIDD)-mediated reprograming of lipid metabolism in cancer. Nat Commun 2022; 13:2493. [PMID: 35524156 PMCID: PMC9076827 DOI: 10.1038/s41467-022-30159-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 04/05/2022] [Indexed: 12/13/2022] Open
Abstract
IRE1α is constitutively active in several cancers and can contribute to cancer progression. Activated IRE1α cleaves XBP1 mRNA, a key step in production of the transcription factor XBP1s. In addition, IRE1α cleaves select mRNAs through regulated IRE1α-dependent decay (RIDD). Accumulating evidence implicates IRE1α in the regulation of lipid metabolism. However, the roles of XBP1s and RIDD in this process remain ill-defined. In this study, transcriptome and lipidome profiling of triple negative breast cancer cells subjected to pharmacological inhibition of IRE1α reveals changes in lipid metabolism genes associated with accumulation of triacylglycerols (TAGs). We identify DGAT2 mRNA, encoding the rate-limiting enzyme in TAG biosynthesis, as a RIDD target. Inhibition of IRE1α, leads to DGAT2-dependent accumulation of TAGs in lipid droplets and sensitizes cells to nutritional stress, which is rescued by treatment with the DGAT2 inhibitor PF-06424439. Our results highlight the importance of IRE1α RIDD activity in reprograming cellular lipid metabolism. IRE1α cleaves several mRNAs upon accumulation of misfolded proteins. Here the authors show that active IRE1α cleaves DGAT2 mRNA encoding the rate-limiting enzyme in the synthesis of triacylglycerols, suggesting a role of IRE1α in reprogramming lipid metabolism in cancer cells.
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Affiliation(s)
- Aitor Almanza
- Apoptosis Research Centre, National University of Ireland, Galway, H91 W2TY, Ireland.,School of Biological and Chemical Sciences, National University of Ireland, Galway, H91 W2TY, Ireland
| | - Katarzyna Mnich
- Apoptosis Research Centre, National University of Ireland, Galway, H91 W2TY, Ireland.,School of Biological and Chemical Sciences, National University of Ireland, Galway, H91 W2TY, Ireland
| | - Arnaud Blomme
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Claire M Robinson
- Apoptosis Research Centre, National University of Ireland, Galway, H91 W2TY, Ireland.,School of Biological and Chemical Sciences, National University of Ireland, Galway, H91 W2TY, Ireland
| | | | | | - Eoghan P McGrath
- Apoptosis Research Centre, National University of Ireland, Galway, H91 W2TY, Ireland.,School of Biological and Chemical Sciences, National University of Ireland, Galway, H91 W2TY, Ireland
| | - Matthieu Le Gallo
- Inserm U1242, University of Rennes, Rennes, France.,Centre de lutte contre le cancer Eugène Marquis, Rennes, France
| | | | - Johannes V Swinnen
- Department of Oncology, Laboratory of Lipid Metabolism and Cancer, KU Leuven Cancer Institute, Leuven, Belgium
| | - Aristotelis Chatziioannou
- e-NIOS Applications PC, 25 Alexandros Pantou str., 17671, Kallithea, Greece.,Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou str, 11527, Athens, GR, Greece
| | - Eric Chevet
- Inserm U1242, University of Rennes, Rennes, France.,Centre de lutte contre le cancer Eugène Marquis, Rennes, France
| | - Adrienne M Gorman
- Apoptosis Research Centre, National University of Ireland, Galway, H91 W2TY, Ireland.,School of Biological and Chemical Sciences, National University of Ireland, Galway, H91 W2TY, Ireland
| | - Afshin Samali
- Apoptosis Research Centre, National University of Ireland, Galway, H91 W2TY, Ireland. .,School of Biological and Chemical Sciences, National University of Ireland, Galway, H91 W2TY, Ireland.
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3
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Gamradt S, Hasselmann H, Taenzer A, Brasanac J, Stiglbauer V, Sattler A, Sajitz-Hermstein M, Kierszniowska S, Ramien C, Nowacki J, Mascarell-Maricic L, Wingenfeld K, Piber D, Ströhle A, Kotsch K, Paul F, Otte C, Gold SM. Reduced mitochondrial respiration in T cells of patients with major depressive disorder. iScience 2021; 24:103312. [PMID: 34765928 PMCID: PMC8571492 DOI: 10.1016/j.isci.2021.103312] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 08/16/2021] [Accepted: 10/15/2021] [Indexed: 11/18/2022] Open
Abstract
Converging evidence indicates that major depressive disorder (MDD) and metabolic disorders might be mediated by shared (patho)biological pathways. However, the converging cellular and molecular signatures remain unknown. Here, we investigated metabolic dysfunction on a systemic, cellular, and molecular level in unmedicated patients with MDD compared with matched healthy controls (HC). Despite comparable BMI scores and absence of cardiometabolic disease, patients with MDD presented with significant dyslipidemia. On a cellular level, T cells obtained from patients with MDD exhibited reduced respiratory and glycolytic capacity. Gene expression analysis revealed increased carnitine palmitoyltransferase IA (CPT1a) levels in T cells, the rate-limiting enzyme for mitochondrial long-chain fatty acid oxidation. Together, our results indicate metabolic dysfunction in unmedicated, non-overweight patients with MDD on a systemic, cellular, and molecular level. This evidence for reduced mitochondrial respiration in T cells of patients with MDD provides translation of previous animal studies regarding a putative role of altered immunometabolism in depression pathobiology. MDD patients display signs of metabolic imbalance on a systemic level Mitochondrial respiration and glycolysis are decreased in T cells of MDD patients Key cellular metabolic markers negatively correlate with depression severity Increased expression of CPT1a in T cells correlates with many serum metabolites
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Affiliation(s)
- Stefanie Gamradt
- Charité – Universitätsmedizin Berlin, Klinik für Psychiatrie und Psychotherapie, Campus Benjamin Franklin, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Helge Hasselmann
- Charité – Universitätsmedizin Berlin, Klinik für Psychiatrie und Psychotherapie, Campus Benjamin Franklin, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Aline Taenzer
- Charité – Universitätsmedizin Berlin, Klinik für Psychiatrie und Psychotherapie, Campus Benjamin Franklin, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Jelena Brasanac
- Charité – Universitätsmedizin Berlin, Klinik für Psychiatrie und Psychotherapie, Campus Benjamin Franklin, Hindenburgdamm 30, 12203 Berlin, Germany
- Charité – Universitätsmedizin Berlin and Max Delbrueck Center for Molecular Medicine, NeuroCure Clinical Research Center (NCRC), Campus Mitte, 10117 Berlin, Germany
| | - Victoria Stiglbauer
- Charité – Universitätsmedizin Berlin, Klinik für Psychiatrie und Psychotherapie, Campus Benjamin Franklin, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Arne Sattler
- Charité – Universitätsmedizin Berlin, Klinik für Allgemein- und Viszeralchirurgie, Campus Benjamin Franklin, 12203 Berlin, Germany
| | | | | | - Caren Ramien
- Institut für Neuroimmunologie und Multiple Sklerose (INIMS), Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg Eppendorf, 20251 Hamburg, Germany
| | - Jan Nowacki
- Charité – Universitätsmedizin Berlin, Klinik für Psychiatrie und Psychotherapie, Campus Benjamin Franklin, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Lea Mascarell-Maricic
- Charité – Universitätsmedizin Berlin, Klinik für Psychiatrie und Psychotherapie, Campus Mitte, 10117 Berlin, Germany
| | - Katja Wingenfeld
- Charité – Universitätsmedizin Berlin, Klinik für Psychiatrie und Psychotherapie, Campus Benjamin Franklin, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Dominique Piber
- Charité – Universitätsmedizin Berlin, Klinik für Psychiatrie und Psychotherapie, Campus Benjamin Franklin, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Andreas Ströhle
- Charité – Universitätsmedizin Berlin, Klinik für Psychiatrie und Psychotherapie, Campus Mitte, 10117 Berlin, Germany
| | - Katja Kotsch
- Charité – Universitätsmedizin Berlin, Klinik für Allgemein- und Viszeralchirurgie, Campus Benjamin Franklin, 12203 Berlin, Germany
| | - Friedemann Paul
- Charité – Universitätsmedizin Berlin and Max Delbrueck Center for Molecular Medicine, NeuroCure Clinical Research Center (NCRC), Campus Mitte, 10117 Berlin, Germany
| | - Christian Otte
- Charité – Universitätsmedizin Berlin, Klinik für Psychiatrie und Psychotherapie, Campus Benjamin Franklin, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Stefan M. Gold
- Charité – Universitätsmedizin Berlin, Klinik für Psychiatrie und Psychotherapie, Campus Benjamin Franklin, Hindenburgdamm 30, 12203 Berlin, Germany
- Institut für Neuroimmunologie und Multiple Sklerose (INIMS), Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg Eppendorf, 20251 Hamburg, Germany
- Charité – Universitätsmedizin Berlin, Medizinische Klinik m.S. Psychosomatik, Campus Benjamin Franklin, 12203 Berlin, Germany
- Corresponding author
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4
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Schubert C, Winter M, Ebert‐Jung A, Kierszniowska S, Nagel‐Wolfrum K, Schramm T, Link H, Winter S, Unden G. C4
‐dicarboxylates and
l
‐aspartate utilization by
Escherichia coli
K‐12 in the mouse intestine:
l
‐aspartate as a major substrate for fumarate respiration and as a nitrogen source. Environ Microbiol 2021; 23:2564-2577. [DOI: 10.1111/1462-2920.15478] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 03/12/2021] [Accepted: 03/18/2021] [Indexed: 11/29/2022]
Affiliation(s)
- Christopher Schubert
- Institute for Molecular Physiology Johannes Gutenberg‐University Mainz Mainz 55099 Germany
| | - Maria Winter
- Department of Microbiology UT Southwestern Medical Center Dallas TX 75287 USA
| | - Andrea Ebert‐Jung
- Institute for Molecular Physiology Johannes Gutenberg‐University Mainz Mainz 55099 Germany
| | | | - Kerstin Nagel‐Wolfrum
- Institute for Molecular Physiology Johannes Gutenberg‐University Mainz Mainz 55099 Germany
| | - Thorben Schramm
- Max Planck Institute for Terrestrial Microbiology Karl‐von‐Frisch‐Straße 10 Marburg 35043 Germany
| | - Hannes Link
- Max Planck Institute for Terrestrial Microbiology Karl‐von‐Frisch‐Straße 10 Marburg 35043 Germany
| | - Sebastian Winter
- Department of Microbiology UT Southwestern Medical Center Dallas TX 75287 USA
| | - Gottfried Unden
- Institute for Molecular Physiology Johannes Gutenberg‐University Mainz Mainz 55099 Germany
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5
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Lampe L, Jentzsch M, Kierszniowska S, Levashina EA. Metabolic balancing by miR-276 shapes the mosquito reproductive cycle and Plasmodium falciparum development. Nat Commun 2019; 10:5634. [PMID: 31822677 PMCID: PMC6904670 DOI: 10.1038/s41467-019-13627-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 11/14/2019] [Indexed: 12/21/2022] Open
Abstract
The blood-feeding behavior of Anopheles females delivers essential nutrients for egg development and drives parasite transmission between humans. Plasmodium growth is adapted to the vector reproductive cycle, but how changes in the reproductive cycle impact parasite development remains unclear. Here, we show that the bloodmeal-induced miR-276-5p fine-tunes the expression of branched-chain amino acid transferase to terminate the reproductive cycle. Silencing of miR-276 prolongs high rates of amino acid (AA) catabolism and increases female fertility, suggesting that timely termination of AA catabolism restricts mosquito investment into reproduction. Prolongation of AA catabolism in P. falciparum-infected females also compromises the development of the transmissible sporozoite forms. Our results suggest that Plasmodium sporogony exploits the surplus mosquito resources available after reproductive investment and demonstrate the crucial role of the mosquito AA metabolism in within-vector parasite proliferation and malaria transmission. Plasmodium growth is adapted to the reproductive cycle of mosquitoes, but underlying mechanisms are unclear. Here, Lampe et al. show that the blood-meal induced miR-276 balances the termination of the mosquito amino acid catabolism and egg development, providing nutrients for Plasmodium sporozoite development.
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Affiliation(s)
- Lena Lampe
- Vector Biology Unit, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117, Berlin, Germany.,Physiology and Metabolism Laboratory, Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Marius Jentzsch
- Vector Biology Unit, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117, Berlin, Germany
| | | | - Elena A Levashina
- Vector Biology Unit, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117, Berlin, Germany.
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6
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Veyel D, Sokolowska EM, Moreno JC, Kierszniowska S, Cichon J, Wojciechowska I, Luzarowski M, Kosmacz M, Szlachetko J, Gorka M, Méret M, Graf A, Meyer EH, Willmitzer L, Skirycz A. PROMIS, global analysis of PROtein-metabolite interactions using size separation in Arabidopsis thaliana. J Biol Chem 2018; 293:12440-12453. [PMID: 29853640 PMCID: PMC6093232 DOI: 10.1074/jbc.ra118.003351] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/25/2018] [Indexed: 12/19/2022] Open
Abstract
Small molecules not only represent cellular building blocks and metabolic intermediates, but also regulatory ligands and signaling molecules that interact with proteins. Although these interactions affect cellular metabolism, growth, and development, they have been largely understudied. Herein, we describe a method, which we named PROtein–Metabolite Interactions using Size separation (PROMIS), that allows simultaneous, global analysis of endogenous protein–small molecule and of protein–protein complexes. To this end, a cell-free native lysate from Arabidopsis thaliana cell cultures was fractionated by size-exclusion chromatography, followed by quantitative metabolomic and proteomic analyses. Proteins and small molecules showing similar elution behavior, across protein-containing fractions, constituted putative interactors. Applying PROMIS to an A. thaliana extract, we ascertained known protein–protein (PPIs) and protein–metabolite (PMIs) interactions and reproduced binding between small-molecule protease inhibitors and their respective proteases. More importantly, we present examples of two experimental strategies that exploit the PROMIS dataset to identify novel PMIs. By looking for similar elution behavior of metabolites and enzymes belonging to the same biochemical pathways, we identified putative feedback and feed-forward regulations in pantothenate biosynthesis and the methionine salvage cycle, respectively. By combining PROMIS with an orthogonal affinity purification approach, we identified an interaction between the dipeptide Tyr–Asp and the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase. In summary, we present proof of concept for a powerful experimental tool that enables system-wide analysis of PMIs and PPIs across all biological systems. The dataset obtained here comprises nearly 140 metabolites and 5000 proteins, which can be mined for putative interactors.
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Affiliation(s)
- Daniel Veyel
- From the Department Willmitzer, Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam and
| | - Ewelina M Sokolowska
- From the Department Willmitzer, Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam and
| | - Juan C Moreno
- From the Department Willmitzer, Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam and
| | | | - Justyna Cichon
- From the Department Willmitzer, Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam and
| | - Izabela Wojciechowska
- From the Department Willmitzer, Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam and
| | - Marcin Luzarowski
- From the Department Willmitzer, Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam and
| | - Monika Kosmacz
- From the Department Willmitzer, Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam and
| | - Jagoda Szlachetko
- From the Department Willmitzer, Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam and
| | - Michal Gorka
- From the Department Willmitzer, Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam and
| | | | - Alexander Graf
- From the Department Willmitzer, Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam and
| | - Etienne H Meyer
- From the Department Willmitzer, Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam and
| | - Lothar Willmitzer
- From the Department Willmitzer, Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam and
| | - Aleksandra Skirycz
- From the Department Willmitzer, Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam and
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7
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Ziv T, Chalifa-Caspi V, Denekamp N, Plaschkes I, Kierszniowska S, Blais I, Admon A, Lubzens E. Dormancy in Embryos: Insight from Hydrated Encysted Embryos of an Aquatic Invertebrate. Mol Cell Proteomics 2017; 16:1746-1769. [PMID: 28729386 DOI: 10.1074/mcp.ra117.000109] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Indexed: 11/06/2022] Open
Abstract
Numerous aquatic invertebrates remain dormant for decades in a hydrated state as encysted embryos. In search for functional pathways associated with this form of dormancy, we used label-free quantitative proteomics to compare the proteomes of hydrated encysted dormant embryos (resting eggs; RE) with nondormant embryos (amictic eggs; AM) of the rotifer Brachionus plicatilisA total of 2631 proteins were identified in rotifer eggs. About 62% proteins showed higher abundance in AM relative to RE (Fold Change>3; p = 0.05). Proteins belonging to numerous putative functional pathways showed dramatic changes during dormancy. Most striking were changes in the mitochondria indicating an impeded metabolism. A comparison between the abundance of proteins and their corresponding transcript levels, revealed higher concordance for RE than for AM. Surprisingly, numerous highly abundant dormancy related proteins show corresponding high mRNA levels in metabolically inactive RE. As these mRNAs and proteins degrade at the time of exit from dormancy they may serve as a source of nucleotides and amino acids during the exit from dormancy. Because proteome analyses point to a similarity in functional pathways of hydrated RE and desiccated life forms, REs were dried. Similar hatching and reproductive rates were found for wet and dried REs, suggesting analogous pathways for long-term survival in wet or dry forms. Analysis by KEGG pathways revealed a few general strategies for dormancy, proposing an explanation for the low transcriptional similarity among dormancies across species, despite the resemblance in physiological phenotypes.
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Affiliation(s)
- Tamar Ziv
- From the ‡Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Vered Chalifa-Caspi
- §National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Nadav Denekamp
- ¶Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Inbar Plaschkes
- §National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | - Idit Blais
- **Division of Reproductive Endocrinology and IVF, Department of Obstetrics and Gynecology, Carmel Medical Center, Haifa, Israel
| | - Arie Admon
- From the ‡Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Esther Lubzens
- From the ‡Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel;
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8
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Veyel D, Kierszniowska S, Kosmacz M, Sokolowska EM, Michaelis A, Luzarowski M, Szlachetko J, Willmitzer L, Skirycz A. System-wide detection of protein-small molecule complexes suggests extensive metabolite regulation in plants. Sci Rep 2017; 7:42387. [PMID: 28205532 PMCID: PMC5304321 DOI: 10.1038/srep42387] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 12/30/2016] [Indexed: 11/09/2022] Open
Abstract
Protein small molecule interactions are at the core of cell regulation controlling metabolism and development. We reasoned that due to the lack of system wide approaches only a minority of those regulatory molecules are known. In order to see whether or not this assumption is true we developed an effective approach for the identification of small molecules having potential regulatory role that obviates the need of protein or small molecule baits. At the core of this approach is a simple biochemical co-fractionation taking advantage of size differences between proteins and small molecules. Metabolomics based analysis of small molecules co-fractionating with proteins identified a multitude of small molecules in Arabidopsis suggesting the existence of numerous, small molecules/metabolites bound to proteins representing potential regulatory molecules. The approach presented here uses Arabidopsis cell cultures, but is generic and hence applicable to all biological systems.
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Affiliation(s)
- Daniel Veyel
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | | | - Monika Kosmacz
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | | | - Aenne Michaelis
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Marcin Luzarowski
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Jagoda Szlachetko
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Lothar Willmitzer
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
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9
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Skirycz A, Kierszniowska S, Méret M, Willmitzer L, Tzotzos G. Medicinal Bioprospecting of the Amazon Rainforest: A Modern Eldorado? Trends Biotechnol 2016; 34:781-790. [PMID: 27113632 DOI: 10.1016/j.tibtech.2016.03.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/21/2016] [Accepted: 03/23/2016] [Indexed: 12/25/2022]
Abstract
Ignorant of the New World, Europeans believed in El Dorado, a hidden city of immense wealth in gold. Many consider the Amazonian forest to be a medicinal treasure chest and potentially the largest drug dispensary in the world. Yet, the quest to obtain drugs from indigenous tropical plants remains elusive. Here, we assess the potential of new technologies to tap into the metabolic diversity of tropical plants. We also consider how regulations affect access to plant resources. We conclude that, although the road to this medicinal El Dorado may be long and arduous, many other smaller but still valuable finds are hidden along the way.
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Affiliation(s)
- Aleksandra Skirycz
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany; Previous affiliation: ITV Institute, Vale. S.A., Belem, Brazil.
| | | | | | - Lothar Willmitzer
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - George Tzotzos
- Department of Agriculture, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy; Previous affiliation: ITV Institute, Vale. S.A., Belem, Brazil
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10
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Perlikowski D, Kierszniowska S, Sawikowska A, Krajewski P, Rapacz M, Eckhardt Ä, Kosmala A. Remodeling of Leaf Cellular Glycerolipid Composition under Drought and Re-hydration Conditions in Grasses from the Lolium-Festuca Complex. Front Plant Sci 2016; 7:1027. [PMID: 27486462 PMCID: PMC4950141 DOI: 10.3389/fpls.2016.01027] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 06/30/2016] [Indexed: 05/22/2023]
Abstract
Drought tolerant plant genotypes are able to maintain stability and integrity of cellular membranes in unfavorable conditions, and to regenerate damaged membranes after stress cessation. The profiling of cellular glycerolipids during drought stress performed on model species such as Arabidopsis thaliana does not fully cover the picture of lipidome in monocots, including grasses. Herein, two closely related introgression genotypes of Lolium multiflorum (Italian ryegrass) × Festuca arundinacea (tall fescue) were used as a model for other grass species to describe lipid rearrangements during drought and re-hydration. The genotypes differed in their level of photosynthetic capacity during drought, and in their capacity for membrane regeneration after stress cessation. A total of 120 lipids, comprising the classes of monogalactosyldiacyloglycerol, digalactosyldiacyloglycerol, sulfoquinovosyldiacylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, diacylglicerol, and triacylglicerol, were analyzed. The results clearly showed that water deficit had a significant impact on lipid metabolism in studied forage grasses. It was revealed that structural and metabolic lipid species changed their abundance during drought and re-watering periods and some crucial genotype-dependent differences were also observed. The introgression genotype characterized by an ability to regenerate membranes after re-hydration demonstrated a higher accumulation level of most chloroplast and numerous extra-chloroplast membrane lipid species at the beginning of drought. Furthermore, this genotype also revealed a significant reduction in the accumulation of most chloroplast lipids after re-hydration, compared with the other introgression genotype without the capacity for membrane regeneration. The potential influence of observed lipidomic alterations on a cellular membrane stability and photosynthetic capacity, are discussed. HIGHLIGHTS A higher drought tolerance of grasses could be associated with an earlier lipidome response to a stress signal and with a membrane regeneration after stress cessation accompanied by a turnover of chloroplast lipids.
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Affiliation(s)
- Dawid Perlikowski
- Department of Environmental Stress Biology, Institute of Plant Genetics, Polish Academy of SciencesPoznan, Poland
| | | | - Aneta Sawikowska
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of SciencesPoznan, Poland
| | - Paweł Krajewski
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of SciencesPoznan, Poland
| | - Marcin Rapacz
- Department of Plant Physiology, University of Agriculture in KrakowKrakow, Poland
| | - Änne Eckhardt
- Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
| | - Arkadiusz Kosmala
- Department of Environmental Stress Biology, Institute of Plant Genetics, Polish Academy of SciencesPoznan, Poland
- *Correspondence: Arkadiusz Kosmala
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Szymanski WG, Kierszniowska S, Schulze WX. Metabolic labeling and membrane fractionation for comparative proteomic analysis of Arabidopsis thaliana suspension cell cultures. J Vis Exp 2013:e50535. [PMID: 24121251 DOI: 10.3791/50535] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Plasma membrane microdomains are features based on the physical properties of the lipid and sterol environment and have particular roles in signaling processes. Extracting sterol-enriched membrane microdomains from plant cells for proteomic analysis is a difficult task mainly due to multiple preparation steps and sources for contaminations from other cellular compartments. The plasma membrane constitutes only about 5-20% of all the membranes in a plant cell, and therefore isolation of highly purified plasma membrane fraction is challenging. A frequently used method involves aqueous two-phase partitioning in polyethylene glycol and dextran, which yields plasma membrane vesicles with a purity of 95% (1). Sterol-rich membrane microdomains within the plasma membrane are insoluble upon treatment with cold nonionic detergents at alkaline pH. This detergent-resistant membrane fraction can be separated from the bulk plasma membrane by ultracentrifugation in a sucrose gradient (2). Subsequently, proteins can be extracted from the low density band of the sucrose gradient by methanol/chloroform precipitation. Extracted protein will then be trypsin digested, desalted and finally analyzed by LC-MS/MS. Our extraction protocol for sterol-rich microdomains is optimized for the preparation of clean detergent-resistant membrane fractions from Arabidopsis thaliana cell cultures. We use full metabolic labeling of Arabidopsis thaliana suspension cell cultures with K(15)NO3 as the only nitrogen source for quantitative comparative proteomic studies following biological treatment of interest (3). By mixing equal ratios of labeled and unlabeled cell cultures for joint protein extraction the influence of preparation steps on final quantitative result is kept at a minimum. Also loss of material during extraction will affect both control and treatment samples in the same way, and therefore the ratio of light and heave peptide will remain constant. In the proposed method either labeled or unlabeled cell culture undergoes a biological treatment, while the other serves as control (4).
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Arsova B, Kierszniowska S, Schulze WX. The use of heavy nitrogen in quantitative proteomics experiments in plants. Trends Plant Sci 2012; 17:102-12. [PMID: 22154826 DOI: 10.1016/j.tplants.2011.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 10/28/2011] [Accepted: 11/04/2011] [Indexed: 05/04/2023]
Abstract
In the growing field of plant systems biology, there is an undisputed need for methods allowing accurate quantitation of proteins and metabolites. As autotrophic organisms, plants can easily metabolize different nitrogen isotopes, resulting in proteins and metabolites with distinct molecular mass that can be separated on a mass spectrometer. In comparative quantitative experiments, treated and untreated samples are differentially labeled by nitrogen isotopes and jointly processed, thereby minimizing sample-to-sample variation. In recent years, heavy nitrogen labeling has become a widely used strategy in quantitative proteomics and novel approaches have been developed for metabolite identification. Here, we present an overview of currently used experimental strategies in heavy nitrogen labeling in plants and provide background on the history and function of this quantitation technique.
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Affiliation(s)
- Borjana Arsova
- Max Planck Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Golm, Germany
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13
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Keinath NF, Kierszniowska S, Lorek J, Bourdais G, Kessler SA, Shimosato-Asano H, Grossniklaus U, Schulze WX, Robatzek S, Panstruga R. PAMP (pathogen-associated molecular pattern)-induced changes in plasma membrane compartmentalization reveal novel components of plant immunity. J Biol Chem 2010; 285:39140-9. [PMID: 20843791 PMCID: PMC2998143 DOI: 10.1074/jbc.m110.160531] [Citation(s) in RCA: 229] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 09/15/2010] [Indexed: 12/23/2022] Open
Abstract
Plasma membrane compartmentalization spatiotemporally regulates cell-autonomous immune signaling in animal cells. To elucidate immediate early protein dynamics at the plant plasma membrane in response to the bacterial pathogen-associated molecular pattern (PAMP) flagellin (flg22) we employed quantitative mass spectrometric analysis on detergent-resistant membranes (DRMs) of Arabidopsis thaliana suspension cells. This approach revealed rapid and profound changes in DRM protein composition following PAMP treatment, prominently affecting proton ATPases and receptor-like kinases, including the flagellin receptor FLS2. We employed reverse genetics to address a potential contribution of a subset of these proteins in flg22-triggered cellular responses. Mutants of three candidates (DET3, AHA1, FER) exhibited a conspicuous defect in the PAMP-triggered accumulation of reactive oxygen species. In addition, these mutants showed altered mitogen-activated protein kinase (MAPK) activation, a defect in PAMP-triggered stomatal closure as well as altered bacterial infection phenotypes, which revealed three novel players in elicitor-dependent oxidative burst control and innate immunity. Our data provide evidence for dynamic elicitor-induced changes in the membrane compartmentalization of PAMP signaling components.
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Affiliation(s)
- Nana F. Keinath
- From the Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Sylwia Kierszniowska
- the Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm, Germany
| | - Justine Lorek
- From the Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Gildas Bourdais
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, United Kingdom, and
| | - Sharon A. Kessler
- the Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland
| | - Hiroko Shimosato-Asano
- the Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland
| | - Ueli Grossniklaus
- the Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland
| | - Waltraud X. Schulze
- the Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm, Germany
| | - Silke Robatzek
- From the Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Ralph Panstruga
- From the Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
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Keinath NF, Kierszniowska S, Lorek J, Bourdais G, Kessler SA, Shimosato-Asano H, Grossniklaus U, Schulze WX, Robatzek S, Panstruga R. PAMP (pathogen-associated molecular pattern)-induced changes in plasma membrane compartmentalization reveal novel components of plant immunity. J Biol Chem 2010. [PMID: 20843791 DOI: 10.1074/m110.160531] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
Plasma membrane compartmentalization spatiotemporally regulates cell-autonomous immune signaling in animal cells. To elucidate immediate early protein dynamics at the plant plasma membrane in response to the bacterial pathogen-associated molecular pattern (PAMP) flagellin (flg22) we employed quantitative mass spectrometric analysis on detergent-resistant membranes (DRMs) of Arabidopsis thaliana suspension cells. This approach revealed rapid and profound changes in DRM protein composition following PAMP treatment, prominently affecting proton ATPases and receptor-like kinases, including the flagellin receptor FLS2. We employed reverse genetics to address a potential contribution of a subset of these proteins in flg22-triggered cellular responses. Mutants of three candidates (DET3, AHA1, FER) exhibited a conspicuous defect in the PAMP-triggered accumulation of reactive oxygen species. In addition, these mutants showed altered mitogen-activated protein kinase (MAPK) activation, a defect in PAMP-triggered stomatal closure as well as altered bacterial infection phenotypes, which revealed three novel players in elicitor-dependent oxidative burst control and innate immunity. Our data provide evidence for dynamic elicitor-induced changes in the membrane compartmentalization of PAMP signaling components.
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Affiliation(s)
- Nana F Keinath
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
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Kierszniowska S, Walther D, Schulze WX. Ratio-dependent significance thresholds in reciprocal 15N-labeling experiments as a robust tool in detection of candidate proteins responding to biological treatment. Proteomics 2009; 9:1916-24. [PMID: 19260003 DOI: 10.1002/pmic.200800443] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Metabolic labeling of plant tissues with (15)N has become widely used in plant proteomics. Here, we describe a robust experimental design and data analysis workflow implementing two parallel biological replicate experiments with reciprocal labeling and series of 1:1 control mixtures. Thereby, we are able to unambiguously distinguish (i) inherent biological variation between cultures and (ii) specific responses to a biological treatment. The data analysis workflow is based on first determining the variation between cultures based on (15)N/(14)N ratios in independent 1:1 mixtures before biological treatment is applied. In a second step, ratio-dependent SD is used to define p-values for significant deviation of protein ratios in the biological experiment from the distribution of protein ratios in the 1:1 mixture. This approach allows defining those proteins showing significant biological response superimposed on the biological variation before treatment. The proposed workflow was applied to a series of experiments, in which changes in composition of detergent resistant membrane domains was analyzed in response to sucrose resupply after carbon starvation. Especially in experiments involving cell culture treatment (starvation) prior to the actual biological stimulus of interest (resupply), a clear distinction between culture to culture variations and biological response is of utmost importance.
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Kierszniowska S, Seiwert B, Schulze WX. Definition of Arabidopsis sterol-rich membrane microdomains by differential treatment with methyl-beta-cyclodextrin and quantitative proteomics. Mol Cell Proteomics 2008; 8:612-23. [PMID: 19036721 PMCID: PMC2667346 DOI: 10.1074/mcp.m800346-mcp200] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Plasma membranes are dynamic compartments with key functions in solute transport, cell shape, and communication between cells and the environment. In mammalian cells and yeast, the plasma membrane has been shown to be compartmented into so-called lipid rafts, which are defined by their resistance to treatment with non-ionic detergents. In plants, the existence of lipid rafts has been postulated, but the precise composition of this membrane compartment is still under debate. Here we were able to experimentally clearly distinguish (i) true sterol-dependent “raft proteins” and (ii) sterol-independent “non-raft” proteins and co-purifying “contaminants” in plant detergent-resistant membranes. We used quantitative proteomics techniques involving 15N metabolic labeling and specific disruption of sterol-rich membrane domains by methyl-β-cyclodextrin. Among the sterol-dependent proteins we found an over-representation of glycosylphosphatidylinositol-anchored proteins. A large fraction of these proteins has functions in cell wall anchoring. We were able to distinguish constant and variable components of plant sterol-rich membrane microdomains based on their responsiveness to the drug methyl-β-cyclodextrin. Predominantly proteins with signaling functions, such as receptor kinases, G-proteins, and calcium signaling proteins, were identified as variable members in plant lipid rafts, whereas cell wall-related proteins and specific proteins with unknown functions make up a core set of sterol-dependent plant plasma membrane proteins. This allows the plant to maintain a balance between static anchoring of cell shape forming elements and variable adjustment to changing external conditions.
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Affiliation(s)
- Sylwia Kierszniowska
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Golm, Germany
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