Fakultät Naturwissenschaften

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Biologie, Ernährungs-wissenschaften und Lebensmittelwissenschaften sind die Schwerpunkte der Fakultät. Die Forschung befasst sich mit Schlüsselthemen der Life Sciences.

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Adaptation of model organisms and environmental bacilli to glyphosate gives insight to species-specific peculiarities of the shikimate pathway
(2024) Schwedt, Inge; Commichau, Fabian M.
Glyphosate (GS), the active ingredient of the popular herbicide Roundup, inhibits the 5-enolpyruvyl shikimate-3-phosphate (EPSP) synthase of the shikimate pathway, which is present in archaea, bacteria, Apicomplexa, algae, fungi, and plants. In these organisms, the shikimate pathway is essential for de novo synthesis of aromatic amino acids, folates, quinones and other metabolites. Therefore, the GS-dependent inhibition of the EPSP synthase results in cell death. Previously, it has been observed that isolates of the soil bacteria Burkholderia anthina and Burkholderia cenocepacia are resistant to high amounts of GS. In the framework of this PhD thesis, it could be demonstrated that B. anthina isolates are not intrinsically resistant to GS. However, B. anthina rapidly adapts to the herbicide at the genome level and the characterization of GS-resistant suppressor mutants led to the discovery of a novel GS resistance mechanism. In B. anthina, the acquisition of loss-of-function mutations in the ppsR gene increases GS resistance. The ppsR gene encodes a regulator of the phosphoenolpyruvate (PEP) synthetase PpsA. In the absence of a functional PpsR protein, the bacteria synthesize more PEP, which competes with GS for binding in the active site of the EPSP synthase, increasing GS resistance. The EPSP synthase in B. anthina probably does not allow changes in the amino acid sequence as it is the case in other organisms. Indeed, the Gram-negative model organism Escherichia coli evolves GS resistance by the acquisition of mutations that either reduce the sensitivity of the EPSP synthase or increase the cellular concentration of the enzyme. Unlike E. coli, the EPSP synthase is also critical for the viability of Gram-positive model bacterium Bacillus subtilis. This observation is surprising because the enzyme belongs to the class of GS-insensitive EPSP synthases. In fact, the EPSP synthase is essential for growth of B. subtilis. The determination of the nutritional requirements allowing the growth of B. subtilis and E. coli mutants lacking EPSP synthase activity revealed that the demand for shikimate pathway intermediates is higher in the former organism. This finding explains why laboratory as well as environmental Bacilli exclusively adapt to GS by the mutational inactivation of glutamate transporter genes. Here, it was also shown that a B. subtilis mutant lacking EPSP synthase activity grows in minimal medium only when additional mutations accumulate in genes involved in the regulation of aerobic/anaerobic metabolism and central carbon metabolism. The characterization of these additional mutants will help to elucidate the peculiarities of the shikimate pathway in B. subtilis. Moreover, the mutants could be useful to identify the aromatic amino acid transporters that still await their discovery.
Agrogentechnik und Biotechpflanzenproduktion : Entwicklung, Stand und Zukunftspotential
(2016) Kuhn, Ekkehard
Pflanzen sind die Nahrungsgrundlage für Mensch und Tier und werden es bleiben. Was unverfälschte Natur zu bieten hat, konnte nie befriedigen, doch war ein langer, weit in die vorchristliche Zeit zurückreichender Weg zurückzulegen, um von essbaren Wildpflanzen und einfachen Landrassen zu den heutigen Hochleistungssorten bei Getreide, Soja, Raps und anderen zu gelangen. Auch heute ist das Potential der klassischen Pflanzenzüchtung noch keineswegs erschöpft. Genomsequenzierung, auf molekulare Marker gestützte Identifizierung züchterisch wertvoller Merkmale und andere früher unbekannte Methoden können Züchtungsprogramme vereinfachen und die Sortenentwicklung beschleunigen. Es bleibt aber eine prinzipielle Schranke, welche die konventionelle Pflanzenzüchtung von wenigen Ausnahmen abgesehen nicht überwinden kann: Sie kann die Artgrenzen nicht überspringen und bleibt auf die Nutzung des arteigenen Genvorrats angewiesen. Das änderte sich um 1985, als es erstmals gelang, bakterielle Gene in dafür gut geeignete Modellpflanzen wie den Tabak einzuführen und zwar so, dass sie „exprimiert“ wurden, d. h. ein funktionelles Proteinprodukt lieferten und sich stabil an die sexuellen Nachkommen dieser ersten transgenen Pflanzen vererbten. Zehn Jahre später begann der kommerzielle Anbau von herbizidresistentem und wenig später insektenresistentem Mais in den USA und Kanada. Es war die Geburtsstunde der Agrogentechnik. Heute werden transgene Kulturpflanzen dort, wo ihre prinzipiellen Gegner weniger Einfluss haben als hierzulande, auf mehr als 180 Millionen ha Ackerland angebaut. Mehr als eine Milliarde Menschen und ein Mehrfaches an Nutztieren haben sich bis heute von „Genpflanzen“ und daraus hergestellten Nahrungs- und Futtermitteln ernährt. Der Grund für den Erfolg der neuen Technik liegt darin, dass sie messbare wirtschaftliche und ökologische Vorzüge hat, die sich in niedrigeren Umweltbelastungen, höheren Erträgen und deutlichen Einkommensverbesserungen der landwirtschaftlichen Betriebe niederschlagen. Während man die Vorteile der Agrogentechnik heute leicht erkennen kann, sind die ihr zugeschriebenen Risiken spekulativ geblieben. Es gibt weder zwingende theoretische Argumente noch praktische Erfahrungen, die dazu berechtigen, der gentechnischen Pflanzenzüchtung ein gegenüber traditionellen Verfahren größeres Gefahrenpotential zuzuschreiben. Ihre realisierbaren Anwendungen gehen über den gegenwärtig noch dominierenden Anbau herbizid- und insektenresistenter Ackerpflanzen weit hinaus. Sie umfassen Nahrungspflanzen mit erhöhter Krankheitsresistenz, verbesserter Trockentoleranz, besserer Verträglichkeit aus ihnen hergestellter Lebensmittel, ausgeglichenem Gehalt an Aminosäuren, Vitaminen und Spurenelementen ebenso wie Industriepflanzen zur Produktion von Grund- und Wirkstoffen für die Chemie- und Pharmaindustrie. An diesen Entwicklungen arbeiten öffentliche und private Forschungseinrichtungen überall in der Welt. Der Mangel an nutzbarem Ackerland, Trinkwasser und sich abzeichnende Folgen des Klimawandels für die Landwirtschaft erzeugen einen wachsenden Druck zur möglichst wirkungsvollen Nutzung aller verfügbaren Ressourcen. Zwar kann die Agrogentechnik das Welternährungsproblem ebensowenig dauerhaft lösen wie irgendeine andere Technik, solange das exponentielle Wachstum der Erdbevölkerung nicht zum Stillstand kommt. Sie vermag aber die Folgen der Übervölkerung abzumildern; denn sie leistet einen wesentlichen Beitrag zur Verbesserung der Grundversorgung und zu einer effizienteren, die Naturvorräte schonenden Landwirtschaft. Die Verdrängung der konventionellen Sorten durch transgene wird deshalb weitergehen. Transgene Ackerpflanzen der ersten Generation, die überwiegend nur ein transgenes Merkmal tragen, werden gegenwärtig rasch durch modernere Stapelsorten ersetzt, die zwei oder mehrere Transgene exprimieren. Sie sind oft herbizidtolerant und gleichzeitig gegen alle wichtigen Schädlinge resistent, die in den jeweiligen Anbaugebieten vorkommen. Gleichzeitig kommen immer mehr Sorten auf den Markt, die nicht nur für die Produzenten Vorteile haben sondern auch ernährungsphysiologisch wertvoller sind als ihre konventionellen Vorläufer. Am Ende dieser Entwicklung werden die konventionellen Sorten auf dem Agrarweltmarkt kaum noch eine Rolle spielen. Dieses Buch behandelt Geschichte, Methoden, Entwicklungsstand und Zukunftspotential der Agrogentechnik, beschreibt typische Vertreter dieses Kulturpflanzentyps und gibt anhand ausgewählter noch im Versuchsstadium stehender Prototypen einen Ausblick auf die kommende Entwicklung und ihre absehbaren Auswirkungen auf die Tier- und Pflanzenproduktion.
Aktivierung eines neuartigen Apoptose-Signalweges durch den Proteinkinaseinhibitor Staurosporin
(2009) Daubrawa, Merle; Graeve, Lutz
The protein kinase inhibitor staurosporine induces apoptosis via the activation of the intrinsic pathway. First staurosporine was described as a specific PKC inhibitor. Today it is known as a broad range kinase inhibitor and is used as a potent apoptosis inductor. However, the mechanism of the apoptotic effect remains elusive. Furthermore, staurosporine obviously exhibit the potential to eliminate chemotherapy resistant tumors by the induction of a novel intrinsic apoptotic signaling pathway. Different derivatives of staurosporine, e.g. UCN-01, PKC-412 or Enzastaurin are already tested in clinical trials phase I-II for cancer therapy. In the present work it could be shown that overexpression of Bcl-2 does not impede the caspase-dependent induction of apoptosis in J16- and JE6.1-Jurkat T-lymphocytes or in DT40 B-lymphocytes following staurosporine treatment . After generation of apaf-1 -/- DT40 cells it was demonstrated that staurosporine induces apoptosis despite the absence of Apaf-1 and therefore independently of the apoptosome. Together with the generated caspase-9 -/- DT40 cells, caspase-9 was identified as the central effector protein of both staurosporine-induced apoptotic pathways. The involvement of published and putative caspase-9 kinases could not be confirmed by the usage of specific inhibitors. Using phospho-mimicking and phospho-deficient caspase-9 variants, S183 could be identified as an essential phosphorylation site during staurosporine-induced apoptosis. In addition, after treatment with anticancer drugs apoptosome formation was blocked by an N-terminal tag of caspase-9. However, this tag could not prevent staurosporine-induced apoptosis. In further studies the potential role of cathepsines for this novel apoptosis signaling pathway could be analysed by their specific inhibition. In order to investigate the involvement of multiple kinases in this novel apoptotic signaling pathway, combination experiments with specific inhibitors of the respective kinases should be accomplished. Further investigations should clarify whether the influence of S183 on staurosporine-induced apoptosis is based on conformational alteration or on phosphorylation of caspase-9. The generation of additional caspase-9 variants including deltaCARD-caspase-9 or non-cleavable caspase-9 could lead to a deeper understanding of the role of caspase-9 for staurosporine-induced apoptosis. For this purpose caspase-9 -/- DT40 cells and cells reconstituted with different caspase-9 variants could be employed. The phosphorylation pattern of caspase-9 could be determined by mass spectrometric analysis. Xenograft or chorio allantois membrane models were used to investigate if the staurosporine derivative UCN-01 is also able to induce this novel apoptosis signaling pathway in vivo. The identification of both the mechanisms and the effector proteins of this staurosporine-induced apoptotic signaling pathway should provide the opportunity to develop novel agents for the elimination of chemotherapy-resistant tumors.
Analysis of aging-related changes and influencing factors on the metabolome of beef
(2023) Bischof, Greta; Gibis, Monika
Aging of beef is necessary to improve its flavor and tenderness. There are two most common aging types, dry-aging and wet-aging. Dry-aged beef is often associated with a higher eating quality than wet-aged beef. The term “dry-aged beef” is not legally defined, so authentication methods are needed to protect the consumers from food fraud. During beef aging, the metabolome of beef changes due to the postmortem metabolism. This dissertation focuses on the aging method as a postmortem process and the resulting changes in the metabolome. As a hypothesis of this study, it was postulated that the detection of these metabolic changes due to aging of beef is feasible by 1H NMR spectroscopy and based on these measurements the evaluation of an authentication model for the aging method of beef is possible. In order to test this hypothesis, a sample preparation and measurement method was developed and based on this, potential influencing factors such as sampling position in muscle, breed and sex were investigated on the metabolome of fresh and aged beef. In the first part of this thesis, the sample preparation and the 1H NMR measurement method were developed. In the sample preparation, the polar fraction of the metabolome was extracted from 200 mg of beef, allowing 24 samples to be prepared in parallel. The sample preparation and the measurement method were validated, and the first aged beef samples were analyzed to check if the aging-related changes in the metabolome could be detected by this method. In the second part of this thesis, the sampling position in the muscle were analyzed for changes or differences in the metabolome due to its location in the muscle. The results showed that the metabolome changes along the length of the M. longissimus thoracis et lumborum, but the influence of the aging type and aging time was more pronounced in the metabolome of beef. The comparison of the surface and the inner part of wet-aged and dry-aged beef showed that the metabolome of dry-aged beef differed greatly between the surface and the inner part, despite the exclusion of the moisture content by freeze-drying and the low microbial load. There were only slight differences between the surface and the inner part for wet-aged beef, which could be due to the influence of microbiota and their metabolites. Therefore, the sampling location in the M. longissimus thoracis et lumborum was determined as precisely as possible for the further studies. The muscles were cut into ten pieces from cranial to caudal and dry-aged or wet-aged for 0, 7, 14, 21, and 28 days, in duplicates. The third part of this thesis focuses on the potential influencing factors such as breed and sex of the animals. Fresh and aged beef samples from three cattle types (heifer, cow, and young bull) and two different breeds (‘Fleckvieh’ and ‘Schwarzbunt’) were analyzed by targeted and non-targeted 1H NMR spectroscopy. Both factors were shown to influence the metabolome of fresh and aged beef. Therefore, these factors had to be included in the authentication model based on both targeted and non-targeted model. The calculation of the authentication model was the main part of this thesis and showed a good prediction of cattle type, breed, aging time and aging type of beef. The authentication model was based on the combination of multiple models of PLS-R and PLS-DA. The model for predicting the cattle type showed an accuracy of 99 %, and the models for predicting the breed depending on the cattle type showed an accuracy of 100 %. Aging time could be predicted with an error of 2.28 days. The statistical models for aging type were separated by aging time based on the determination of aging time. The model for predicting the aging type of 28-day aged samples had an accuracy of 99 %. The other statistical models for predicting aging type were additionally separated by cattle type and breed, and their accuracy ranged from 90 % to 100 %. In conclusion, an authentication model to determine the cattle type, breed, aging time and aging type of beef was developed in this dissertation. Therefore, it is possible to authenticate beef samples using a single 1H NMR spectrum. In future studies, it would be useful to extend this authentication model to other samples of other breeds and influencing factors.
Antioxidants Attenuate Heat Shock Induced Premature Senescence of Bovine Mesenchymal Stem Cells
(2022) Nir, Dana; Ribarski-Chorev, Ivana; Shimoni, Chen; Strauss, Carmit; Frank, Jan; Schlesinger, Sharon
Mesenchymal stem cells (MSC) have many roles that are important for the body’s proper functioning. When the MSC pool is damaged, it is often correlated with impaired development or health of the organism. MSC are known for their anti-inflammatory, immunomodulatory and trophic characteristics that play an important role in the physiological homeostasis of many tissues. Heat shock impairs MSC capacity by inducing the generation of reactive oxygen species and mitochondrial dysfunction, which, in turn, send the cells into a state of premature senescence. Here, we pre-exposed MSC to melatonin, resveratrol, or curcumin, which are natural antioxidative compounds, and tested the protective effects of these substances from oxidative stress and aging. Our data showed that pre-exposure of MSC to antioxidants decreased reactive oxygen species while mitochondrial damage remained high. Additionally, although the proliferation of the cells was slow, antioxidants protected the cells from premature senescence, and subsequent cytokine release was prevented. We conclude that while elevated temperatures directly cause mitochondrial damage, senescence is induced by elevated ROS levels. We suggest that heat shock alters cell and tissue homeostasis by several independent mechanisms; however, reducing tissue senescence will reduce damage and provide a pathway to overcome physiological challenges in animals.
Application of fluorescent proteins for functional dissection of the drosophila visual system
(2021) Smylla, Thomas; Wagner, Krystina; Huber, Armin
The Drosophila eye has been used extensively to study numerous aspects of biological systems, for example, spatio-temporal regulation of differentiation, visual signal transduction, protein trafficking and neurodegeneration. Right from the advent of fluorescent proteins (FPs) near the end of the millennium, heterologously expressed fusion proteins comprising FPs have been applied in Drosophila vision research not only for subcellular localization of proteins but also for genetic screens and analysis of photoreceptor function. Here, we summarize applications for FPs used in the Drosophila eye as part of genetic screens, to study rhodopsin expression patterns, subcellular protein localization, membrane protein transport or as genetically encoded biosensors for Ca2+ and phospholipids in vivo. We also discuss recently developed FPs that are suitable for super-resolution or correlative light and electron microscopy (CLEM) approaches. Illustrating the possibilities provided by using FPs in Drosophila photoreceptors may aid research in other sensory or neuronal systems that have not yet been studied as well as the Drosophila eye.
Applied molecular bioprocess control using RNA thermometers : exploiting temperature responsive elements for rhamnolipid production
(2022) Noll, Philipp; Hausmann, Rudolf
The highest titer reported for heterologous Rhamnolipid (RL) production is 14.9 g/L. However, biomass generation, as a large carbon sink, was a significant drawback in this process with roughly 50 more biomass than product produced. This problem is addressed in this thesis leveraging temperature as control variable and a molecular temperature sensor, an RNA thermometer (RNAT). RNAT generally refers to secondary loop structures, in the 5’ untranslated region of the mRNA, that form at certain temperatures and therefore regulate translation in dependence of temperature. The ROSE (repression of heat shock gene expression) RNAT evaluated in the first original research article in the heterologous system P. putida KT2440 pSynpro8oT_rhlAB originates from P. aeruginosa. The ROSE element regulates, in dependence of ambient temperature, the translation of rhlA and via a polar effect also the translation of rhlB therefore indirectly RL synthesis. It was found that in the ROSE RNAT-controlled system, the RL production rate was 60% higher at cultivations of 37°C than at 30°C. However, besides the regulatory effect of the RNAT, as revealed by control experiments, multiple unspecific metabolic effects may be equally responsible for the increase in production rate. After screening for even more efficient regulatory structures, a fourU RNAT was identified. Natively, this fourU RNAT regulates the expression of the heat shock gene agsA of Salmonella enterica and its regulatory capability can easily be modified by site-directed mutagenesis. The experimental data collected in the second original research article confirms the functionality of the fourU RNAT in the heterologous RL production system. The data suggested improved regulatory capabilities of the fourU RNAT compared to the ROSE element and a major effect of temperature on RL production rates and yields. The average RL production rate increased by a factor of 11 between 25°C and 38°C. Control experiments confirmed that a major part of this increase originates from the regulatory effect of the fourU RNAT rather than from an unspecific metabolic effect. With this system YP/X values well above 1 (about 1.4 gRL/gBM) could be achieved mitigating the problem of high biomass formation compared to product synthesis. Also, YP/S values of about 0.2 gRL/gGlc at elevated temperatures of 37-38°C were reached in shake flasks. The system was subsequently tested in a proof-of-concept bioreactor process involving a temperature switch. With this simple batch experiment and a temperature switch from 25°C to 38°C not only a partial decoupling of biomass formation from product synthesis was achieved but also an around 25% higher average specific rhamnolipid production rate reached compared to the so far best performing heterologous RL production process reported in literature (average specific production rate: 24 mg/(g h) vs. 32 mg/(g h)). However, to achieve higher titers while reducing side product formation a suitable feeding strategy and more complex temperature profiles may be required. Temperature variations in turn cause several metabolic changes, many of which are complex and interdependent. Models that describe biological processes as a function of temperature are thus essential for improved process understanding. The goal of the peer reviewed review article “Modeling and Exploiting Microbial Temperature Response”, shown in this thesis, was to present an overview of various temperature models, aid comprehension of model intent and to facilitate selection and application. Since not all metabolic interdependencies and mechanisms during temperature variation are known for the reasonable connection of input-output relationships, a suitable modeling approach seemed to be neural networks. Neural networks as black box models do not require mechanistic a priori knowledge but representative historic datasets. To collect training data, different temperature profiles or constant temperatures for a bioreactor process with P. putida KT2440 pSynpro8oT_rhlAB were applied and concentration curves for biomass, glucose and RL recorded. Subsequently, the data was fed into the neural network to compute RL titer as output. An exponential temperature profile yielded at the highest RL value of approx. 9 g (around 13 g/L) less biomass (around 12 g/L) than product. These values were reached after only 30 h consuming just 45 g of glucose. Hence, at this timepoint 36 weight-% of the consumed glucose could be assigned to mono-RL (YP/S = 0.19 gRL/gGlc) and biomass (YX/S = 0.17 gBM/gGlc. The so far best performing heterologous RL production process, yielded 23.2 g (14.9 g/L) mono-RL from >250 g of consumed glucose (YP/S = 0.10 gRL/gGlc) in >70 h using the same strain and medium but a constant temperature of 30°C.
ATP4 and Wnt-signaling are required for ciliogenesis and left-right axis development of Xenopus
(2012) Walentek, Peter; Blum, Martin
The vertebrate body plan displays left-right (LR) asymmetries of organ placement superimposed on an overt bilaterally symmetrical organization. Symmetry is broken during embryogenesis, and asymmetric gene expression precedes asymmetric organ morphogenesis. The proton/potassium pump ATP4 was shown to play a role in LR-development of the frog Xenopus laevis as well as in other deuterostomes. Two opposing models of symmetry-breakage were proposed, the ?ion-flux? and the ?leftward flow? model. The former proposed that symmetry was broken by LR-asymmetric expression of the a-subunit of ATP4 during cleavage stages. The latter claimed a cilia-based leftward flow at the gastrocoel roof plate (GRP) to take center stage during neurulation, i.e. a day later in development. In the present thesis work, the role of ATP4a in symmetry-breakage was re-addressed and evidence for symmetrical expression and function of ATP4a was gathered. ATP4a was shown to be required for two Wnt-signaling dependent steps during the setup of cilia driven leftward flow at the GRP: (1) Wnt/b-catenin (b-cat) dependent expression of Foxj1 during gastrulation, and (2) Wnt/planar cell polarity (PCP) dependent posterior localization of motile cilia during neurulation. These data challenge the ?ion-flux? hypothesis and argue for a conserved ATP4- and cilia-dependent symmetry-breakage mechanism throughout the vertebrates. Furthermore, the function of Wnt-signaling components was analyzed in the context of GRP-formation: The receptor Frizzled 8 (Fz8) and b-cat were required for Foxj1 expression during gastrulation. Morphogenesis of the GRP, posterior polarization of motile cilia and expression of Xnr1 and Coco in somitic cells were all required for LR-development. Loss of non-canonical Xwnt11b-signaling perturbed these process, suggesting that non-canonical Wnt-signaling branches, in addition to Wnt/PCP, were relevant for LR-development. ATP4-mediated Wnt-signaling was also required for Foxj1 expression and motile cilia in other epithelia during Xenopus development, i.e. the skin, floor plate and the ependymal cell layer. In the floor plate b-cat was required for Foxj1 expression downstream of Hedgehog-signaling. In the skin mucociliary epithelium ATP4a and Wnt/b-cat were required downstream of Notch/Delta-mediated cell-type specification of multiciliated cells. This was also true for a new cell type of serotonergic cells described here, which was characterized morphologically, by analysis of gene expression and response to manipulations of Wnt- and Notch/Delta-signaling. In summary, the data presented in this thesis suggest a conserved function of ATP4a and Wnt-signaling in vertebrate symmetry-breakage and Foxj1-dependent ciliogenesis in Xenopus.
The Bacillus phage SPβ : a model system to study the lysis-lysogeny regulatory network and antiphage defense systems
(2024) Kohm, Katharina; Commichau, Fabian M.
Although bacteriophages are considered the most abundant biological entities on our planet, they are less well-studied compared to their host. Being intracellular parasites, phages rely on the metabolic processes of their bacterial hosts for their replication. Phages that use the host exclusively to produce virions are called virulent phages and the reproduction cycle is called the lytic cycle. The lytic cycle is accompanied by lysis and, thus, the killing of the host cell. Temperate phages can choose between the virulent or lysogenic lifecycle. Lysogeny or the lysogenic cycle is a type of viral reproduction in which no virus particles are produced, instead, the genetic material of the phage is replicated and then passed on to the daughter cells. The viral genome can be present as part of the bacterial chromosome or as a circular or linear plasmid molecule and is referred to as a prophage. Since temperate phages can influence the mutual interactions with other bacteria, growth, metabolic pathways or pathogenicity of their host, it is important to understand how temperate phages control their lysogenic life cycle and which genes are involved. Repression usually occurs through the interaction between a repressor and specific binding sites, which are mostly located in the promoter regions of the lytic genes. SPβ is a temperate phage of the model bacterium Bacillus subtilis. In contrast to its host, many aspects of the life cycle of SPβ have been little studied and many genes have not been assigned a function. Not only are SPβ-like phages widespread within the genus Bacillus and of greater importance to their hosts than previously thought, but they also exhibit a novel lysogeny management system. With regard to the control and regulation of the lysis-lysogeny network, it is already partially known which gene products are involved in the decision, establishment and resolvement of lysogeny. The maintenance and resolvement of lysogeny of SPβ was investigated in more detail in this thesis. To gain more insight into the regulation and control of lysogeny, the SPβ c2 mutant was characterized in this work. This mutant is unable to maintain its lysogenic state when exposed to heat, suggesting the alteration of a key regulatory element. This work demonstrated that the SPβ c2 phenotype is due to a single nucleotide exchange in the mrpR (yopR) gene that renders the encoded MrpRG136E protein temperature-sensitive. Furthermore, it was shown that this protein acts as a repressor of lytic gene expression. This occurs through the binding of the repressor to several conserved elements in the genome of the SPβ prophage. Further biochemical analysis revealed that the G136E exchange makes MrpR less stable and reduces its affinity for DNA binding. Structural characterization of MrpR revealed that the protein is a DNA-binding protein with a similar protein fold to tyrosine recombinases. However, the repressor function is independent of functional recombinase activity. In addition, a mutagenesis approach was used to identify the region within the protein that is essential for the function of the repressor. This work also identified further players in the lysogeny management system, with the YosL protein being crucial for the induction of the lytic cycle. However, YosL cannot activate the lytic cycle of SPβ alone. In addition, the core genome of SPβ-like phages was defined and new integration loci were identified in this work. Apart from a better understanding of lysis-lysogeny regulation and phagehost relationships, the characterization of the SPβ c2 mutant also led to the identification of a previously unknown phage defense system. The defense system is encoded on a plasmid and leads to a decrease in phage titer and a change in plaque morphology. It could be shown that the spbB locus, which ensures the segregation stability of the plasmid and codes for two open reading frames, is also responsible for the resistance to SPβ c2 and related phages. Further studies have shown that the spbB gene and the downstream region, which presumably encodes an RNA element and a terminator, play a crucial role in mediating resistance. The second open reading frame of the spbB locus is irrelevant for the mediation of phage resistance. Overall, this work contributes to a better understanding of the phage-host relationship.
Backmittel mit fermentativ angereicherten Hydrokolloiden
(2021) Seitter, Michael Friedrich Hermann; Hertel, Christian
Lactic acid bacteria (LAB) are involved in fermentation of sourdoughs and able to produce exopolysaccharides (EPS). Screening of 190 LAB of different species and genera showed that 82% are able to produce EPS. Whereby, 28% a strong or very strong production exhibited. It becomes evident that strains of species L. reuteri, L. sanfranciscensis, L. frumenti and L. pontis, could be identified as effective EPS producer. The molecular weight of the synthetized EPS was larger than 5*106 Dalton. Glucan was formed almost of L. reuteri strains. To identify the effect of commercial hydrocolloids on bread staling, baking trials were performed. The parameter crumb hardness using Texture-Profile-Analysis and retrogradation of starch using Differential Scanning Calorimetry were chosen. Staling of wheat breads was dependent on the flour quality. Breads produced using weak flours and straight dough method showed faster staling. Addition of isolated EPS produced by L. sanfranciscensis LTH 1729 (Glu/Fru ratio: 1:6) and LTH 2590 (Glu/Fru ratio: 1:45) was more effective in retarding the rate of staling compared to hydrocolloids guar gum and xanthan. Baking trials with chemical acidified sponges showed that swelling and endogenous enzyme activities exerts no positive effect on the rate of staling. In contrast to sponges with fermentative enriched EPS, which exhibits a delayed rate of staling. This effect could be verified in mixed wheat breads (rye : wheat, 50:50). Frozen storage of doughs revealed no influence on the rate of staling. Production of an EPS enriched dried sourdough (baking improver) using optimized fermentation conditions was performed using L. sanfranciscensis LTH 1729. 3% dosage of the baking improver showed similar staling rate compared to control, however with 2% higher water absorption. Thus, addition of hydrocolloids and EPS, respectively, leads to an increase in dough yield of 1 1.5%. The width-height ratio was comparable in all doughs, except the xanthan supplemented. After adjusting the doughs to 500 FE, all doughs showed similar results in measurements with Bohlin-Rheometer. Doughs with added hydrocolloids as well as EPS were less sticky. Fermented sponge doughs with enriched EPS showed higher stickiness compared to not enriched. This could be traced back to residual not metabolized amounts of sucrose. EPS addition affects extensibility of doughs less compared to gum guar and xanthan. Negative influence on dough structure using acidic sponges was compensated with EPS enriched ones. Addition of guar gum and xanthan effect in a viscosity increase during gelatinization. Whereas, EPS and EPS containing sponges showed no effect on viscosity. Frozen storage of 10 days reveals lower dough stability and gas retention. Doughs were less elastic and stickier. Dough resistance decreased and elasticity increased. By addition of EPS these effects could be compensated. The gas retention capability of EPS supplemented frozen doughs was identical not frozen ones. Addition of 3% baking improver produced by spray dried EPS enriched sourdough to doughs increased the water absorption by 2%, whereas almost no change on dough rheological parameters resulted. Dough stability and gas retention was considerably improved. Dough stickiness and resistance decreased. No effect in viscosity during gelatinization. Summarized, the results of the present work show the optimization and manufacturing of a “clean label” baking improver, produced thru EPS enriched fermentation of sourdoughs. As well as the application of the improver and the impact of on dough processing and fresh keeping of frozen dough and baked goods.
Die Bedeutung von AQUAPORIN INTERACTOR 1 (AQI1) für die Zelltodregulation in Pflanzen
(2014) Glink, Eva Katharina; Pfitzner, Artur J. P.
Programmed cell death (PCD) is an important process during development, senescence and pathogen defence in plants and in animals. It is a genetically regulated and targeted cell suicide of single cells, for benefit of the whole organism. In plants, PCD is of great importance, especially in the course of the “hypersensitive response” (HR). For protecting themselves against harmful intruders, infected plant cells are directly deposed of by PCD. The developing local lesions act as a barrier between host plant and pathogen. This prevents the systemic expansion of biotrophic pathogens within the whole plant. The induction of PCD involves complex signal transduction pathways. Reactive oxygen species (ROS), in particular H₂O₂, play an important role as signal molecules during PCD. The transport of H₂O₂ across cell membranes is conducted by aquaporins. As the vitality of cells depends on intracellular H₂O₂-levels, a spatiotemporal control of this H₂O₂-transport is indispensable. AQUAPORIN INTERACTOR 1 (AQI1) was isolated as a potential regulator of the channel function of aquaporins. AQI1 is a plant protein with sequence homology to the mammal aminoacylase 1. It is known, that aminoacylases catalyse the hydrolysis of acyl-amino acids. However, the physiological function of these enzymes is still unclear. This study represents the first characterisation of an aminoacylase (AQI1) in plants. The physiological function of AQI1 as a regulator of aquaporins, as well as the underlying molecular mechanisms, have been analysed. In addition to deacetylation of amino acids, a second function of the protein AQI1 was discovered. AQI1 interferes with the channel activity of aquaporins by protein-protein interaction. In this way, AQI1 is able to inhibit the H₂O₂-, and to a certain extent also the H₂O-influx, through aquaporins. Probably, this happens by blocking the aquaporinpore. Due to this function, AQI1 is a major component in cell death regulation in plants. During the „hypersensitive response“ (HR), which is induced as a result of pathogen attack, AQI1 accumulates to high levels to prevent the influx of toxic amounts of H₂O₂ into neighbouring cells. This ensures a local control of PCD. In addition, AQI1 seems to be involved in regulation of senescence processes. It could be demonstrated, that AQI1 accumulates in a gradient from juvenile to senescent leaves, due to degradation in older tissues. By this age-dependent accumulation, AQI1 could contribute to the vitality of leaves, by preventing the influx of excessive amounts of H₂O₂ into the cell.
Die Bedeutung von Aquaporin interagierenden Proteinen für die Zelltodregulation bei Pflanzen und Tieren
(2020) Straub, Anna Katharina; Pfitzner, Artur J. P.
Hydrogen peroxide plays a crucial role as a signalling molecule in the induction of cell death in plants and animals. To mediate signalling and induce apoptosis in a cell, hydrogen peroxide molecules need to be transported across different membranes to their target site. In plants and animals, integral membrane proteins called aquaporins, facilitate the transport of hydrogen peroxide between cell compartments by channelling the signalling molecule across membranes. Plant aquaporins are regulated by proteins called Aquaporin Interactor 1 and 2 (AQI1 and AQI2). AQI2 is a plant homolog of AQI1. Both proteins function as inhibitors of aquaporins by binding to the channels resulting in prevention of water and hydrogen peroxide influx. Aquaporin Interactor 1 binds preferentially to the aquaporin tonoplast intrinsic protein TIP1.1, while Aquaporin Interactor 2 exhibits a binding preference to the aquaporin plasma membrane intrinsic protein PIP2.2. Aquaporin Interactor 1 is located in the vacuole or associated to the tonoplast membrane. In contrast, results obtained for Aquaporin Interactor 2 suggest that it is located in the apoplast. This is compatible with the hypothesis that tonoplast aquaporins can be regulated by AQI1, whereas plasma membrane aquaporins on the other hand are regulated by AQI2. The enzyme Aminoacylase 1 is known to hydrolyse N-acetylated amino acids. It is a zinc-binding metalloenzyme with a wide range of substrates. However, its preferred substrate is N-acetyl-Methionine. N-acetyl-Methionine can also be hydrolysed by the plant homolog AQI1. The plant enzyme also needs metal ions as co-factors. Of note, no aminoacylase activity was found for AQI2. Experiments using aqi1 knock-out mutants of Arabidopsis thaliana and Nicotiana tabacum clearly show, that hydrolysis of N-acetyl-Methionine can only be accomplished by AQI1. However, the aminoacylase activity of AQI1 is not needed for the ability to bind to aquaporins. The data show that the aminoacylase activity and the ability to bind aquaporins are two separate functions of the protein Aquaporin Interactor 1. Based on current knowledge, it must be assumed, that AQI2 acts only as an aquaporin-regulating protein. After pathogen attack an increased aminoacylase activity could be detected in the affected plant tissue. This AQI1 induction can be observed both after agrobacteria infiltration and after infection with the tobacco mosaic virus. This suggests a role for AQI1 in pathogen defence. Another aquaporin interacting protein is BHRF1, an anti-apoptotic protein originating from the Epstein-Barr virus. To date, an interaction between BHRF1 and aquaporins could only be detected with plant aquaporins. Transgenic BHRF1 N. tabacum plants show spontaneously occurring cell death events apparent by necrotic plant tissue. These necrotic areas are caused by BHRF1 interacting with plant aquaporins and several proteins of the G-protein signalling pathway inducing cell death. By binding to the aquaporins, BHRF1 is able to replace the endogenous aquaporin interaction partners AQI1 and AQI2. Thus, a precise aquaporin regulation by endogenous AQI1 and AQI2 is no longer guaranteed. Moreover, results show that BHRF1 can bind the Arabidopsis glucose sensor AtRGS1 (regulator of G-protein signalling). AtRGS1 is a combination of a G-protein coupled receptor and a RGS protein. The RGS domain causes the hydrolysis of GTP bound to the Gα subunit. Further experiments showed, an interaction of BHRF1 with human RGS proteins. Therefore, BHRF1 could also have a possible effect on G-protein signalling in humans. The results of this study demonstrate the importance of a precise regulation of aquaporins in cell death regulation. Deregulation caused by viral BHRF1, leads to cell death events. BHRF1 presumably competes with the endogenous interaction partners of aquaporins and of the G-protein-signalling pathway, ultimately resulting in the deregulation of various signalling pathways.
Die Bedeutung von Aquaporinen und ihren Interaktionspartnern für die Zelltodregulation in Pflanzen
(2011) Hoch, Tanja; Pfitzner, Artur J. P.
Programmed cell death (PCD, apoptosis) is an induced cell suicide process that plays an important role during the differentiation and pathogen defense responses of plants and animals. BHRF1 (?BamHI fragment H rightward open reading frame no. 1?) is a cell-death modulating protein of the Epstein-Barr virus (EBV), a human lymphotrophic herpes virus. The expression of BHRF1 in transgenic plants led to the formation of necrotic lesions. Further experiments showed that BHRF1 associated necrotic lesions are caused due to stress, senescence and pathogen defense responses. Yeast-two-hybrid-screening of a tobacco cDNA library identified two different aquaporins as partners for interacting with BHRF1. Aquaporins were identified as water channels/carriers within red blood cells, but are also present in all other organisms. Over the last years, more information was gathered indicating that, apart from transporting water, aquaporins had other functional activities. E. g. Henzler and Steudle (2000) demonstrated that aquaporins can act as hydrogen peroxide channels in the algae Chara corallina. Furthermore, publications by Bienert et al. (2006), indicating that aquaporins in plants as well as in animals are also able to transport H2O2. Hydrogen peroxide and other reactive oxygen species (ROS) have long been recognized as important signal molecules during the pathogen defense response in plants, therefore establishing a logical connection between cell death and aquaporins for the first time. It was assumed that the aquaporins NtPIP2.2a, NtPIP2.2b und NtTIP1.1a identified during the yeast-two-hybrid-screen can act as H2O2 channels. In further experiments it could indeed be established that these aquaporins have the ability to transport H2O2 in yeast cells. Yeasts expressing aquaporins could be influenced in their H2O2 sensitivity by the expression of BHRF1. BHRF1 without transmembrane domain (BHRF1deltaTMwt) led to an enhanced H2O2 sensitivity and also to an increase in cell death. In addition, the transient expression of aquaporin could induce necrotic lesions and cell death in Nicotiana benthamiana. Deletion experiments identified a common binding domain for interacting with BHRF1 in these aquaporins. This binding domain consists of the conserved region containing the first NPA motive (?loop? B) that is also half of one pore. Further studies showed that BHRF1 interacts with all kinds of different aquaporins from plants, animals (rAQP8) and humans (hAQP1). BHRF1 most likely binds with the alpha3 helix to the highly conserved NPA region of aquaporins. A cellular protein showing sequence homology to M20 proteases and aminoacylases was isolated when looking for interaction partners of aquaporins in plants. Like BHRF1, this protein binds to the conserved NPA region of the aquaporins. Although the cellular substrate for this protein has to be found yet, an interesting observation was made. Co-expression of the isolated aminoacylase with NtTIP1.1a or NtPIP2.2b in Nicotiana benthamiana led to the inhibition of cell death induced by these aquaporins.
Der Beitrag von Neurofascin zur Entstehung und Lokalisation von Gephyrinclustern während der inhibitorischen Synaptogenese im ZNS
(2008) Burkarth, Nadine; Volkmer, Hansjürgen
Membrane-bound cell adhesion molecules (CAMs) were discovered to be key players in initiating excitatory synapse formation in the CNS. However, so far little is known about the role of CAMs in inhibitory synapse development. In particular, a functional link between CAMs and the clustering of postsynaptic scaffold component gephyrin, which is a critical determinant of y-aminobutyric acid A (GABAA) clustering, still needs to be elaborated. Neurofascin belongs to the L1-subgroup of the immunoglobuline like CAMs (IgCAMs). In vivo Neurofascin has been shown to direct the formation and localization of GABAergic Input on cerebellar Purkinje neurons. Thus it serves as a candidate molecule recruiting gephyrin to inhibitory postsynaptic sites. At early stages of inhibitory synaptogenesis, formation of gephyrin clusters and their translocation to the axon hillock correlated with a somatic expression of neurofascin in rat hippocampal neurons. Furthermore, a neurofascin splice variant lacking the extracellular fifth fibronectine-III like domain (NF-5te FN-III) was predominantely expressed at early stages of synapse formation. In contrast expression of NF+5te FN-III harbouring the fifth fibronectine-III like domain was prominent only in adult brain. Transfection of expression vectors for different splice variants and deletion mutants of neurofascin revealed that the embryonic neurofascin isoform NF-5te FN-III is required for the formation of gephyrin clusters. This process is presumably dependent on extracellular interactions with molecules on pre- and postsynaptic terminals, respectively. However, possible interaction partners for neurofascin are unknown. Point mutations in the cytoplasmatic domain of neurofascin inhibited the formation of gephyrin clusters suggesting intracellular signal transduction pathways triggered by neurofascin. Furthermore, expression of neurofascin is necessary for the translocation of gephyrin clusters to the axon hillock of hippocampal neurons as shown by shRNA-mediated knockdown. In addition, overexpression of an embryonic neurofascin isoform was sufficient for functional rescue after knockdown of endogenous neurofascin. Expression of NF-5te FN-III resulted in the accumulation of exogenous GFP-Gephyrin at the axon initial segment AIS suggesting a functional link between neurofascin and gephyrin. However, colocalization studies in HEK293 and PC12E2 cells, respectively, did not provide an indication of direct neurofascin gephyrin interactions leading to the observed effects.
Biochemical investigations on genetically modified oil crops
(2009) Mekawi, Enas; Schwack, Wolfgang
The main purpose of this study was to develop a method of purification and characterization of Cry1Ab isolated from MON810 genetically modified maize. The second object was to study the effect of the genetic modification of MON810 and high-oleic sunflower on the oil composition. Therefore, the following investigations were performed: (1) Quantification of Cry1Ab toxin in different corn plant parts. (2) Development of a suitable method for purification of Cry1Ab from MON810. (3) Establishment of characterization method for Cry1Ab by mass spectrometry with regard to high peptide sequence coverage. (4) Evaluation of the effect of genetic modification on the oil composition compared with the conventional traits. The following results were obtained: Screening of Cry1Ab by ELISA is the most predominant technique for determination of Cry toxin content in plants. The determination of the toxin concentration resulted in highest levels for leaves (26.8 µg/g dry matter), while it was 1.5, and 1.0 µg/g for stalks and grains respectively. In our study, toxin content in leaves was about six times higher than in a previous study. There are no data available for the dry weight content of Bt toxins in stalk and grain, which could be compared to the obtained results. Although MON810 maize is one of the major genetically modified crops, informations on the character of the Cry1Ab purified from the MON810 maize is still limited, although such data are important for safety assessment studies. To my best knowledge, this study is the first investigation charactizing Cry1Ab toxin isolated from MON810 maize. The results of the present investigation indicated that the separation of the Cry1Ab protein from MON810 leaf extracts by HPLC techniques was not efficient. MALDI-TOF analyses showed that the major component separated with Cry1Ab was β-D glucosidase, which may be due to resembled isoelectric points. However, immuno-affinity purification using self-prepared affinity columns was very efficient to isolate pure Cry1Ab from MON810. The characterization of purified Cry1Ab was successfully done by SDS-PAGE, Western blot analysis and MS techniques. MALDI-TOF MS analyses were useful for component screening of Cry1Ab. Results showed that Cry1Ab is subjected to truncation by plant proteases into a core toxin with approximately 69 kDa. LC(ESI)-MS/MS gave a higher sequencing coverage of Cry1Ab (73 % of peptide sequence) compared to MALDI-TOF analysis (41% of peptide sequence). Further studies revealed that Cry1Ab had no detectable potential carbohydrates which might be covalently linked to the protein. The capillary electrophoresis technique was used for determination of the Cry1Ab purified from MON810 maize and proved to be a suitable method for determination of the Cry1Ab, but it was not successful for the detection of very low quantities (less than 0.03 mg/ml). Peptide mapping is one of the most powerful tools for protein identification and characterization. The use of HPTLC with the relatively new plates (ProteoChrom) was identified as a convenient tool for peptide mapping as compared to capillary electrophoresis, especially if put into consideration that HPTLC is less costly than capillary electrophoresis. The HPTLC method was able to resolve 13 peptides, while capillary electrophoresis resolved 19 peptides, obtained from the digested Cry1Ab toxin. Concerning lipid analyses, fatty acids and sterols were determined by gas chromatography, tocopherols by HPLC. For the determination of phospholipids, an HPTLC method was developed, resulting in lower detection limits than reported in previous studies. The present study proved that the genetic modification did not significantly affect the contents of fatty acids, sterols, tocopherols and phospholipids in transgenic maize oil. Apart from the increased amount of oleic acid in high-oleic sunflower oil, the genetic modification in sunflower did not produce unexpected effects on the oil composition. Therefore, with regard to the oil composition, both oils from genetically modified plants will be as safe as conventional oil types.
Bioethanol production from lignocellulosic biomass
(2023) Hoppert, Luis; Kölling, Ralf
The aim of this thesis was to develop a high gravity second-generation bioethanol process and investigate the effects of a high solid loading. The insights gained from the initial experiments helped to understand the underlying mechanism behind the limitations of a high solid loading. Based on these findings, strategies were developed to overcome these limitations.
Biogenese und Virusassembly des filamentösen Coliphagen M13
(2012) Ploß, Martin; Kuhn, Andreas
Taxonomically, the bacteriophage M13 is assigned to the single-stranded DNA phage and belongs to the family of Inoviridae. For propagation the Gram-negative bacteria Escherichia coli with F-pili is required. The host cell is not lysed by the phage. New findings about the M13 phage biogenesis are presented here within four essential areas of the M13 phage cycle concerning the sections infection, assembly, and phage secretion. Phage adsorption experiments in which the host bacterium E. coli K38 was infected by M13 phage showed that the phage adsorption to the cells takes place within the first 5 minutes and because of a limitation of F-pili per cell a maximum of 7 phages per cell were found to be adsorbed. The insertion of the phage coat protein gp9 into the cytoplasmic membrane of the host cell was verified by the periplasmic location of antigenic epitopes introduced into the N-terminal domain of gp9. The membrane insertion of gp9 was found to depend on the host protein YidC. Plasmid-encoded gp9 exhibiting antigenic epitopes at the N-terminal domain did not interfere with the assembly of new progeny phage. Therefore, the development of a phage display system with gp9 by introducing short peptide sequences (17 ? 36 amino acids) is feasible. After overexpression of gp1/11 assembly complexes in E. coli and size exclusion chromatography, respectively, the complex was characterized and a molecular weight of ~ 300 kDa was assigned. Examinations of the purified gp1/11 assembly complexes by transmission electron microscopy (TEM) revealed ring-like structures with ~ 7 ? 8 nm in inner diameter and ~ 11 ? 12 nm in outer diameter. The investigation of M13 wild-type infection showed that the secretion of new progeny phage starts after a short lag period (eclipse). An infected E. coli cell secreted upto 925 progeny in a time period of 115 minutes which corresponds to an average of 7 secreted phages per minute. The generation time of the infected E. coli K38 cells rose from 24 minutes to 48 minutes. Experiments were carried out with genetically manipulated phages which were hindered to synthesize the major coat protein gp8 in the host cell by a nonsense mutation in the phage genome. Therefore, phage replication was only observed in host cells bearing plasmid encoding gene 8. Since the quantity of the protein was limited the lag period (eclipse) was extended to 12 minutes and the efficiency of phage secretion was decreased to about 2 phages per minute. The M13 phage secretion from infected E. coli cells was visualized by atomic force microscopy (AFM). The identity of the phage was verified by labeling with protein-A conjugated gold and transmission electron microscopy (TEM). The secretion of M13 progeny was first observed at the cell poles of E. coli and then spreaded within 4 minutes along the cell surface. After 16 minutes the secretion was observed over the entire cell surface.
Bioinformatische Analyse und funktionelle Charakterisierung von strukturellen Genvarianten in ADME-Genen in humaner Leber
(2016) Tremmel, Roman; Zanger, Ulrich M.
Pharmacogenetics is the study about inter-individual genetic variation that influences the response to drugs and other xenobiotics. A major part of this variation is due to hepatic drug metabolism with enzymes, transporters and receptors involved in the ab-sorption, distribution, metabolism and the excretion of drugs, xenobiotics and endoge-nous substances and collectively defined as ADME-genes. Genetic factors along with environmental and endogenous factors, including gender, age, inflammation processes and others are known to influence the expression and activity of ADME-genes. These influences can affect drug response, side effects or toxicity. According to newly published data, the human genome of any subject differs from a reference genome at 4.1 to 5.0 million positions. More than 99.9% of these differences are single nucleotide polymorphisms (SNP) or short insertions or deletions. Further-more, a person carries up to 2,500 structural variants, including copy number variations (CNV) affecting ~20 million bases (1000 Genomes Project Consortium et al., 2015). Thus structural variants affect more bases than SNPs. Per definition the CNVs are du-plicated or deleted DNA segments greater than 1kb and it was shown that they cover at least 12-30% of the human genome. Genome-wide studies investigating the function-ality of CNVs in the fruit fly, the mouse and in humans showed that there are genes whose expression is clearly affected by CNVs (dosage-sensitve), but also genes show-ing lower expression with increased copy number (dosage reversed) or genes without any expression alterations despite different copy number (dosage-insensitive). A prominent example of CNVs influencing drug metabolism is the phase I gene CYP2D6. Carriers of reduced or amplified gene copies show significantly altered ex-pression and enzyme activity levels and also a different drug metabolism of substrates like codeine (opioid) or tamoxifen (selective estrogen receptor antagonist) in compari-son to carriers with normal copy status of two. Genotyping of CYP2D6 gene copy num-ber may thus help to adjust drug dosage in a genotype dependent manner. In this work I investigated if further ADME-genes are affected by CNVs and if these variants have a functional impact on the expression phenotype and drug metabolism. The distribution of CNVs in the most important ADME-genes (n=340) was investigated in three independent cohorts using CNV data in a public accessible database of ge-nomic variants (DGV; dgv.tcag.ca), processed SNP microarray data of paired samples of healthy (n=269) and tumor (n=351) liver tissue of the TCGA project (http://cancergenome.nih.gov/) and ADME-panel based exon next generation sequenc-ing (NGS) applied on 150 well documented human liver samples of an in-house cohort (IKP148). For the NGS data analysis a method was developed and optimized to esti-mate the relative copy number of the ADME genes or every single exon via the read depth. The results were validated using qPCR with specific TaqMan assays. RNA-sequencing data of 50 healthy TCGA liver samples, and normalised expression data from microarray experiments applied to lymphoblastoid cell lines (LCL) from the HapMap samples and the 150 human liver samples (IKP148) were used to analyse the association between CNVs and the mRNA expression. Furthermore, in the IKP148 liver samples protein and enzymatic activity levels were available or measured using West-ernBlot and mass spectrometry for selected ADME-genes. All pharmacologically important CNVs of phase I and phase II genes, including CYP2A6, CYP2D6, GSTM1, GSTT1, SULT1A1 and UGT2B17 could be confirmed in all datasets. CNVs which were known, but so far not functionally assessed were found in the phase I and II genes CES1, CYP2E1, CYP21A2, UGT2B15 and UGT2B28. In this work rare CNVs (<1%) were mainly found for transporters like ABCA2, SLC2A4 and SLC47A1. The analysis of the read depth in the IKP148 samples data revealed hybrid genes for CYP2A6 and CYP2D6 with their pseudogenes and allowed a fine mapping of the different alleles. The functional analysis further confirmed the positive association between CNVs and the mRNA expression of CYP2A6, CYP2D6, GSTM1, GSTT1, SULT1A1 and UGT2B17 in all three cohorts. The combination of all data from the NGS project in the IKP148 liver subjects, including SNP and CNV genotypes showed that 11% and 53% of the variability of CYP2A6 and CYP2D6 enzyme activity were explained by the genetic factors. In contrast the mRNA expression of the genes CES1 and CYP2E1 was not dependent of the CNV pattern in healthy liver tissue (IKP148 and TCGA) and lymphoblastoid cell lines. A detailed analysis of the protein and enzyme activity levels (chlorzoxazone-6-hydroxylation) of CYP2E1 confirmed the dosage-insensitivity in the IKP148 liver sub-jects. The dosage compensation can be principally explained by different mechanisms and could be tissue or tumor specific. Furthermore, CNV-linked genetic variants, altered miRNA regulation, incomplete inclusion of regulatory elements or coding sequences, hybridgenes, monoallelic expression, feedback loops or epigenetics could be factors which mask the CNV effect. In this work a haplotype analysis of the CYP2E1 region identified SNPs which were linked to the duplication and a reduced expression phenotype in persons with European ancestry. Using in silico prediction tools we found a relation of one of the linked SNPs in the 3’UTR with additional predicted miRNA bind-ing sites potentially regulating additional CYP2E1 gene copies. The CNV influence on the mRNA expression of the genes CYP21A2, UGT2B25 and UGT2B28 was inconsistent. Although CYP21A2 deletions were associated with a de-creased expression, gene duplications showed normal expression levels compared to samples with two copies. A significant influence of UGT2B28 CNVs was found in LCLs but not in human liver samples (IKP148 and TCGA). In total 7 of 17, 2 of 12 and 3 of 14 ADME genes showed a significant association between expression and CNV type in the IKP148, TCGA and LCLs of the HapMap samples, respectively. In the TCGA cancer tissue nearly all ADME-genes carry CNVs and in 30% of the genes a significant correlation was observed. With cooperation partners further polymorphisms and phenotypes of SULT1A1 and CYP2E1 were analyzed. CYP2E1: In this part of the thesis factors influencing the risk of developing differentiat-ed thyroid carcinoma (DTC) were investigated. Known risk factors for the progression of DTC are genetic and environmental factors, including ionizing radiations, previous thyroid diseases, and hormone factors. It has been speculated that dietary acrylamide intake correlates with the DTC formation. The acrylamide molecule is metabolized by CYP2E1 to the reactive carcinogenic glycidamide. The enzymatic reaction is probably dependent on the CYP2E1 genotype. Together with a cooperation partner (Prof. Dr. Landi, University of Pisa, Pisa, Italy) we investigated, whether CYP2E1 variants influ-ence the DTC risk. Prof. Landi and colleagues used a case-control-cohort and a haplo-type approach and observed a significant association between a tag-SNP rs2480258 (A allele), which covers variants in intron eight and the 3’UTR, and an increased DTC risk. In the human liver samples (IKP148) the rs2480258 genotypes were assessed using an imputation analysis and it was shown that particularly the A allele of the SNP reduce significantly the mRNA and protein expression and the enzyme activity. An in silico prediction for the molecular mechanism suggested that miR570 specifically down regulates the transcripts in carriers of the A allele. These results indicated that the inter-individual CYP2E1 activity as well as acrylamide (similar to glycidamide) influences the risk for DTC. SULT1A1: Methyleugenol, a secondary metabolite present in herbs such as basil or laurel is metabolized in humans by sulfation to a reactive product which can covalently bind to DNA. The resulting DNA adducts are mutagenic and can promote carcinogene-sis. Our cooperation partner Prof. Dr. Hans-Rudolf Glatt (German Institute for Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal, Germany) had shown, that the meth-yleugenol metabolism takes place in the liver of mice and is mainly catalyzed by the phase II enzyme SULT1A1. To investigate these facts in humans, the methyleugenol DNA-adduct levels were measured by the cooperation partner in liver tissues (n=121; IKP148) using mass spectrometry. In this work the SULT1A1 protein levels were de-termined using western blot analysis and the relation between the DNA adducts as well as the SULT1A1 expression and the SULT1A1 CNVs was assessed. The SULT1A1 mRNA and protein expression were significantly correlated to the DNA adducts, e.g. higher SULT1A1 expression resulted in higher adduct levels. This emphasized the role of SULT1A1 in the in vivo metabolism in human liver samples. As mentioned above, there were individuals (IKP148) carrying one, two, three, four and five copies of SULT1A1. Deletions were found less frequent (4%) than duplications (36%). The CNVs were significantly associated with the SULT1A1 mRNA and protein expression. This result was consistent to previous studies investigating the association between SULT1A1 CNVs and enzyme activity. The methyleugenol DNA adduct levels were also significantly associated to the SULT1A1 copy number. Carriers of at least three gene copies exhibited a 2.8-fold higher DNA adduct level compared to donors carrying only one SULT1A1 gene copy. As a consequence this could mean that individuals with mul-tiple SULT1A1 copies reach faster, more often and more easily critical and ultimate adduct levels which increase the risk for developing cancer. Future studies should clari-fy whether methyleugenol intake as well as the individual SULT1A1 CNV make-up in-fluences the risk of cancer.
Biotechnological conversion of lignocellulose hydrolyzates : model microorganisms for a bio-based economy
(2020) Horlamus, Felix; Hausmann, Rudolf
Lignocellulose has substantial potential as a carbon source in a bio-based economy. It is the most abundant renewable raw material on earth and is available in large quantities as waste from the agriculture, food and wood industry. It is composed mainly of the polymers lignin, cellulose and hemicellulose. In contrast to glucose derived from cellulose, hemicellulose sugars often remain unused although 60 billion tons of hemicelluloses are produced annually. Hemicelluloses are a group of heterogeneous polysaccharides consisting of different monomers such as D xylose, D arabinose, D mannose and D galactose. Lignocellulose is mostly depolymerized in order to obtain fermentable sugars. During the depolymerization process, inhibitors such as organic acids or furan aldehydes can be formed or released, which could be problematical for biotechnological processes. The aim of this thesis was to develop and evaluate bacterial-based biotechnological processes capable of using hemicellulose sugars as a source of carbon. First, Pseudomonas putida KT2440 was chosen. Pseudomonades are claimed as a promising chassis in biotechnology due to their versatile and robust metabolism. Unlike other Pseudomonades, the strain KT2440 is classified as biosafety level 1 in the American Type Culture Collection (ATCC). However, these bacteria can metabolize glucose as the only lignocellulose monosaccharide. Cellvibrio japonicus was the second selected bacterium. This strain is not yet established as a microbial host in biotechnology, but can degrade a huge portfolio of plant cell wall polysaccharides and is also classified as biosafety level 1 in ATCC. The topic of the first publication was to engineer P. putida KT2440 strains for metabolizing the hemicellulose monosaccharides xylose and arabinose and characterize their growth behavior. Initially, an arabinose metabolizing strain with the araBAD operon and a xylose metabolizing strain with xylAB operon was constructed. Later on, these strains were cultivated in minimal salt medium with glucose, xylose and arabinose as carbon sources in Erlenmeyer flasks. The recombinant P. putida KT2440 strains metabolized xylose and arabinose with high growth rates comparable to glucose. It turned out that both engineered strains were able to grow on both pentoses as well as on mixtures of glucose xylose and arabinose. The intent of the second publication was to evaluate P. putida KT2440 as a platform model organism for bioconversion of lignocellulose hydrolyzates. Strains were cultivated in minimal salt medium with several hydrolyzates as carbon source in Erlenmeyer flask and bioreactor. In addition, the growth-inhibiting effect of major toxic substances contained in lignocellulose hydrolyzates on P. putida KT2440 was analyzed via cultivation experiments. Several suitable hydrolyzates were figured out for this strain. Formic acid and acetic acid proved to be relatively unproblematic under pH neutral conditions, whereas furfural and hydroxymethylfurfural (HMF) had a negative effect on the bacterial growth. A diauxic-like growth behavior was revealed via fed batch bioreactor cultivations, since pentoses were almost not consumed with sufficient glucose supply. Consequently, feed-medium was added step-by-step in the next experiment. The applied feed profile did lead to an almost complete metabolization of xylose. The purpose of the third publication was to evaluate C. japonicus as a potential host strain for the one‐step bioconversion of xylans into rhamnolipids. Cultivation experiments were performed in Erlenmeyer flasks filled with minimal salt medium and containing different carbon sources. Furthermore, the strain was transformed with the plasmid pSynPro8oT carrying rhlA (encodes acetyltransferase) and rhlB (encodes rhamnosyltransferase I) to complete the rhamnolipid metabolism. The strain grew on all main lignocellulose monosaccharides as well as, on different xylans. Mono rhamnolipids were produced with the engineered strain using xylans as carbon source. This is particularly interesting as most industrially relevant bacteria are not able to depolymerize wood polymers. As the product yields were quite low, there are still many challenges in order to achieve an economically efficient process. Nevertheless, to the best of our knowledge, it is the first published one step bioconversion of hemicellulose polymers into rhamnolipids. In total, P. putida KT2440 turned out as a flexible and powerful model organism and two xylose and arabinose metabolizing strains were constructed. Moreover, bioreactor cultivations with lignocellulose hydrolyzates were performed and a feeding strategy to overcome diauxic-like growth behavior was presented. A proof of concept for a one-step bioconversion of xylans into rhamnolipids with a recombinant C. japonicus strain was successfully demonstrated.
Broad time‐dependent transcriptional activity of metabolic genes of E. coli O104:H4 strain C227/11Φcu in a soil microenvironment at low temperature
(2023) Detert, Katharina; Währer, Jonathan; Nieselt, Kay; Schmidt, Herbert
In the current study, metabolic genes and networks that influence the persistence of pathogenic Escherichia coli O104:H4 strain C227/11Φcu in agricultural soil microenvironments at low temperature were investigated. The strain was incubated in alluvial loam (AL) and total RNA was prepared from samples at time point 0, and after 1 and 4 weeks. Differential transcriptomic analysis was performed by RNA sequencing analysis and values obtained at weeks 1 and 4 were compared to those of time point 0. We found differential expression of more than 1500 genes for either time point comparison. The two lists of differentially expressed genes were then subjected to gene set enrichment of Gene Ontology terms. In total, 17 GO gene sets and 3 Pfam domains were found to be enriched after 1 week. After 4 weeks, 17 GO gene sets and 7 Pfam domains were statistically enriched. Especially stress response genes and genes of the primary metabolism were particularly affected at both time points. Genes and gene sets for uptake of carbohydrates, amino acids were strongly upregulated, indicating adjustment to a low nutrient environment. The results of this transcriptome analysis show that persistence of C227/11Φcu in soils is associated with a complex interplay of metabolic networks.

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