Biochemie und Chemie
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The bile acid activated transcription factor farnesoid X receptor (FXR) regulates numerous metabolic processes and is a rising target for the treatment of hepatic and metabolic disorders. FXR agonists have revealed efficacy in treating non-alcoholic steatohepatitis (NASH), diabetes and dyslipidemia. Here we characterize imatinib as first-in-class allosteric FXR modulator and report the development of an optimized descendant that markedly promotes agonist induced FXR activation in a reporter gene assay and FXR target gene expression in HepG2 cells. Differential effects of imatinib on agonist-induced bile salt export protein and small heterodimer partner expression suggest that allosteric FXR modulation could open a new avenue to gene-selective FXR modulators.
The following thesis is concerned with the elucidation of structural changes of RNA molecules during the time course of dynamic processes that are commonly denoted as folding reactions. In contrast to the field of protein folding, the concept of RNA folding comprises not only folding reactions itself but also refolding- or conformational switching- and assembly processes (see chapter III). The method in this thesis to monitor these diverse processes is high resolution liquid-state NMR spectroscopy. To understand the reactions is of considerable interest, because most biological active RNA molecules function by changing their conformation. This can be either an intrinsic property of their respective sequence or may happen in response to a cellular signal such as small molecular ligand binding (like in the aptamer and riboswitch case), protein or metal binding. The first part of the thesis (chapters II & III) provides a general overview over the field of RNA structure and RNA folding. The two chapters aim at introducing the reader into the current status of research in the field. Chapters II is structured such that primary structure is first described then secondary and tertiary structure elements of RNA structure. A special emphasis is given to bistable RNA systems that are functionally important and represent models to understand fundamental questions of RNA conformational switching. RNA folding in vitro as well as in vivo situations is discussed in Chapter III. The following chapters IV and V also belong to the introduction part and review critically the NMR methods that were used to understand the nature and the dynamics of the conformational/structural transitions in RNA. A general overview of NMR methods quantifying dynamics of biomolecules is provided in chapter IV. A detailed discussion of solvent exchange rates and time-resolved NMR, as the two major techniques used, follows. In the final chapter V of the first part the NMR parameters used in structure calculation and structure calculation itself are conferred. The second part of the thesis, which is the cumulative part, encompasses the conducted original work. Chapter VI reviews the general NMR techniques applied and explains their applicability in the field of RNA structural and biochemical studies in several model cases. Chapter VII describes the achievement of a complete resonance assignment of an RNA model molecule (14mer cUUCGg tetral-loop RNA) and introduces a new technique to assign quaternary carbon resonances of the nucleobases. Furthermore, it reports on a conformational analysis of the sugar backbone in this RNA hairpin molecule in conjunction with a parameterization of 1J scalar couplings. Achievements: • Establishment of two new NMR pulse-sequences facilitating the assignment of quaternary carbons in RNA nucleobases • First complete (99.5%) NMR resonance assignment of an RNA molecule (14mer) including 1H, 13C, 15N, 31P resonances • Description of RNA backbone conformation by a complete set of NMR parameters • Description of the backbone conformational dependence in RNA of new NMR parameters (1J scalar couplings) Chapters VII & VIII summarize the real-NMR studies that were conducted to elucidate the conformational switching events of several RNA systems. Chapter VIII gives an overview on the experiments that were accomplished on three different bistable RNAs. These molecules where chosen to be good model systems for RNA refolding reactions and so consequently served as reporters of conformational switching events of RNA secondary structure elements. Achievements: • First kinetic studies of RNA refolding reactions with atomic resolution by NMR • Application of [new] RT-NMR techniques either regarding the photolytic initiation of the reaction or regarding the readout of the reaction • Discovery of different RNA refolding mechanisms for different RNA molecules Deciphering of a general rule for RNA refolding methodology to conformational switching processes of RNA tertiary structure elements. The models for these processes were a) the guanine-dependent riboswitch RNA and b) the minimal hammerhead ribozyme. Achievements: • NMR spectroscopic assignment of imino-resonances of the hypoxanthine bound guanine-dependent riboswitch RNA • Application of RT-NMR techniques to monitor the ligand induced conformational switch of the aptamer domain of the guanine-dependent riboswitch RNA at atomic resolution • Translation of kinetic information into structural information • Deciphering a folding mechanism for the guanine riboswitch aptamer domain • Application of RT-NMR techniques to monitor the reaction of the catalytically active mHHR RNA at atomic resolution In the appendices the new NMR pulse-sequences and the experimental parameters are described, which are not explicitly treated in the respective manuscripts.
The conformational dynamics induced by ligand binding to the tetracycline-binding aptamer is monitored via stopped-flow fluorescence spectroscopy and time-correlated single photon counting experiments. The fluorescence of the ligand is sensitive to changes within the tertiary structure of the aptamer during and after the binding process. In addition to the wild-type aptamer, the mutants A9G, A13U and A50U are examined, where bases important for regulation are changed to inhibit the aptamer’s function. Our results suggest a very fast two-step-mechanism for the binding of the ligand to the aptamer that can be interpreted as a binding step followed by a reorganization of the aptamer to accommodate the ligand. Binding to the two direct contact points A13 and A50 was found to occur in the first binding step. The exchange of the structurally important base A9 for guanine induces an enormous deceleration of the overall binding process, which is mainly rooted in an enhancement of the back reaction of the first binding step by several orders of magnitude. This indicates a significant loss of tertiary structure of the aptamer in the absence of the base A9, and underlines the importance of pre-organization on the overall binding process of the tetracycline-binding aptamer.
Die Bedeutung der Toleranztests für die Diagnostik der diabetischen Vorstadien wird aus den pathophysiologischen Voraussetzungen abgeleitet. Die Methode der Wahl ist der einzeitige orale Glucosetoleranztest mit 100g Glucose (oder Glucoseoligosacchariden). Dieses Verfahren erfaßt die wesentlichen physiologisch wichtigen Funktionen, was für den intravenösen Glucosetoleranztest und für den Tolbutamidtest nicht gilt. Gleichzeitig ist der orale Toleranztest am einfachsten durchzuführen. Lediglich bei Störungen im Gastrointestinalbereich kann der intravenöse Glucosetoleranztest angezeigt sein. Es gibt keine wichtige Indikation für den Tolbutamidtest.
Die verschiedenen Störmöglichkeiten sowie Fehlermöglichkeiten bei der Durchführung des Glucosetoleranztests werden besprochen.
Das Gleichgewicht zwischen den Sphingolipiden Ceramid und Sphingosin-1-Phosphat (S1P) spielt eine entscheidende Rolle für das Schicksal einer Zelle. Es ist bekannt, dass Ceramid proapoptotisch wirkt, wohingegen S1P antiapoptotische und entzündungshemmende Signalwege induziert [6]. Eine Beeinflussung der Sphingolipid-metabolisierenden Enzyme sowie eine daraus resultierende gestörte Balance zwischen Ceramid und S1P ist somit ein Merkmal diverser entzündlicher Krankheiten wie der Asthma bronchiale, der Colitis ulcerosa [148] oder auch verschiedenen Arten von Tumoren [199]. Das Hauptziel dieser Arbeit lag in der Untersuchung der Ceramid-abbauenden neutralen Ceramidase (NCDase) und der S1P-synthetisierenden Sphingosinkinase 1 (SK1) in verschiedenen Nierenzellen. Ein Fokus wurde dabei auf die Regulierung dieser Enzyme durch entzündungshemmende Corticosteroide in Ratten Mesangiumzellen gelegt, wobei diese Zellen entscheidend in der Entstehung entzündlicher Nierenerkrankungen wie einer Glomerulonephritis sind. Weiterhin wurde der Einfluss der Mutation putativer Phosphorylierungsstellen der NCDase auf die Regulierung dieses Enzyms in HEK293 Zellen untersucht und in einem dritten Teil der Arbeit schließlich die Expression und die Funktion der SK1 in der humanen Niere im Vergleich zum Nierenzellkarzinom analysiert.
Es konnte gezeigt werden, dass Glucocorticoide (GCs) Mesangiumzellen durch eine Steigerung der intrazellulären S1P-Konzentrationen vor durch Stress induzierter Apoptose schützen. Diese Beeinflussung des Sphingolipid-Rheostats beruhte auf einer gesteigerten mRNA- und Proteinexpression der Sphingosinkinase 1 (SK1) und der neutralen Ceramidase (NCDase). Außerdem wurde nachgewiesen, dass der Promotor der NCDase durch GCs aktivierbar ist und dass zwei Glucocorticoid-responsive-Elemente (GREs) innerhalb der Promotorsequenz durch die Bindung von Glucocorticoidrezeptoren (GRs) diese Aktivierung bewirken. In vivo Experimente mit isolierten Glomeruli, die aus mit Dexamethason behandelten Mäusen gewonnen wurden, zeigten ebenfalls eine Erhöhung der mRNA-Expression und Aktivität der SK1 sowie eine gesteigerte Proteinexpression der NCDase. Somit wurde erstmals ein direkter Einfluss von GCs auf den Sphingolipidmetabolismus in Mesangiumzellen beschrieben.
In einem zweiten Teil dieser Arbeit wurde gezeigt, dass eine Mutation zweier putativer Proteinkinase C (PKC)-Phosphorylierungsstellen (T253A und T420/23A) in der Sequenz der murinen NCDase zu einem verlangsamten Reifungsprozess dieses Enzyms führt. Western Blot-Analysen ergaben, dass der überexprimierte NCDase-WT zwei unterschiedlich glykosylierte Isoformen mit einem Molekulargewicht von 120 und 130 kDa exprimiert, welche stetig durch einen aktiven Prozess sezerniert werden. Im Gegensatz dazu war in den Mutanten ausschließlich die 130 kDa-Form im Zellkulturüberstand und die 120 kDa-Form im Lysat zu finden. Im Gegensatz zum WT lokalisierten die Mutanten lediglich an intrazellulären Membranen und nicht zusätzlich an der Plasmamembran. In Lysaten von Zellen die die Mutanten exprimierten, konnte eine verringerte relative Aktivität gemessen werden, die der sezernierten mutierten Formen hingegen war erhöht. Daher wurde vermutet, dass die 130 kDa-Form die reife Plasmamembran-gebundene und anschließend sezernierte, aktivere Isoform der NCDase darstellt. Die Inkubation von Mesangiumzellen mit Zellkulturüberständen, die den sezernierten NCDase-WT enthielten, führte zum Schutz vor durch Stress induzierter Apoptose. Somit kann eine auto- bzw. parakrine Funktion der sezernierten NCDase angenommen werden.
Dem dritten Teil der Arbeit lag die erstmalige Beschreibung der SK1-Expression in der gesunden humanen Niere zugrunde. Es konnte gezeigt werden, dass diese im Zytoplasma sowie an Membranen von Zellen des proximalen Tubulus sowie in geringerem Maße in Podozyten und Mesangiumzellen des Glomerulus exprimiert wird. Im Gegensatz dazu wurde die SK1 in Biopsien von Patienten mit Nierentumor im Nukleus gefunden. Die Untersuchung der SK1-Expression in 5 verschiedenen Nierentumorzelllinien im Vergleich zu Epithelzellen des proximalen Tubulus (Human Kidney 2 - HK2-Zellen) ergaben, dass sowohl die Protein- als auch die mRNA-Expression der SK1 in Föhn-Zellen stark erhöht, in ACHN3-Zellen hingegen signifikant niedriger war. Zudem konnte auch in den Föhn-Zellen eine nukleäre Expression der SK1 nachgewiesen werden. Die Behandlung von HK2-, ACHN3- und Föhn-Zellen mit dem Transforming Growth Factor-ß2 (TGF-ß2) resultierte in einer transkriptionellen Steigerung der SK1-Expression. Die Herunterregulierung der SK1 in diesen Zellen führte zu einem Arrest der Zellen in der S Phase, wohingegen die Überexpression der SK1 in den ACHN3-Zellen zu einem signifikanten Schutz vor Apoptose führte.
Zusammenfassend sind die Sphingolipid-metabolisierenden Enzyme NCDase und SK-1 ein interessanter therapeutischer Ansatzpunkt zur Behandlung von Krankheiten, die mit pathologischen Prozessen wie Entzündung, Apoptose und Proliferation einhergehen, wie es bei Glomerulonephritiden und bei Nierentumoren der Fall ist.
The near and far UV spectra of the aminoboranes (Me2N)n B X3-n, n = 1, 2, 3, Me=CH3, X= H, Me, F, Cl, Br are presented. In most of the monoamino boranes the π→π * transitions dominate. In the di- and triamino boranes there were additionally found a Rydberg series and some single Rydberg transitions, partly preceding the π→π * band. The Rydberg assignments were settled particularly by comparing the band positions of the compounds relatively to their ionization energies.
Life and biological resilience rely on the execution of precise gene expression profiles. A key mechanism to ensure cellular homeostasis is the regulation of protein synthesis. Recent studies have unveiled an intrinsic regulatory capacity of ribosomes, previously considered mere executors of mRNA translation. Neurons in particular finely regulate protein synthesis, at both global and local levels. This sustains their complex morphology and allows them to rapidly transmit, integrate, and respond to external stimuli. In this thesis, I investigated the neuronal ribosome and how subcellular environments and physiological perturbations shape it, by profiling its molecular composition, functional interconnections, and cellular distribution.
First, I used genetic engineering, biochemical purification, and mass spectrometry, to characterize in an unbiased manner the translation machinery specifically from excitatory and inhibitory neurons of the mouse cortex. I found that neuronal ribosomes commonly interact with RNA-binding proteins, components of the cytoskeleton, and proteins associated with the endoplasmic reticulum and vesicles. In line with the requirement for local protein synthesis in the distal parts of neurons, we observed that neuronal ribosomes preferentially interact with proteins involved in cellular transport. Remarkably, I observed a strong association between ribosomes and pre-synaptic vesicles, which suggests a potential regulatory interaction between local translation and neuronal activity.
Intriguingly, I and others have observed mRNAs encoding for core ribosomal proteins (RPs) among the genes most enriched in neuronal processes. This observation challenges two historical assumptions of ribosome biology: (1) new RPs are incorporated only into newly forming ribosomes, and (2) this incorporation occurs only in the nucleus and perinuclear region. In my PhD, I aimed to directly test these two assumptions and if proven wrong ask whether and why neurons would localize RP mRNAs far from their known assembly site.
Employing a combination of metabolic labeling and highly sensitive mass spectrometry techniques, I discovered that a subset of RPs rapidly and dynamically binds on and off mature ribosomes. Strikingly, this incorporation does not depend on the supply of new ribosomes from the nucleus. Therefore, my data refuted the assumption that ribosomes are built and degraded as a unit and revealed a more dynamic view of these machines, which can actively exchange core components. In particular, I found that the association of certain exchanging RPs is influenced by location (e.g., cell body versus neurites) and cellular state (e.g., post-oxidative stress). Neurons may use this mechanism to repair and/or specialize their protein synthesis machinery in a rapid and context-dependent manner.
Finally, I asked whether some steps of ribosome biogenesis could also take place in distal processes. Although most steps of ribosome assembly occur within the nucleus, the final stages of maturation are known to occur in the cytosol. By combining several imaging and biochemical approaches, I found that cytosolic (but not nuclear) pre-ribosomal particles are present in neuronal processes. Through the incorporation of new RPs into these immature particles, neurons may be able to locally “turn on” previously incompetent ribosomes. This may enable regions near synapses to enhance and customize their translational capacity, independently of the central pool of ribosomes from the cell body. Indeed, I observed that synaptic plasticity induces a maturation of cytosolic pre-ribosomes.
In summary, this thesis shows how neuronal ribosomes can sense cellular states, respond by adjusting their core composition, and in doing so influence the local capacity for protein synthesis. By overturning long-held assumptions in ribosome biology, this work highlights new molecular mechanisms of gene expression and enriches our understanding of the rapid and dynamic strategies cells employ to operate, thrive, and adaptively respond to environmental changes.
Lentiviral vectors mediate gene transfer into dividing and most non-dividing cells. Thereby, they stably integrate the transgene into the host cell genome. For this reason, lentiviral vectors are a promising tool for gene therapy. However, safety and efficiency of lentiviral mediated gene transfer still needs to be optimised. Ideally, cell entry should be restricted to the cell population relevant for a particular therapeutic application. Furthermore, lentiviral vectors able to transduce quiescent lymphocytes are desirable. Although many approaches were followed to engineer retroviral envelope proteins, an effective and universally applicable system for retargeting of lentiviral cell entry is still not available. Just before the experimental work of this thesis was started, retargeting of measles virus (MV) cell entry was achieved. This virus has two types of envelope glycoproteins, the hemagglutinin (H) protein responsible for receptor recognition and the fusion (F) protein mediating membrane fusion. For retargeting, the H protein was mutated in its interaction sites for the native MV receptors and a ligand or a single-chain antibody (scAb) was fused to its ectodomain. It was hypothesised that the retargeting system of MV can be transferred to lentiviral vectors by pseudotyping human immunodeficiency virus-1 (HIV-1) derived vector particles with the MV glycoproteins. As the unmodified MV glycoproteins did not pseudotype HIV vectors, two F and 15 H protein variants carrying stepwise truncations or amino acid (aa) exchanges in their cytoplasmic tails were screened for their ability to form MV-HIV pseudotypes. The combinations Hcd18/Fcd30, Hcd19/Fcd30 and Hcd24+4A/Fcd30 led to most efficient pseudotype formation with titers above 10exp6 transducing units /ml, using concentrated particles. The F cytoplasmic tail was truncated by 30 aa and the H cytoplasmic tail was truncated by 18, 19 or 24 residues with four added alanines after the start methionine in the latter case. Western blot analysis indicated that particle incorporation of the MV glycoproteins was enhanced upon truncation of their cytoplasmic tails. With the MV-HIV vectors high titers on different cell lines expressing one or both MV receptors were obtained, whereas MV receptor-negative cells remained untransduced. Titers were enhanced using an optimal H to F plasmid ratio (1:7) during vector particle production. Based on the described pseudotyping with the MV glycoprotein variants, HIV vectors retargeted to the epidermal growth factor receptor (EGFR) or the B cell surface marker CD20 were generated. For the production of the retargeted vectors MVaEGFR-HIV and MVaCD20-HIV, Fcd30 together with a native receptor blind Hcd18 protein, displaying at its ectodomain either the ligand EGF or a scAb directed against CD20 were used. With these vectors, gene transfer into target receptor-positive cells was several orders of magnitude more efficient than into control cells. The almost complete absence of background transduction of non-target cells was e.g. demonstrated in mixed cell populations, where the CD20-targeting vector selectively eliminated CD20-positive cells upon suicide gene transfer. Remarkably, transduction of activated primary human CD20-positive B cells was much more efficient with the MVaCD20-HIV vector than with the standard pseudotype vector VSV-G-HIV. Even more surprisingly, MVaCD20-HIV vectors were able to transduce quiescent primary human B cells, which until then had been resistant towards lentiviral gene transfer. The most critical step during the production of MV-HIV pseudotypes was the identification of H cytoplasmic tail mutants that allowed pseudotyping while retaining the fusion helper function. In contrast to previously inefficient targeting strategies, the reason for the success of this novel targeting system must be based on the separation of the receptor recognition and fusion functions onto two different proteins. Furthermore, with the CD20-targeting vector transduction of quiescent B cells was demonstrated for the first time. Own data and literature data suggest that CD20 binding and hyper-cross-linking by the vector particles results in calcium influx and thus activation of quiescent B cells. Alternatively this feature may be based on a residual binding activity of the MV glycoproteins to the native MV receptors that is insufficient for entry but induces cytoskeleton rearrangements dissolving the post-entry block of HIV vectors. Hence, in this thesis efficient retargeting of lentiviral vectors and transduction of quiescent cells was combined. This novel targeting strategy should be easily adaptable to many other target molecules by extending the modified MV H protein with appropriate specific domains or scAbs. It should now be possible to tailor lentiviral vectors for highly selective gene transfer into any desired target cell population with an unprecedented degree of efficiency.
Identifizierung neuer Bindungspartner von Gephyrin, einem Strukturprotein inhibitorischer Synapsen
(2002)
Synapsen sind spezialisierte Zellkontakte, die der Kommunikation von Nervenzellen dienen. Für eine effiziente Signalübertragung ist es erforderlich, daß an diesem Prozeß beteiligte Proteine präzise und in hoher Dichte an der Synapse angereichert vorliegen. Die selektive Akkumulation von Glyzinrezeptoren sowie der verbreitetesten GABAARezeptoren an inhibitorischen Synapsen wird durch das periphere Membranprotein Gephyrin vermittelt. Gephyrin bindet direkt an die β-Untereinheit des Glyzinrezeptors und kann diesen vermittels seiner Affinität zu polymerisiertem Tubulin am Zytoskelett verankern. Um mehr über die Rolle dieses Proteins in der Entwicklung und Funktion von inhibitorischen Synapsen zu erfahren, sollten in der vorliegenden Arbeit neue Interaktionspartner von Gephyrin identifiziert werden. Hierzu wurde das Zwei-Hybrid-System in Saccharomyces cerevisiae zur Analyse einer cDNA-Bank aus dem Gehirn von Ratten verwendet. Dies resultierte in der Sequenzaufklärung von 24 potentiellen Gephyrin-bindenden Proteinen. Von diesen erwiesen sich vier in einem weiteren Bindungsexperiment als positiv und kommen daher als hochaffine Interaktionspartner in Frage. Es handelte sich um die eng verwandten Dynein light chains-1 und -2 (Dlc-1/-2), den Natrium-Kalzium-Austauscher NCX2 und ein Fragment eines bisher unbekannten Proteins, das nicht weiter untersucht wurde. Im Einklang mit einer möglichen Interaktion zwischen NCX2 und Gephyrin gelang es zu zeigen, daß NCX2 sowie das verwandte Protein NCX3 in neuronalen Primärkulturen an inhibitorischen Synapsen mit Gephyrin-Immunreaktivität kolokalisierten. Der Schwerpunkt der vorliegenden Arbeit lag in der Untersuchung der Interaktion zwischen Gephyrin und Dlc-1/-2. Die Bindedomäne von Gephyrin für Dlc-1/-2 konnte auf den Bereich von Aminosäuren 181-243 eingegrenzt werden, und eine Gephyrinmutante ohne dieses Bindemotiv wies keine Affinität zu Dlc-1/-2 auf. Sowohl endogenes als auch rekombinant exprimiertes Dlc-Protein kolokalisierte mit aus der Überexpression in HEK-Zellen resultierenden zytosolischen Gephyrinaggregaten. Weiter gelang die Coimmunpräzipitation von Komplexen aus Gephyrin und Dlc-1/-2 aus transfizierten HEK-Zellen, und bakteriell exprimierte GST-Fusionsproteine von Dlc-1 bzw. Gephyrin reicherten den jeweils anderen Bindungspartner aus Hirnextrakt an. In neuronalen Primärkulturen waren Dlc-Proteine zu großen Anteilen zytoplasmatisch lokalisiert, darüberhinaus jedoch in Abhängigkeit von der Zelldichte an inhibitorischen Synapsen angereichert. Dlc-1/-2 sind Komponenten der Motorproteinkomplexe Dynein und Myosin-Va, in welchen sie möglicherweise als Adapter für zu transportierende Lasten dienen. Es ist daher denkbar, daß Gephyrin über Dlc-1/-2 mit einem aktiven Transportprozess verbunden wird. Zur Untersuchung dieser Frage wurden EGFP-epitopmarkierte Gephyrinproteine in hippokampalen Neuronen exprimiert und auf ihre subzelluläre Lokalisation untersucht. Sowohl EGFP-Gephyrin als auch die Deletionsmutante ohne Dlc-Bindemotiv waren zuverlässig an inhibitorischen Synapsen angereichert, ein Lokalisationsdefekt aufgrund fehlender Dlc-Bindung wurde nicht beobachtet. Dieses Ergebnis spricht gegen eine essentielle Rolle von Dlc-1/-2 und möglicherweise assoziierten Motorproteinen im Transport von Gephyrin zur Synapse. Aktiver Transport kann jedoch andere Funktionen im Zusammenhang mit der subzellulären Lokalisation von Gephyrin haben, wie etwa im retrograden Transport zum Zellkörper des Neurons. Diese Frage wird in weiteren Experimenten zu untersuchen sein.
Singlet oxygen (1Δg) was generated by a microwave discharge and bubbled through a solution of chlorophyll-a in dibutylphtalate at approximately 10-20 torr. It not only excited the dye to its first singlet state but also produced oxidized species which generated a very long lasting weak chemiluminescence. From quenching experiments for the generation of the excited species could computer simulation.