TY - JOUR A1 - Brothers, Soren M. A1 - Hilt, Sabine A1 - Attermeyer, Katrin A1 - Grossart, Hans-Peter A1 - Kosten, Sarian A1 - Lischke, Betty A1 - Mehner, Thomas A1 - Meyer, Nils A1 - Scharnweber, Inga Kristin A1 - Köhler, Jan T1 - A regime shift from macrophyte to phytoplankton dominance enhances carbon burial in a shallow, eutrophic lake JF - Ecosphere : the magazine of the International Ecology University N2 - Ecological regime shifts and carbon cycling in aquatic systems have both been subject to increasing attention in recent years, yet the direct connection between these topics has remained poorly understood. A four-fold increase in sedimentation rates was observed within the past 50 years in a shallow eutrophic lake with no surface in-or outflows. This change coincided with an ecological regime shift involving the complete loss of submerged macrophytes, leading to a more turbid, phytoplankton-dominated state. To determine whether the increase in carbon (C) burial resulted from a comprehensive transformation of C cycling pathways in parallel to this regime shift, we compared the annual C balances (mass balance and ecosystem budget) of this turbid lake to a similar nearby lake with submerged macrophytes, a higher transparency, and similar nutrient concentrations. C balances indicated that roughly 80% of the C input was permanently buried in the turbid lake sediments, compared to 40% in the clearer macrophyte-dominated lake. This was due to a higher measured C burial efficiency in the turbid lake, which could be explained by lower benthic C mineralization rates. These lower mineralization rates were associated with a decrease in benthic oxygen availability coinciding with the loss of submerged macrophytes. In contrast to previous assumptions that a regime shift to phytoplankton dominance decreases lake heterotrophy by boosting whole-lake primary production, our results suggest that an equivalent net metabolic shift may also result from lower C mineralization rates in a shallow, turbid lake. The widespread occurrence of such shifts may thus fundamentally alter the role of shallow lakes in the global C cycle, away from channeling terrestrial C to the atmosphere and towards burying an increasing amount of C. KW - calcite precipitation KW - CO2 emissions KW - global carbon cycle KW - metabolism KW - regime shift KW - sedimentation KW - submerged macrophytes KW - temperate zone KW - trophic status Y1 - 2013 U6 - https://doi.org/10.1890/ES13-00247.1 SN - 2150-8925 VL - 4 IS - 11 PB - Wiley CY - Washington ER - TY - JOUR A1 - Calderan-Rodrigues, Maria Juliana A1 - Luzarowski, Marcin A1 - Monte-Bello, Carolina Cassano A1 - Minen, Romina Ines A1 - Zühlke, Boris M. A1 - Nikoloski, Zoran A1 - Skirycz, Aleksandra A1 - Caldana, Camila T1 - Proteogenic dipeptides are characterized by diel fluctuations and target of rapamycin complex-signaling dependency in the model plant Arabidopsis thaliana JF - Frontiers in plant science : FPLS N2 - As autotrophic organisms, plants capture light energy to convert carbon dioxide into ATP, nicotinamide adenine dinucleotide phosphate (NADPH), and sugars, which are essential for the biosynthesis of building blocks, storage, and growth. At night, metabolism and growth can be sustained by mobilizing carbon (C) reserves. In response to changing environmental conditions, such as light-dark cycles, the small-molecule regulation of enzymatic activities is critical for reprogramming cellular metabolism. We have recently demonstrated that proteogenic dipeptides, protein degradation products, act as metabolic switches at the interface of proteostasis and central metabolism in both plants and yeast. Dipeptides accumulate in response to the environmental changes and act via direct binding and regulation of critical enzymatic activities, enabling C flux distribution. Here, we provide evidence pointing to the involvement of dipeptides in the metabolic rewiring characteristics for the day-night cycle in plants. Specifically, we measured the abundance of 13 amino acids and 179 dipeptides over short- (SD) and long-day (LD) diel cycles, each with different light intensities. Of the measured dipeptides, 38 and eight were characterized by day-night oscillation in SD and LD, respectively, reaching maximum accumulation at the end of the day and then gradually falling in the night. Not only the number of dipeptides, but also the amplitude of the oscillation was higher in SD compared with LD conditions. Notably, rhythmic dipeptides were enriched in the glucogenic amino acids that can be converted into glucose. Considering the known role of Target of Rapamycin (TOR) signaling in regulating both autophagy and metabolism, we subsequently investigated whether diurnal fluctuations of dipeptides levels are dependent on the TOR Complex (TORC). The Raptor1b mutant (raptor1b), known for the substantial reduction of TOR kinase activity, was characterized by the augmented accumulation of dipeptides, which is especially pronounced under LD conditions. We were particularly intrigued by the group of 16 dipeptides, which, based on their oscillation under SD conditions and accumulation in raptor1b, can be associated with limited C availability or photoperiod. By mining existing protein-metabolite interaction data, we delineated putative protein interactors for a representative dipeptide Pro-Gln. The obtained list included enzymes of C and amino acid metabolism, which are also linked to the TORC-mediated metabolic network. Based on the obtained results, we speculate that the diurnal accumulation of dipeptides contributes to its metabolic adaptation in response to changes in C availability. We hypothesize that dipeptides would act as alternative respiratory substrates and by directly modulating the activity of the focal enzymes. KW - dipeptide KW - diel cycle KW - metabolism KW - TOR signaling KW - protein-metabolite KW - interactions KW - carbon limitation KW - amino acid Y1 - 2021 U6 - https://doi.org/10.3389/fpls.2021.758933 SN - 1664-462X VL - 12 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Catchpole, Gareth A1 - Platzer, Alexander A1 - Weikert, Cornelia A1 - Kempkensteffen, Carsten A1 - Johannsen, Manfred A1 - Krause, Hans A1 - Jung, Klaus A1 - Miller, Kurt A1 - Willmitzer, Lothar A1 - Selbig, Joachim A1 - Weikert, Steffen T1 - Metabolic profiling reveals key metabolic features of renal cell carcinoma JF - Journal of cellular and molecular medicine : a journal of translational medicine N2 - Recent evidence suggests that metabolic changes play a pivotal role in the biology of cancer and in particular renal cell carcinoma (RCC). Here, a global metabolite profiling approach was applied to characterize the metabolite pool of RCC and normal renal tissue. Advanced decision tree models were applied to characterize the metabolic signature of RCC and to explore features of metastasized tumours. The findings were validated in a second independent dataset. Vitamin E derivates and metabolites of glucose, fatty acid, and inositol phosphate metabolism determined the metabolic profile of RCC. alpha-tocopherol, hippuric acid, myoinositol, fructose-1-phosphate and glucose-1-phosphate contributed most to the tumour/normal discrimination and all showed pronounced concentration changes in RCC. The identified metabolic profile was characterized by a low recognition error of only 5% for tumour versus normal samples. Data on metastasized tumours suggested a key role for metabolic pathways involving arachidonic acid, free fatty acids, proline, uracil and the tricarboxylic acid cycle. These results illustrate the potential of mass spectroscopy based metabolomics in conjunction with sophisticated data analysis methods to uncover the metabolic phenotype of cancer. Differentially regulated metabolites, such as vitamin E compounds, hippuric acid and myoinositol, provide leads for the characterization of novel pathways in RCC. KW - kidney cancer KW - metabolism KW - metabolomics KW - metastasis Y1 - 2011 U6 - https://doi.org/10.1111/j.1582-4934.2009.00939.x SN - 1582-1838 VL - 15 IS - 1 SP - 109 EP - 118 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Fichtner, Franziska A1 - Olas, Justyna Jadwiga A1 - Feil, Regina A1 - Watanabe, Mutsumi A1 - Krause, Ursula A1 - Hoefgen, Rainer A1 - Stitt, Mark A1 - Lunn, John Edward T1 - Functional features of Trehalose-6-Phosphate Synthase 1 BT - an essential enzyme in Arabidopsis JF - The Plant Cell N2 - Tre6P synthesis by TPS1 is essential for embryogenesis and postembryonic growth in Arabidopsis, and appropriate Suc signaling by Tre6P is dependent on the noncatalytic domains of TPS1. In Arabidopsis (Arabidopsis thaliana), TREHALOSE-6-PHOSPHATE SYNTHASE1 (TPS1) catalyzes the synthesis of the sucrose-signaling metabolite trehalose 6-phosphate (Tre6P) and is essential for embryogenesis and normal postembryonic growth and development. To understand its molecular functions, we transformed the embryo-lethal tps1-1 null mutant with various forms of TPS1 and with a heterologous TPS (OtsA) from Escherichia coli, under the control of the TPS1 promoter, and tested for complementation. TPS1 protein localized predominantly in the phloem-loading zone and guard cells in leaves, root vasculature, and shoot apical meristem, implicating it in both local and systemic signaling of Suc status. The protein is targeted mainly to the nucleus. Restoring Tre6P synthesis was both necessary and sufficient to rescue the tps1-1 mutant through embryogenesis. However, postembryonic growth and the sucrose-Tre6P relationship were disrupted in some complementation lines. A point mutation (A119W) in the catalytic domain or truncating the C-terminal domain of TPS1 severely compromised growth. Despite having high Tre6P levels, these plants never flowered, possibly because Tre6P signaling was disrupted by two unidentified disaccharide-monophosphates that appeared in these plants. The noncatalytic domains of TPS1 ensure its targeting to the correct subcellular compartment and its catalytic fidelity and are required for appropriate signaling of Suc status by Tre6P. KW - cyanobacterial sucrose-phosphatase KW - trehalose 6-phosphate KW - vegetative growth KW - crystal-structure KW - gene-expression KW - thaliana KW - metabolism KW - phosphorylation KW - reveals KW - proteins Y1 - 2020 U6 - https://doi.org/10.1105/tpc.19.00837 SN - 0032-0781 SN - 1471-9053 VL - 32 IS - 6 SP - 1949 EP - 1972 PB - Oxford University Press CY - Oxford ER - TY - JOUR A1 - Hocher, Berthold A1 - Haumann, Hannah A1 - Rahnenführer, Jan A1 - Reichetzeder, Christoph A1 - Kalk, Philipp A1 - Pfab, Thiemo A1 - Tsuprykov, Oleg A1 - Winter, Stefan A1 - Hofmann, Ute A1 - Li, Jian A1 - Püschel, Gerhard Paul A1 - Lang, Florian A1 - Schuppan, Detlef A1 - Schwab, Matthias A1 - Schaeffeler, Elke T1 - Maternal eNOS deficiency determines a fatty liver phenotype of the offspring in a sex dependent manner JF - Epigenetics : the official journal of the DNA Methylation Society N2 - Maternal environmental factors can impact on the phenotype of the offspring via the induction of epigenetic adaptive mechanisms. The advanced fetal programming hypothesis proposes that maternal genetic variants may influence the offspring's phenotype indirectly via epigenetic modification, despite the absence of a primary genetic defect. To test this hypothesis, heterozygous female eNOS knockout mice and wild type mice were bred with male wild type mice. We then assessed the impact of maternal eNOS deficiency on the liver phenotype of wild type offspring. Birth weight of male wild type offspring born to female heterozygous eNOS knockout mice was reduced compared to offspring of wild type mice. Moreover, the offspring displayed a sex specific liver phenotype, with an increased liver weight, due to steatosis. This was accompanied by sex specific differences in expression and DNA methylation of distinct genes. Liver global DNA methylation was significantly enhanced in both male and female offspring. Also, hepatic parameters of carbohydrate metabolism were reduced in male and female offspring. In addition, male mice displayed reductions in various amino acids in the liver. Maternal genetic alterations, such as partial deletion of the eNOS gene, can affect liver metabolism of wild type offspring without transmission of the intrinsic defect. This occurs in a sex specific way, with more detrimental effects in females. This finding demonstrates that a maternal genetic defect can epigenetically alter the phenotype of the offspring, without inheritance of the defect itself. Importantly, these acquired epigenetic phenotypic changes can persist into adulthood. KW - Epigenetics KW - eNOS KW - Fetal programming KW - fatty liver KW - metabolism Y1 - 2016 U6 - https://doi.org/10.1080/15592294.2016.1184800 SN - 1559-2294 SN - 1559-2308 VL - 11 SP - 539 EP - 552 PB - Routledge, Taylor & Francis Group CY - Philadelphia ER - TY - JOUR A1 - Islam, Khan M. Shaiful A1 - Schaeublin, H. A1 - Wenk, C. A1 - Wanner, Michael A1 - Liesegang, Annette T1 - Effect of dietary citric acid on the performance and mineral metabolism of broiler JF - Journal of animal physiology and animal nutrition N2 - The objective of this study was to investigate the effect of dietary citric acid (CA) on the performance and mineral metabolism of broiler chicks. A total of 1720 Ross PM3 broiler chicks (days old) were randomly assigned to four groups (430 in each) and reared for a period of 35 days. The diets of groups 1, 2, 3 and 4 were supplemented with 0%, 0.25%, 0.75% or 1.25% CA by weight respectively. Feed and faeces samples were collected weekly and analysed for acid insoluble ash, calcium (Ca), phosphorus (P) and magnesium (Mg). The pH was measured in feed and faeces. At the age of 28 days, 10 birds from each group were slaughtered; tibiae were collected from each bird for the determination of bone mineral density, total ash, Ca, P, Mg and bone-breaking strength, and blood was collected for the measurement of osteocalcin, serum CrossLaps (R), Ca, P, Mg and 1,25(OH)(2)Vit-D in serum. After finishing the trial on day 37, all chicks were slaughtered by using the approved procedure. Birds that were fed CA diets were heavier (average body weights of 2030, 2079 and 2086 g in the 0.25%, 0.75% and 1.25% CA groups, respectively, relative to the control birds (1986 g). Feed conversion efficiency (weight gain in g per kg of feed intake) was also higher in birds of the CA-fed groups (582, 595 and 587 g/kg feed intake for 0.25%, 0.75% and 1.25% CA respectively), relative to the control birds (565 g/kg feed intake). The digestibility of Ca, P and Mg increased in the CA-fed groups, especially for the diets supplemented with 0.25% and 0.75% CA. Support for finding was also indicated in the results of the analysis of the tibia. At slaughter, the birds had higher carcass weights and higher graded carcasses in the groups that were fed the CA diets. The estimated profit margin was highest for birds fed the diet containing 0.25% CA. Birds of the 0.75% CA group were found to have the second highest estimated profit margin. Addition of CA up to a level of 1.25% of the diet increased performance, feed conversion efficiency, carcass weight and carcass quality, but only in numerical terms. The addition of CA up to 0.75% significantly increased the digestibility of macro minerals, bone ash content, bone mineral density and bone strength of the broiler chicks. It may, therefore, be concluded that the addition of 0.75% CA in a standard diet is suitable for growth, carcass traits, macromineral digestibility and bone mineral density of broiler chicks. KW - broiler chicks KW - dietary citric acid KW - calcium KW - phosphorus KW - metabolism KW - performance Y1 - 2012 U6 - https://doi.org/10.1111/j.1439-0396.2011.01225.x SN - 0931-2439 VL - 96 IS - 5 SP - 808 EP - 817 PB - Wiley-Blackwell CY - Hoboken ER - TY - THES A1 - Küken, Anika T1 - Predictions from constraint-based approaches including enzyme kinetics N2 - The metabolic state of an organism reflects the entire phenotype that is jointly affected by genetic and environmental changes. Due to the complexity of metabolism, system-level modelling approaches have become indispensable tools to obtain new insights into biological functions. In particular, simulation and analysis of metabolic networks using constraint-based modelling approaches have helped the analysis of metabolic fluxes. However, despite ongoing improvements in prediction of reaction flux through a system, approaches to directly predict metabolite concentrations from large-scale metabolic networks remain elusive. In this thesis, we present a computational approach for inferring concentration ranges from genome-scale metabolic models endowed with mass action kinetics. The findings specify a molecular mechanism underling facile control of concentration ranges for components in large-scale metabolic networks. Most importantly, an extended version of the approach can be used to predict concentration ranges without knowledge of kinetic parameters, provided measurements of concentrations in a reference state. We show that the approach is applicable with large-scale kinetic and stoichiometric metabolic models of organisms from different kingdoms of life. By challenging the predictions of concentration ranges in the genome-scale metabolic network of Escherichia coli with real-world data sets, we further demonstrate the prediction power and limitations of the approach. To predict concentration ranges in other species, e.g. model plant species Arabidopsis thaliana, we would rely on estimates of kinetic parameters (i.e. enzyme catalytic rates) since plant-specific enzyme catalytic rates are poorly documented. Using the constraint-based approach of Davidi et al. for estimation of enzyme catalytic rates, we obtain values for 168 plant enzymes. The approach depends on quantitative proteomics data and flux estimates obtained from constraint-based model of plant leaf metabolism integrating maximal rates of selected enzymes, plant-specific constraints on fluxes through canonical pathways, and growth measurements from Arabidopsis thaliana rosette under ten conditions. We demonstrate a low degree of plant enzyme saturation, supported by the agreement between concentrations of nicotinamide adenine dinucleotide, adenosine triphosphate, and glyceraldehyde 3-phosphate, based on our maximal in vivo catalytic rates, and available quantitative metabolomics data. Hence, our results show genome-wide estimation for plant-specific enzyme catalytic rates is feasible. These can now be readily employed to study resource allocation, to predict enzyme and metabolite concentrations using recent constrained-based modelling approaches. Constraint-based methods do not directly account for kinetic mechanisms and corresponding parameters. Therefore, a number of workflows have already been proposed to approximate reaction kinetics and to parameterize genome-scale kinetic models. We present a systems biology strategy to build a fully parameterized large-scale model of Chlamydomonas reinhardtii accounting for microcompartmentalization in the chloroplast stroma. Eukaryotic algae comprise a microcompartment, the pyrenoid, essential for the carbon concentrating mechanism (CCM) that improves their photosynthetic performance. Since the experimental study of the effects of microcompartmentation on metabolic pathways is challenging, we employ our model to investigate compartmentation of fluxes through the Calvin-Benson cycle between pyrenoid and stroma. Our model predicts that ribulose-1,5-bisphosphate, the substrate of Rubisco, and 3-phosphoglycerate, its product, diffuse in and out of the pyrenoid. We also find that there is no major diffusional barrier to metabolic flux between the pyrenoid and stroma. Therefore, our computational approach represents a stepping stone towards understanding of microcompartmentalized CCM in other organisms. This thesis provides novel strategies to use genome-scale metabolic networks to predict and integrate metabolite concentrations. Therefore, the presented approaches represent an important step in broadening the applicability of large-scale metabolic models to a range of biotechnological and medical applications. N2 - Der Stoffwechsel eines Organismus spiegelt den gesamten Phänotyp wieder, welcher durch genetische und umweltbedingte Veränderungen beeinflusst wird. Aufgrund der Komplexität des Stoffwechsels sind Modellierungsansätze, welche das ganzheitliches System betrachten, zu unverzichtbaren Instrumenten geworden, um neue Einblicke in biologische Funktionen zu erhalten. Insbesondere die Simulation und Analyse von Stoffwechselnetzwerken mithilfe von Constraint-basierten Modellierungsansätzen hat die Analyse von Stoffwechselflüssen erleichtert. Trotz kontinuierlicher Verbesserungen bei der Vorhersage des Reaktionsflusses durch ein System, sind Ansätze zur direkten Vorhersage von Metabolitkonzentrationen aus metabolischen Netzwerken kaum vorhanden. In dieser Arbeit stellen wir einen Ansatz vor, mit welchem Konzentrationsbereiche aus genomweiten metabolischen Netzwerken, die mit einer Massenwirkungskinetik ausgestattet sind, abgeleitet werden können. Die Ergebnisse zeigen einen molekularen Mechanismus auf, welcher der Steuerung von Konzentrationsbereichen für Komponenten in metabolischen Netzwerken zugrunde liegt. Eine erweiterte Version des Ansatzes kann verwendet werden, um Konzentrationsbereiche ohne Kenntnis der kinetischen Parameter vorherzusagen, vorausgesetzt, dass Messungen von Konzentrationen in einem Referenzzustand vorhanden sind. Wir zeigen, dass der Ansatz mit kinetischen und stöchiometrischen Stoffwechselmodellen von Organismen aus verschiedenen taxonomischen Reichen anwendbar ist. Indem wir die Vorhersagen von Konzentrationsbereichen im genomweiten Stoffwechselnetzwerk von Escherichia coli mit realen Datensätzen validieren, demonstrieren wir die Vorhersagekraft und die Grenzen des Ansatzes. Um Konzentrationsbereiche in anderen Spezies vorherzusagen, z.B. der Modellpflanzenspezies Arabidopsis thaliana, stützen wir uns auf Schätzungen der kinetischen Parameter (d.h. der katalytischen Enzymraten), da tatsächlich gemessene, pflanzenspezifische katalytische Enzymraten nur unzureichend dokumentiert sind. Unter Verwendung des Constraint-basierten Ansatzes von Davidi et al. zur Abschätzung der katalytischen Enzymraten erhalten wir Werte für 168 pflanzliche Enzyme. Der Ansatz hängt von quantitativen Proteomikdaten und Schätzungen des Reaktionsflusses ab, die aus einem Constraint-basierten Modell des Pflanzenblattmetabolismus unter Einbeziehung der maximalen Raten ausgewählter Enzyme, pflanzenspezifischen Einschränkungen des Flusses durch kanonische Pfade und Wachstumsmessungen aus Rosetten von Arabidopsis thaliana unter zehn Bedingungen erhalten wurden. Wir fanden einen niedrigen Grad an Sättigung der Pflanzenenzyme, der durch die Übereinstimmung zwischen den Konzentrationen von Nicotinamidadenindinukleotid, Adenosintriphosphat und Glycerinaldehyd-3-phosphat auf der Grundlage unserer maximalen in vivo katalytischen Raten und den verfügbaren quantitativen Metabolomikdaten gestützt wird. Daher zeigen unsere Ergebnisse, dass genomweite Schätzungen für pflanzenspezifische Enzymkatalyseraten möglich sind. Diese können nun leicht verwendet werden, um die Ressourcenzuweisung zu untersuchen und die Enzym- und Metabolitenkonzentrationen unter Verwendung neuerer Constraint-basierter Modellierungsansätze vorherzusagen. Constraint-basierte Methoden berücksichtigen kinetische Mechanismen und entsprechende Parameter nicht direkt. Daher wurden einige Methoden entwickelt, welche die Reaktionskinetik approximieren und systemumfassende kinetische Modelle zu parametrisieren. Wir präsentieren eine systembiologische Strategie zur Erstellung eines vollständig parametrisierten Modells von Chlamydomonas reinhardtii, welches die Mikrokompartimentierung im Chloroplaststroma berücksichtigt. Eukaryotische Algen besitzen ein Mikrokompartiment, den Pyrenoiden, der für den Kohlenstoffkonzentrationsmechanismus (KKM) unerlässlich ist und die Photosyntheseleistung verbessert. Die experimentelle Untersuchung der Auswirkungen der Mikrokompartimentierung auf Stoffwechselwege stellt eine Herausforderung dar. Daher verwenden wir unser Modell um die Kompartimentierung von Reaktionsflüssen durch den Calvin-Benson-Zyklus zwischen Pyrenoid und Stroma zu untersuchen. Unser Modell sagt voraus, dass Ribulose-1,5-Bisphosphat, das Substrat von Rubisco, und 3-Phosphoglycerat , das Produkt, in den Pyrenoid hinein und aus ihm heraus diffundieren. Weiter stellen wir fest, dass es keine wesentliche Diffusionsbarriere zwischen dem Pyrenoid und dem Stroma gibt. Somit bietet unser Ansatz eine Möglichkeit um ein Verständnis des mikrokompartimentierten KKM auch in anderen Organismen zu erlangen. Diese Dissertation zeigt neue Strategien um metabolische Netzwerke zur Vorhersage von Metabolitkonzentrationen zu nutzen und selbige zu integrieren. Daher stellen die Ansätze einen wichtigen Schritt zur Anwendbarkeit von genomweiten Stoffwechselmodellen auf eine Reihe von biotechnologischen und medizinischen Anwendungen dar. KW - constraint-based modeling KW - metabolism KW - metabolic networks Y1 - 2020 ER - TY - THES A1 - Laeger, Thomas T1 - Protein-dependent regulation of feeding, metabolism, and development of type 2 diabetes T1 - Proteinabhängige Regulation der Nahrungsaufnahme und des Metabolismus sowie Entstehung des Typ-2-Diabetes BT - FGF21’s biological role BT - die Rolle von FGF21 N2 - Food intake is driven by the need for energy but also by the demand for essential nutrients such as protein. Whereas it was well known how diets high in protein mediate satiety, it remained unclear how diets low in protein induce appetite. Therefore, this thesis aims to contribute to the research area of the detection of restricted dietary protein and adaptive responses. This thesis provides clear evidence that the liver-derived hormone fibroblast growth factor 21 (FGF21) is an endocrine signal of a dietary protein restriction, with the cellular amino acid sensor general control nonderepressible 2 (GCN2) kinase acting as an upstream regulator of FGF21 during protein restriction. In the brain, FGF21 is mediating the protein-restricted metabolic responses, e.g. increased energy expenditure, food intake, insulin sensitivity, and improved glucose homeostasis. Furthermore, endogenous FGF21 induced by dietary protein or methionine restriction is preventing the onset of type 2 diabetes in the New Zealand Obese mouse. Overall, FGF21 plays an important role in the detection of protein restriction and macronutrient imbalance in rodents and humans, and mediates both the behavioral and metabolic responses to dietary protein restriction. This makes FGF21 a critical physiological signal of dietary protein restriction, highlighting the important but often overlooked impact of dietary protein on metabolism and eating behavior, independent of dietary energy content. N2 - Die Nahrungsaufnahme wird nicht nur durch den Bedarf an Energie, sondern auch durch den Bedarf an essenziellen Nährstoffen wie z. B. Protein bestimmt. Es war zwar bekannt, wie proteinreiche Nahrung eine Sättigung vermittelt, jedoch war unklar, wie eine proteinarme Ernährung den Appetit anregt. Ziel dieser Arbeit ist es daher, zu untersuchen, wie Nahrung mit einem niedrigen Proteingehalt detektiert wird und die Anpassung des Organismus im Hinblick auf den Metabolismus und das Ernährungsverhalten erfolgt. Diese Arbeit liefert klare Beweise dafür, dass das aus der Leber stammende Hormon Fibroblast growth factor 21 (FGF21) ein endokrines Signal einer Nahrungsproteinrestriktion ist, wobei der zelluläre Aminosäuresensor general control nonderepressible 2 kinase (GCN2) als Regulator von FGF21 während der Proteinrestriktion fungiert. Im Gehirn vermittelt FGF21 die durch Proteinrestriktion induzierten Stoffwechselreaktionen, z.B. den Anstieg des Energieverbrauches, die Erhöhung der Nahrungsaufnahme und eine Verbesserung der Insulinsensitivität sowie der Glukosehomöostase. Darüber hinaus schützt das durch eine protein- oder methioninarme Diät induzierte FGF21 New Zealand Obese (NZO)-Mäuse, einem Tiermodell für den humanen Typ-2-Diabetes, vor einer Diabetesentstehung. FGF21 spielt bei Nagetieren und Menschen eine wichtige Rolle hinsichtlich der Detektion einer diätetischen Proteinrestriktion sowie eines Ungleichgewichtes der Makronährstoffe zueinander und vermittelt die adaptiven Verhaltens- und Stoffwechselreaktionen. Dies macht FGF21 zu einem kritischen physiologischen Signal der Nahrungsproteinrestriktion und unterstreicht den wichtigen, aber oft übersehenen Einfluss der Nahrungsproteine auf den Stoffwechsel und das Nahrungsaufnahmeverhalten, unabhängig vom Energiegehalt der Nahrung. KW - protein restriction KW - autophagy KW - thermogenesis KW - appetite KW - hyperglycemia KW - methionine restriction KW - bone KW - FGF21 KW - energy expenditure KW - GCN2 KW - metabolism KW - food choice KW - type 2 diabetes Y1 - 2021 ER - TY - THES A1 - Mancini, Carola T1 - Analysis of the effects of age-related changes of metabolic flux on brown adipocyte formation and function N2 - Brown adipose tissue (BAT) is responsible for non-shivering thermogenesis, thereby allowing mammals to maintain a constant body temperature in a cold environment. Thermogenic capacity of this tissue is due to a high mitochondrial density and expression of uncoupling protein 1 (UCP1), a unique brown adipocyte marker which dissipates the mitochondrial proton gradient to produce heat instead of ATP. BAT is actively involved in whole-body metabolic homeostasis and during aging there is a loss of classical brown adipose tissue with concomitantly reduced browning capacity of white adipose tissue. Therefore, an age-dependent decrease of BAT-related energy expenditure capacity may exacerbate the development of metabolic diseases, including obesity and type 2 diabetes mellitus. Given that direct effects of age-related changes of BAT-metabolic flux have yet to be unraveled, the aim of the current thesis is to investigate potential metabolic mechanisms involved in BAT-dysfunction during aging and to identify suitable metabolic candidates as functional biomarkers of BAT-aging. To this aim, integration of transcriptomic, metabolomic and proteomic data analyses of BAT from young and aged mice was performed, and a group of candidates with age-related changes was revealed. Metabolomic analysis showed age-dependent alterations of metabolic intermediates involved in energy, nucleotide and vitamin metabolism, with major alterations regarding the purine nucleotide pool. These data suggest a potential role of nucleotide intermediates in age-related BAT defects. In addition, the screening of transcriptomic and proteomic data sets from BAT of young and aged mice allowed identification of a 60-kDa lysophospholipase, also known as L-asparaginase (Aspg), whose expression declines during BAT-aging. Involvement of Aspg in brown adipocyte thermogenic function was subsequently analyzed at the molecular level using in vitro approaches and animal models. The findings revealed sensitivity of Aspg expression to β3-adrenergic activation via different metabolic cues, including cold exposure and treatment with β3-adrenergic agonist CL. To further examine ASPG function in BAT, an over-expression model of Aspg in a brown adipocyte cell line was established and showed that these cells were metabolically more active compared to controls, revealing increased expression of the main brown-adipocyte specific marker UCP1, as well as higher lipolysis rates. An in vitro loss-of-function model of Aspg was also functionally analyzed, revealing reduced brown adipogenic characteristics and an impaired lipolysis, thus confirming physiological relevance of Aspg in brown adipocyte function. Characterization of a transgenic mouse model with whole-body inactivation of the Aspg gene (Aspg-KO) allowed investigation of the role of ASPG under in vivo conditions, indicating a mild obesogenic phenotype, hypertrophic white adipocytes, impairment of the early thermogenic response upon cold-stimulation and dysfunctional insulin sensitivity. Taken together, these data show that ASPG may represent a new functional biomarker of BAT-aging that regulates thermogenesis and therefore a potential target for the treatment of age-related metabolic disease. KW - adipose tissue KW - aging KW - nutrients KW - metabolism KW - Fettgewebe KW - Alterung KW - Stoffwechsel KW - Nährstoffe Y1 - 2021 U6 - https://doi.org/10.25932/publishup-51266 ER - TY - THES A1 - Mubeen, Umarah T1 - Regulation of central carbon and nitrogen metabolism by Target of Rapamycin (TOR) kinase in Chlamydomonas reinhardtii T1 - Regulation des zentralen Kohlen- und Stickstoff Stoffwechsels durch die Target of Rapamycin Kinase in der Grünalge Chlamydomonas reinhardtii N2 - The highly conserved protein complex containing the Target of Rapamycin (TOR) kinase is known to integrate intra- and extra-cellular stimuli controlling nutrient allocation and cellular growth. This thesis describes three studies aimed to understand how TOR signaling pathway influences carbon and nitrogen metabolism in Chlamydomonas reinhardtii. The first study presents a time-resolved analysis of the molecular and physiological features across the diurnal cycle. The inhibition of TOR leads to 50% reduction in growth followed by nonlinear delays in the cell cycle progression. The metabolomics analysis showed that the growth repression is mainly driven by differential carbon partitioning between anabolic and catabolic processes. Furthermore, the high accumulation of nitrogen-containing compounds indicated that TOR kinase controls the carbon to nitrogen balance of the cell, which is responsible for biomass accumulation, growth and cell cycle progression. In the second study the cause of the high accumulation of amino acids is explained. For this purpose, the effect of TOR inhibition on Chlamydomonas was examined under different growth regimes using stable 13C- and 15N-isotope labeling. The data clearly showed that an increased nitrogen uptake is induced within minutes after the inhibition of TOR. Interestingly, this increased N-influx is accompanied by increased activities of nitrogen assimilating enzymes. Accordingly, it was concluded that TOR inhibition induces de-novo amino acid synthesis in Chlamydomonas. The recognition of this novel process opened an array of questions regarding potential links between central metabolism and TOR signaling. Therefore a detailed phosphoproteomics study was conducted to identify the potential substrates of TOR pathway regulating central metabolism. Interestingly, some of the key enzymes involved in carbon metabolism as well as amino acid synthesis exhibited significant changes in the phosphosite intensities immediately after TOR inhibition. Altogether, these studies provide a) detailed insights to metabolic response of Chlamydomonas to TOR inhibition, b) identification of a novel process causing rapid upshifts in amino acid levels upon TOR inhibition and c) finally highlight potential targets of TOR signaling regulating changes in central metabolism. Further biochemical and molecular investigations could confirm these observations and advance the understanding of growth signaling in microalgae. N2 - Target of Rapamycin (TOR) ist das Zentralprotein eines hochkonservierten Proteinkomplexes, welcher Nährstoff- und Energie Ressourcen für zelluläre Wachstumsprozesse kontengiert. Diese Doktorarbeit beschreibt anhand dreier Studien, wie TOR zu diesem Zweck, in der Grünalge Chlamydomonas reinhardtii, den zentralen Stoffwechsel reguliert. Die erste Studie untersucht dazu das zeitaufgelöste Verhalten von Biomolekülen im Tagesverlauf synchronisiert wachsender Algen. Dabei konnte gezeigt werden, das der TOR Inhibitor Rapamycin das Wachstum um 50% reduziert und den Zellzyklus verzögert. Die Zellzyklus Verzögerung scheint dabei hauptsächlich durch veränderte Stoffwechselprozesse erklärt zu sein. Hierbei konnte gezeigt werden, dass TOR vor allem stickstoffhaltige Stoffwechselprodukte (z.B. Aminosäuren) kontrolliert, welche die Grundlage für Biomasseproduktion, Wachstum und den Zellzyklus bilden. Im Rahmen der zweiten Studie konnte dann der molekulare Mechanismus der Akkumulation der zellulären Aminosäuren aufgeklärt werden. Zu diesem Zweck wurden Fütterungsstudien mit 13C- und 15N-Isotopen durchgeführt. Die Ergebnisse dieser Fütterung konnten klar zeigen, dass die Inhibition von TOR zur verstärkten Aufnahme von Stickstoff in die Zelle und dessen Assimilierung in Aminosäuren führt. Die Aufdeckung dieses neuen, von TOR gesteuerten Prozesses eröffnete somit die Frage, wie die Signalkaskade von TOR zu den Enzymen der Aminosäuresynthese verläuft. Detaillierte phosphoproteomische Studien sollten dieser Frage nachgehen und Zielprotein der TOR Kinase zu identifizieren und regulierte Stoffwechselprozesses zu finden. Dabei stellte sich heraus, dass sowohl verschiedene Enzyme der Aminosäuresynthese als auch Enzyme des zentralen Stoffwechsels innerhalb weniger Minuten stark verändert wurden. Zusammenfassend kann man festhalten das die vorliegende Arbeit detaillierte Stoffwechselanalysen des Stoffwechsels nach einer TOR Inhibition aufdeckt. Hierbei ein neuer Mechanismus zur Regulation der Aminosäuresynthese, nach TOR Inhibition gezeigt werden konnte, welche durch systemische Regulation der Phosphorylierungsmuster zellulärer Proteine kontrolliert wird. Zusätzliche molekulare und biochemische Studien konnten weiterhin zeigen, dass wie TOR das zelluläre Wachstum der photosynthetischen Grünalge kontrolliert und somit steuert. KW - Target of Rapamycin kinase KW - Growth signaling KW - metabolism KW - phosphoproteomics KW - Chlamydomonas KW - Target of Rapamycin kinase KW - Wachstumssignale KW - Stoffwechsel KW - Phosphoproteomik KW - Chlamydomonas Y1 - 2018 ER - TY - JOUR A1 - Scharnweber, Inga Kristin A1 - Andersson, Matilda L. A1 - Chaguaceda, Fernando A1 - Eklöv, Peter T1 - Intraspecific differences in metabolic rates shape carbon stable isotope trophic discrimination factors of muscle tissue in the common teleost Eurasian perch (Perca fluviatilis) JF - Ecology and evolution N2 - Stable isotopes represent a unique approach to provide insights into the ecology of organisms. δ13C and δ15N have specifically been used to obtain information on the trophic ecology and food-web interactions. Trophic discrimination factors (TDF, Δ13C and Δ15N) describe the isotopic fractionation occurring from diet to consumer tissue, and these factors are critical for obtaining precise estimates within any application of δ13C and δ15N values. It is widely acknowledged that metabolism influences TDF, being responsible for different TDF between tissues of variable metabolic activity (e.g., liver vs. muscle tissue) or species body size (small vs. large). However, the connection between the variation of metabolism occurring within a single species during its ontogeny and TDF has rarely been considered. Here, we conducted a 9-month feeding experiment to report Δ13C and Δ15N of muscle and liver tissues for several weight classes of Eurasian perch (Perca fluviatilis), a widespread teleost often studied using stable isotopes, but without established TDF for feeding on a natural diet. In addition, we assessed the relationship between the standard metabolic rate (SMR) and TDF by measuring the oxygen consumption of the individuals. Our results showed a significant negative relationship of SMR with Δ13C, and a significant positive relationship of SMR with Δ15N of muscle tissue, but not with TDF of liver tissue. SMR varies inversely with size, which translated into a significantly different TDF of muscle tissue between size classes. In summary, our results emphasize the role of metabolism in shaping-specific TDF (i.e., Δ13C and Δ15N of muscle tissue) and especially highlight the substantial differences between individuals of different ontogenetic stages within a species. Our findings thus have direct implications for the use of stable isotope data and the applications of stable isotopes in food-web studies. KW - fractionation factors KW - metabolism KW - ontogeny KW - standard metabolic rate KW - tissue types KW - δ13C KW - δ15N Y1 - 2021 SN - 2045-7758 VL - 11 IS - 14 SP - 9804 EP - 9814 PB - John Wiley & Sons, Inc. CY - New Jersey ER - TY - JOUR A1 - Schell, Mareike A1 - Wardelmann, Kristina A1 - Kleinridders, Andre T1 - Untangling the effect of insulin action on brain mitochondria and metabolism JF - Journal of neuroendocrinology N2 - The regulation of energy homeostasis is controlled by the brain and, besides requiring high amounts of energy, it relies on functional insulin/insulin-like growth factor (IGF)-1 signalling in the central nervous system. This energy is mainly provided by mitochondria in form of ATP. Thus, there is an intricate interplay between mitochondrial function and insulin/IGF-1 action to enable functional brain signalling and, accordingly, propagate a healthy metabolism. To adapt to different nutritional conditions, the brain is able to sense the current energy status via mitochondrial and insulin signalling-dependent pathways and exerts an appropriate metabolic response. However, regional, cell type and receptor-specific consequences of this interaction occur and are linked to diverse outcomes such as altered nutrient sensing, body weight regulation or even cognitive function. Impairments of this cross-talk can lead to obesity and glucose intolerance and are linked to neurodegenerative diseases, yet they also induce a self-sustainable, dysfunctional 'metabolic triangle' characterised by insulin resistance, mitochondrial dysfunction and inflammation in the brain. The identification of causal factors deteriorating insulin action, mitochondrial function and concomitantly a signature of metabolic stress in the brain is of utter importance to offer novel mechanistic insights into development of the continuously rising prevalence of non-communicable diseases such as type 2 diabetes and neurodegeneration. This review aims to determine the effect of insulin action on brain mitochondrial function and energy metabolism. It precisely outlines the interaction and differences between insulin action, insulin-like growth factor (IGF)-1 signalling and mitochondrial function; distinguishes between causality and association; and reveals its consequences for metabolism and cognition. We hypothesise that an improvement of at least one signalling pathway can overcome the vicious cycle of a self-perpetuating metabolic dysfunction in the brain present in metabolic and neurodegenerative diseases. KW - brain KW - energy homeostasis KW - inflammation KW - insulin signalling KW - metabolism KW - mitochondrial function Y1 - 2021 U6 - https://doi.org/10.1111/jne.12932 SN - 0953-8194 SN - 1365-2826 VL - 33 IS - 4 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Schwahn, Kevin A1 - Beleggia, Romina A1 - Omranian, Nooshin A1 - Nikoloski, Zoran T1 - Stoichiometric Correlation Analysis: Principles of Metabolic Functionality from Metabolomics Data JF - Frontiers in plant science N2 - Recent advances in metabolomics technologies have resulted in high-quality (time-resolved) metabolic profiles with an increasing coverage of metabolic pathways. These data profiles represent read-outs from often non-linear dynamics of metabolic networks. Yet, metabolic profiles have largely been explored with regression-based approaches that only capture linear relationships, rendering it difficult to determine the extent to which the data reflect the underlying reaction rates and their couplings. Here we propose an approach termed Stoichiometric Correlation Analysis (SCA) based on correlation between positive linear combinations of log-transformed metabolic profiles. The log-transformation is due to the evidence that metabolic networks can be modeled by mass action law and kinetics derived from it. Unlike the existing approaches which establish a relation between pairs of metabolites, SCA facilitates the discovery of higherorder dependence between more than two metabolites. By using a paradigmatic model of the tricarboxylic acid cycle we show that the higher-order dependence reflects the coupling of concentration of reactant complexes, capturing the subtle difference between the employed enzyme kinetics. Using time-resolved metabolic profiles from Arabidopsis thaliana and Escherichia coli, we show that SCA can be used to quantify the difference in coupling of reactant complexes, and hence, reaction rates, underlying the stringent response in these model organisms. By using SCA with data from natural variation of wild and domesticated wheat and tomato accession, we demonstrate that the domestication is accompanied by loss of such couplings, in these species. Therefore, application of SCA to metabolomics data from natural variation in wild and domesticated populations provides a mechanistic way to understanding domestication and its relation to metabolic networks. KW - metabolism KW - systems biology KW - maximal correlation KW - correlation analysis KW - domestication Y1 - 2017 U6 - https://doi.org/10.3389/fpls.2017.02152 SN - 1664-462X VL - 8 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Wagner, Nicole D. A1 - Hillebrand, Helmut A1 - Wacker, Alexander A1 - Frost, Paul C. T1 - Nutritional indicators and their uses in ecology JF - Ecology letters N2 - The nutrition of animal consumers is an important regulator of ecological processes due to its effects on their physiology, life-history and behaviour. Understanding the ecological effects of poor nutrition depends on correctly diagnosing the nature and strength of nutritional limitation. Despite the need to assess nutritional limitation, current approaches to delineating nutritional constraints can be non-specific and imprecise. Here, we consider the need and potential to develop new complementary approaches to the study of nutritional constraints on animal consumers by studying and using a suite of established and emerging biochemical and molecular responses. These nutritional indicators include gene expression, transcript regulators, protein profiling and activity, and gross biochemical and elemental composition. The potential applications of nutritional indicators to ecological studies are highlighted to demonstrate the value that this approach would have to future studies in community and ecosystem ecology. KW - Ecological stoichiometry KW - lipid profiling KW - metabolism KW - nutrient-stress KW - nutrition KW - proteomics KW - transcriptomics Y1 - 2013 U6 - https://doi.org/10.1111/ele.12067 SN - 1461-023X VL - 16 IS - 4 SP - 535 EP - 544 PB - Wiley-Blackwell CY - Hoboken ER -