Synaptic connectivity in micropatterned networks of neuronal cells

The presented thesis describes the formation of functional neuronal networks on an underlying micropattern. Small circuits of interconnected neurons defined by the geometry of the patterned substrate could be observed and were utilised as a model system of reduced complexity for the behaviour of neuronal network formation and activity. The first set of experiments was conducted to investigate aspects of the substrate preparation. Micropatterned substrates were created by microcontact printing of physiological proteins onto polystyrene culture dishes. The substrates displayed a high contrast between the repellant background and the cell attracting pattern, such that neurons seeded onto these surfaces aligned with the stamped structure. Both the patterning process and the cell culture were optimised, yielding highly compliant low-density networks of living neuronal cells. In the second step, cellular physiology of the cells grown on these substrates was investigated by patch-clamp measurements and compared to cells cultivated under control conditions. It could be shown that the growth on a patterned substrate did not result in an impairment of cellular integrity nor that it had an impact on synapse formation or synaptic efficacy. Due to the extremely low-density cell culture that was applied, cellular connectivity through chemical synapses could be observed at the single cell level. Having established that single cells were not negatively affected by the growth on patterned substrates, aspects of network formation were investigated. The formation of physical contact between two cells was analysed through microinjection studies and related to the rate at which functional synaptic contacts formed between two neighbouring cells. Surprisingly, the rate of synapse formation between physically contacting cells was shown to be unaltered in spite of the drastic reduction of potential interaction partners on the micropattern. Additional features of network formation were investigated and found consistent with results reported by other groups: A different rate of synapse formation by excitatory and inhibitory neurons could be reproduced as well as a different rate of frequency-dependent depression at excitatory and inhibitory synapses. Furthermore, regarding simple feedback loops, a significant enrichment of reciprocal connectivity between mixed pairs of excitatory and inhibitory neurons relative to uniform pairs could be demonstrated. This phenomenon has also been described by others in unpatterned cultures [Muller, 1997] and may therefore be a feature underlying neuronal network formation in general. Based on these findings, it can be assumed that inherent features of neuronal behaviour and cellular recognition mechanisms were found in the cultured networks and appear to be undisturbed by patterned growth. At the same time, it was possible to reduce the complexity of the forming networks dramatically in a cell culture on a patterned surface. Thus, features of network architecture and synaptic connectivity could be investigated on the single cell level under highly defined conditions.

Self-assembly of Tetraurea Calix[4]arenes

We have elaborated a multistep strategy to synthesize ABAB-type tetraureas. There are overall nine steps but they involve very simple chemistry. The sequence starts with a 1,3-dialkylation and this is the step in which a difference between distal phenolic units is introduced. The selective ipso-nitration in the next step is based on the difference in reactivity between free phenolic units and alkylated ones. The direct reaction of tetraamino calixarene with tolylisocyanate appears not to be an appropriate method to synthesize 1,3-ditolylurea calixarenes but can be used to get tetraureas of ABBB- and AABB-types in two steps with yields of about 60%. A complete regioselective dimerization was obtained with mono-loop derivatives in which two adjacent urea residues are covalently connected. As predicted/expected the loop prevents the formation of one regioisomer, and only the dimer in which the open-chain residue slips through the loop is formed. To synthesize mono-loop tetraureas 1,2-diBoc protected tetraamino calixarene was acylated with activated di-urethanes under high dilution conditions. Di-loop compounds were synthesized by two different ways. In the reaction of tetraamine and di-urethanes the yield is about 30-40%. The second method is based on the metathesis reaction within a suitable heterodimer. For this strategy, tetraurea derivatives with residues which have terminal double bonds were prepared. The exclusive formation of the heterodimer with tetratosylurea as template is the key point in this strategy. Metathesis followed by hydrogenation give exceptionally good yields (> 80%) of the loop compounds. All the NMR data for di-loop compounds confirm that the loops prevent the interaction of the urea residues which are connected and thus, as expected, the di-loop derivatives do not form homodimers. The heterodimer between di-loop compounds and tetratolylurea (open-chain tetraureas) was the only species observed for a 1:1 mixture in benzene or chloroform. The rational synthesis of bis-[2]catenanes was a consequence of the selective formation of one regioisomer of mono-loop derivatives and the exclusive formation of heterodimers by di-loop derivatives. The formation of interlocking-ring in the synthesis of bis-[2]catenanes is an additional evidence that one open-chain residue slips through the loop in mono- or di-loop derivatives. Exceptionally good yields in the synthesis of bis-[2]catenanes are due to the high preorganization in the dimer which undergoes the metathesis. This preorganization decreases the number of the wrong connections and favors the new connections to be formed. Although the procedure for working up the reaction mixture should be still improved, these results are promising. A C2-symmetrical bis-[2]catenane was successfully resolved by column chromatography using a chiral stationary phase. Thus it should be possible to separate a larger amount to obtain pure enantiomers for further studies.

Präparation, Charakterisierung und elektronische Eigenschaften von dünnen Schichten des Hochtemperatursupraleiters HgReBa 2 Ca n-1 Cu n O y

Ziel dieser Arbeit war die Pr"{a}paration, Charakterisierung und Untersuchung der elektronischen Eigenschaften von d"{u}nnen Schichten des Hochtemperatursupraleiters HgReBa$_{2}$Ca$_{n-1}$Cu$_{n}$O$_{y}$, die mittels gepulster Laser-Deposition hergestellt wurden. Die HgRe1212-Filme zeigen in der AC-Suszeptibilit"{a}t einen scharfen "{U}bergang in die supraleitende Phase bei 124 K mit einer "{U}bergangsbreite von 2 K. Die resistiven "{U}berg"{a}nge der Proben wurden mit zunehmender St"{a}rke des externen Magnetfeldes breiter. Aus der Steigung der Arrheniusplots konnte die Aktivierungsenergie f"{u}r verschiedene Feldst"{a}rken bestimmt werden. Weiterhin wurde die Winkelabh"{a}ngigkeit des Depinning-Feldes $B_{dp}(theta)$ der Filme gemessen. Hieraus wurde ein Anisotropiewert von $gamma$ = 7.7 bei 105 K ermittelt. Dies ist relevant, um den f"{u}r Anwendungen wichtigen Bereich im $T$-$B$-$theta$-Phasenraum des Materials absch"{a}tzen zu k"{o}nnen. Die kritische Stromdichte $J_{c}$ der d"{u}nnen Filme aus HgRe-1212 wurde mit Hilfe eines SQUID-Magnetometers gemessen. Die entsprechenden $M$-$H$ Kurven bzw. das magnetische Moment dieser Filme wurde f"{u}r einen weiten Temperatur- und Feldbereich mit einem magnetischen Feld senkrecht zum Film aufgenommen. F"{u}r einen HgRe-1212-Film konnte bei 5 K eine kritische Stromdichte von 1.2 x 10$^{7}$ A/cm$^{2}$ und etwa 2 x 10$^{6}$ A/cm$^{2}$ bei 77 K ermittelt werden. Es wurde die Magnetfeld- und die Temperaturabh"{a}ngigkeit des Hall-Effekts im normalleitenden und im Mischzustand in Magnetfeldern senkrecht zur $ab$-Ebene bis zu 12 T gemessen. Oberhalb der kritischen Temperatur $T_{c}$ steigt der longitudinale spezifische Widerstand $rho_{xx}$ linear mit der Temperatur, w"{a}hrend der spezifische Hall-Widerstand $rho_{yx}$ sich umgekehrt proportional zur Temperatur "{a}ndert. In der N"{a}he von $T_{c}$ und in Feldern kleiner als 3 T wurde eine doppelte Vorzeichen"{a}nderung des spezifischen Hall-Widerstandes beobachtet. Der Hall-Winkel im Normalzustand, cot $theta_{H}= alpha T^{2} + beta$, folgt einer universellen $textit{T }^{2}$-Abh"{a}ngigkeit in allen magnetischen Feldern. In der N"{a}he des Nullwiderstand-Zustandes h"{a}ngt der spezifische Hall-Widerstand $rho_{yx}$ "{u}ber ein Potenzgesetz mit dem longitudinalen Widerstand $rho_{xx}$ zusammen. Das Skalenverhalten zwischen $rho_{yx}$ und $rho_{xx}$ weist eine starke Feld-Abh"{a}ngigkeit auf. Der Skalenexponent $beta$ in der Gleichung $rho_{yx}$ =A $rho_{xx}^{beta}$ steigt von 1.0 bis 1.7, w"{a}hrend das Feld von 1.0 bis 12 T zunimmt.

Molecular phylogeography of the Woodland Ringlet (Erebia medusa [Denis and Schiffermüller] 1775) in Europe

Phylogeography is a recent field of biological research that links phylogenetics to biogeography through deciphering the imprint that evolutionary history has left on the genetic structure of extant populations. During the cold phases of the successive ice ages, which drastically shaped species’ distributions since the Pliocene, populations of numerous species were isolated in refugia where many of them evolved into different genetic lineages. My dissertation deals with the phylogeography of the Woodland Ringlet (Erebia medusa [Denis and Schiffermüller] 1775) in Central and Eastern Europe. This Palaearctic butterfly species is currently distributed from central France and south eastern Belgium over large parts of Central Europe and southern Siberia to the Pacific. It is absent from those parts of Europe with mediterranean, oceanic and boreal climates. It was supposed to be a Siberian faunal element with a rather homogeneous population structure in Central Europe due to its postglacial expansion out of a single eastern refugium. An already existing evolutionary scenario for the Woodland Ringlet in Central and Eastern Europe is based on nuclear data (allozymes). To know if this is corroborated by organelle evolutionary history, I sequenced two mitochondrial markers (part of the cytochrome oxydase subunit one and the control region) for populations sampled over the same area. Phylogeography largely relies on the construction of networks of uniparentally inherited haplotypes that are compared to geographic haplotype distribution thanks to recent developed methods such as nested clade phylogeographic analysis (NCPA). Several ring-shaped ambiguities (loops) emerged from both haplotype networks in E. medusa. They can be attributed to recombination and homoplasy. Such loops usually avert the straightforward extraction of the phylogeographic signal contained in a gene tree. I developed several new approaches to extract phylogeographic information in the presence of loops, considering either homoplasy or recombination. This allowed me to deduce a consistent evolutionary history for the species from the mitochondrial data and also adds plausibility for the occurrence of recombination in E. medusa mitochondria. Despite the fact that the control region is assumed to have a lack of resolving power in other species, I found a considerable genetic variation of this marker in E. medusa which makes it a useful tool for phylogeographic studies. In combination with the allozyme data, the mitochondrial genome supports the following phylogeographic scenario for E. medusa in Europe: (i) a first vicariance, due to the onset of the Würm glaciation, led to the formation of several major lineages, and is mirrored in the NCPA by restricted gene flow, (ii) later on further vicariances led to the formation of two sub-lineages in the Western lineage and two sub-lineages in the Eastern lineage during the Last Glacial Maximum or Older Dryas; additionally the NCPA supports a restriction of gene flow with isolation by distance, (iii) finally, vicariance resulted in two secondary sub-lineages in the area of Germany and, maybe, to two other secondary sub-lineages in the Czech Republic. The last postglacial warming was accompanied by strong range expansions in most of the genetic lineages. The scenario expected for a presumably Siberian faunal element such as E. medusa is a continuous loss of genetic diversity during postglacial westward expansion. Hence, the pattern found in this thesis contradicts a typical Siberian origin of E. medusa. In contrast, it corroboratess the importance of multiple extra-Mediterranean refugia for European fauna as it was recently assumed for other continental species.

Statistical mechanics of protein complexed and condensed DNA

In this thesis I treat various biophysical questions arising in the context of complexed / ”protein-packed” DNA and DNA in confined geometries (like in viruses or toroidal DNA condensates). Using diverse theoretical methods I consider the statistical mechanics as well as the dynamics of DNA under these conditions. In the first part of the thesis (chapter 2) I derive for the first time the single molecule ”equation of state”, i.e. the force-extension relation of a looped DNA (Eq. 2.94) by using the path integral formalism. Generalizing these results I show that the presence of elastic substructures like loops or deflections caused by anchoring boundary conditions (e.g. at the AFM tip or the mica substrate) gives rise to a significant renormalization of the apparent persistence length as extracted from single molecule experiments (Eqs. 2.39 and 2.98). As I show the experimentally observed apparent persistence length reduction by a factor of 10 or more is naturally explained by this theory. In chapter 3 I theoretically consider the thermal motion of nucleosomes along a DNA template. After an extensive analysis of available experimental data and theoretical modelling of two possible mechanisms I conclude that the ”corkscrew-motion” mechanism most consistently explains this biologically important process. In chapter 4 I demonstrate that DNA-spools (architectures in which DNA circumferentially winds on a cylindrical surface, or onto itself) show a remarkable ”kinetic inertness” that protects them from tension-induced disruption on experimentally and biologically relevant timescales (cf. Fig. 4.1 and Eq. 4.18). I show that the underlying model establishes a connection between the seemingly unrelated and previously unexplained force peaks in single molecule nucleosome and DNA-toroid stretching experiments. Finally in chapter 5 I show that toroidally confined DNA (found in viruses, DNAcondensates or sperm chromatin) undergoes a transition to a twisted, highly entangled state provided that the aspect ratio of the underlying torus crosses a certain critical value (cf. Eq. 5.6 and the phase diagram in Fig. 5.4). The presented mechanism could rationalize several experimental mysteries, ranging from entangled and supercoiled toroids released from virus capsids to the unexpectedly short cholesteric pitch in the (toroidaly wound) sperm chromatin. I propose that the ”topological encapsulation” resulting from our model may have some practical implications for the gene-therapeutic DNA delivery process.

Zellulärer Transport von Myelinproteinen

Während der Myelinbildung im zentralen Nervensystem (ZNS) umwinden Oligodendrozyten mit Ausläufern ihrer Plasmamembran mehrfach das Axon. Myelin ermöglicht die saltatorische Erregungsweiterleitung entlang der Axone und ist zudem für die Aufrechterhaltung der axonalen Integrität erforderlich (Edgar and Garbern, 2004). Ein Oligodendrozyt myelinisiert bis zu 40 Axonsegmente gleichzeitig, wodurch er in seiner aktivsten Myelinisierungsphase 5 bis 50 x 103 µm2 Membranfläche pro Tag produziert (Pfeiffer et al., 1993). Die vollständig ausgebildete Myelinscheide besteht aus Subdomänen mit charakteristischen Protein- und Lipidzusammensetzungen. Die Entwicklung und der Erhalt der komplexen Myelinmembran erfordert die kontinuierliche Kommunikation zwischen Neuronen und Glia-Zellen, die Koordination der Protein- und Lipidsynthese sowie angepasste intrazelluläre Sortier- und Transportwege der Myelinkomponenten. Über die molekularen Mechanismen, die zur Ausbildung des Myelins und seiner Domänen führen, ist bisher nicht sehr viel bekannt. Im Rahmen dieser Arbeit wurden Endo- und Exozytosemechanismen von Myelinproteinen analysiert. Dabei wurden drei Proteine untersucht, die in unterschiedlichen Subdomänen der Myelinmembran des ZNS lokalisiert sind. Das Hauptmyelinprotein Proteolipid Protein (PLP), das Myelin-assoziierte Glykoprotein (MAG) und das Myelin Oligodendrozyten Glykoprotein (MOG). Die Exozytose des Hauptmyelinproteins PLP erfolgt möglicherweise durch sekretorische Lysosomen (Trajkovic et al., 2006) und ist Ca2+-abhängig. Interessanterweise konnte gezeigt werden, dass PLP, MAG und MOG unterschiedlichen endosomalen Transportwegen und Sortierprozessen unterliegen. PLP wird über einen Clathrin-unabhängigen, MAG und MOG hingegen über einen Clathrin-abhängigen Mechanismus endozytiert. Zudem gelangen die Proteine zu unterschiedlichen endosomalen Zielkompartimenten und recyceln zu verschiedenen oligodendroglialen Membrandomänen. Diese Ergebnisse legen nahe, dass die endosomale Sortierung und das Recycling der Myelinproteine, die für die Bildung der Subdomänen erforderliche Umgestaltung der oligodendroglialen Plasmamembran unterstützen.

Atomic force microscopy of biomimetic systems

This thesis was driven by the ambition to create suitable model systems that mimic complex processes in nature, like intramolecular transitions, such as unfolding and refolding of proteins, or intermolecular interactions between different cell compo-nents. Novel biophysical approaches were adopted by employing atomic force mi-croscopy (AFM) as the main measurement technique due to its broad diversity. Thus, high-resolution imaging, adhesion measurements, and single-molecule force distance experiments were performed on the verge of the instrumental capabilities. As first objective, the interaction between plasma membrane and cytoskeleton, me-diated by the linker protein ezrin, was pursued. Therefore, the adsorption process and the lateral organization of ezrin on PIP2 containing solid-supported membranes were characterized and quantified as a fundament for the establishment of a biomimetic model system. As second component of the model system, actin filaments were coated on functionalized colloidal probes attached on cantilevers, serving as sensor elements. The zealous endeavor of creating this complex biomimetic system was rewarded by successful investigation of the activation process of ezrin. As a result, it can be stated that ezrin is activated by solely binding to PIP2 without any further stimulating agents. Additional cofactors may stabilize and prolong the active conformation but are not essentially required for triggering ezrin’s transformation into an active conformation. In the second project, single-molecule force distance experiments were performed on bis-loop tetra-urea calix[4]arene-catenanes with different loading rates (increase in force per second). These macromolecules were specifically designed to investigate the rupture and rejoining mechanism of hydrogen bonds under external load. The entangled loops of capsule-like molecules locked the unbound state of intramolecular hydrogen bonds mechanically, rendering a rebinding observable on the experimental time scale. In conjunction with Molecular Dynamics simulations, a three-well potential of the bond rupture process was established and all kinetically relevant parameters of the experiments were determined by means of Monte Carlo simulations and stochastic modeling. In summary, it can be stated that atomic force microscopy is an invaluable tool to scrutinize relevant processes in nature, such as investigating activation mechanisms in proteins, as shown by analysis of the interaction between F-actin and ezrin, as well as exploring fundamental properties of single hydrogen bonds that are of paramount interest for the complete understanding of complex supramolecular structures.

Fluorescence close to dielectric interfaces

The aim of the work was to study the correlation between the orientation and excited-state lifetimes of organic dyes close to dielectric interfaces. For this purpose, an experimental setup was designed and built, guiding the light through a prism in total internal reflection geometry. Fluorescence intensities and lifetimes for an ensemble of dye molecules were analyzed as a function of the excitation and detection polarizations. Working close to the total internal reflection angle, the differences between polarization combinations were enhanced. A classical electromagnetic model that assumes a chromophore as a couple of point-like electrical dipoles was developed. A numerical method to calculate the excitation and emission of dye molecules embedded in a multilayer system was implemented, by which full simulation of the time resolved fluorescence experiments was achieved. Free organic dyes and organic dyes covalently bound to polyelectrolyte chains were used. The polymer functionalization process avoided aggregation and provided control over the dyes position, within a few nanometers to the interface. Moreover, by varying the pH, the polymer chains could be deposited on different substrates with different conformations and the resulting fluorescence characteristics analyzed. Initially the fluorescence of organic dyes embedded in a polymer matrix was studied as a function of the distance between the fluorophores and the polymer-air interface. The non-radiative decay rate, vacuum decay rate and the relative angle between the excitation and emission dipoles of the chromophores could be determined. Different free organic dyes were deposited onto different dielectric spacers, as close as possible to the air-dielectric interface. Surprisingly, the fluorescence characteristics of dyes deposited onto polyelectrolyte layer were in good agreement with theoretical predictions of dyes in a polymer matrix, even when the layer was only 2 nm thick. When functionalized chains were deposited at low pH, on top of a polyelectrolyte spacer, the fluorescence had the characteristics of emitters embedded in a polymer matrix as well. Surface deposition at high pH showed an intermediate behaviour between emitters embedded in polymer and on top of the surface, in air. In general, for low pH values, the chains are deposited on a substrate in a train-like conformation. For high pH values, the chains are deposited in a loop-like conformation. As a consequence at low pH the functionalized polymer strongly interdigitates with the polyelectrolyte chains of the spacer, bringing most of the dyes inside the polymer. Thus, the fluorophores may experience the polymer as surrounding environment. On the other hand, for high pH values the dye-loaded chains adsorbed have a conformational arrangement of dense loops that extend away from the surface. Therefore many fluorophores experience the air as surrounding environment. Changing the spacer from polyelectrolyte to negatively charged silane produced contradictory results for lifetimes and intensities. The fluorescence intensities indicated the behaviour of emitters embedded in a polymer matrix, regardless of the pH value. On the other hand, for low pH values, the excited-state lifetimes showed that the emitters behaved as in air. For higher pH values, an intermediate behaviour between fluorophores located within and above of a dielectric film was observed. The poor agreement between theoretical and experimental data may be due to the simplified model utilized, by which the dipoles are assumed either in one side or in the other with respect to a geometrical air-dielectric interface. In the case when the dielectric film is constituted by the functionalized polymer chains themselves, reality is more complex and a different model may apply. Nevertheless, possible applications of the technique arise from a qualitative analysis.

Selektiv deblockierbare Diamino-D-Galactose-Scaffolds für die kombinatorische Synthese potentieller RNA-Liganden

Die Aufklärung der Schlüsselrolle der RNA in zahlreichen biologischen Prozessen, die sich aus ihren selektiven Wechselwirkungen mit anderen RNA-Molekülen, Proteinen, Peptiden bzw. Antibiotika ergibt, ist für die Wirkstoffforschung von großer Bedeutung. Die Aminoglycoside und Antibiotika, die durch eine Hemmung der Proteinbiosynthese schon seit längerem bekannt sind, dienen als Leitstrukuren für die Synthese von weiteren Wirkstoffen. Die meisten Aminoglycosid-Antibiotika beinhalten Aminozucker, die mit dem rn2-Desoxystreptamin-Gerüst verbunden sind. Die stereochemische Vielfalt der Substitutionsstellen für Amino- und Hydroxylgruppen in diesem Gerüst und deren beschränkte konformative Flexibilität bieten vielseitige Möglichkeiten, um potenzielle RNA-Liganden so zu gestalten, dass es zu einer spezifischen Erkennung von RNA-Strukturen kommen kann. Ein wichtiger Vertreter dieser Antibiotika, Neomycin B, von dessen Struktur die Entwicklung des Diaminogalactose-Templates abgeleitet wurde, wurde in dieser Arbeit als Leitstruktur gewählt. Die Synthese von Diaminogalactose-Scaffolds wurde zunächst in Lösung durchgeführt. Anschließend wurden die Bausteine 2 und 4 an einen polymeren Träger gebunden.rnNach Prüfung der orthogonalen Stabilität der Schutzgruppen wurde mit den Scaffolds 2 und 4 eine Bibliothek von 65 Verbindungen hergestellt. Mit 42 dieser Verbindungen wurden anschließend Zellassays im Rahmen des Sonderforschungsbereichs 579 (RNA-Liganden-Wechselwirkungen) durchgeführt, um ihre Cytotoxizität zu prüfen. Für einzelne Verbindungen konnten die optimalen Konzentrationen bestimmt werden, bei denen zukünftige Tests für die Tat/TAR Wechselwirkung ohne störende cytotoxische Effekte durchgeführt werden können.rn

The C-4-Dicarboxylate carriers DcuB and DctA of Escherichia coli: function as cosensors and topology

Das fakultativ anaerobe Enterobakterium Escherichia coli nutzt C4-Dicarboxylate sowohl unter aeroben als auch anaeroben Bedingungen als Kohlenstoff- und Energiequelle. Die Aufnahme der C4-Dicarboxylaten und die Energiekonservierung mittels Fumaratatmung wird durch das Zweikomponentensystem DcuSR reguliert. Die Sensorhistidinkinase DcuS und der nachgeschaltete Responseregulator DcuR aktivieren bei Verfügbarkeit von C4-Dicarboxylaten die Expression der Gene für den Succinat Transporter DctA, den anaeroben Fumarat/Succinat Antiporter DcuB, die Fumarase B sowie die Fumaratreduktase FrdABCD. Die Transportproteine DctA und DcuB wiederum regulieren die Expression der DcuSR-abhängigen Gene negativ. Fehlen von DctA oder DcuB resultiert bereits ohne Effektor in einer maximalen Expression von dctA bzw. dcuB. Durch gerichtete und ungerichtete Mutagenese wurde gezeigt, dass die Transportfunktion des Carriers DcuB unabhängig von seiner regulatorischen Funktion ist. DcuB kann daher als Cosensor des DcuSR Systems angesehen werden.rnUnter Verwendung von Reportergenfusionen von C-terminal verkürzten Konstrukten von DcuB mit der Alkalischen Phosphatase und der β-Galactosidase wurde die Topologie des Multitransmembranproteins DcuB bestimmt. Zusätzlich wurde die Zugänglichkeit bestimmter Aminosäurereste durch chemische Modifikation mit membran-durchlässigen und membran-undurchlässigen Thiolreagenzien untersucht. Die erhaltenen Ergebnisse deuten auf die Existenz eines tief in die Membran reichenden, hydrophilen Kanal hin, welcher zum Periplasma hin geöffnet ist. Mit Hilfe der Topologie-Studien, des Hydropathie-Blots und der Sekundärstruktur-Vorhersage wurde ein Modell des Carriers erstellt. DcuB besitzt kurze, periplasmatisch liegende Proteinenden, die durch 12 Transmembranhelices und zwei große hydrophile Schleifen jeweils zwischen TM VII/VIII und TM XI/XII verbunden sind. Die regulatorisch relevanten Reste K353, T396 und D398 befinden sich innerhalb von TM XI sowie auf der angrenzenden cytoplasmatischen Schleife XI-XII. Unter Berücksichtigung der strukturellen und funktionellen Aspekte wurde ein Regulationsmodell erstellt, welches die gemeinsam durch DcuB und DcuS kontrollierte C4-Dicarboxylat-abhängige Genexpression darstellt. rnDer Effekt von DctA und DcuSR auf die Expression einer dctA´-´lacZ Reportergenfusion und auf die aerobe C4-Dicarboxylat-Aufnahme wurde untersucht. In-vivo FRET-Messungen weisen auf eine direkte Wechselwirkung zwischen dem Carrier DctA und dem Sensor DcuS hin. Dieses Ergebnis stützt die Theorie der Regulation von DcuS durch C4-Dicarboxylate und durch die Cosensoren DctA bzw. DcuB mittels direkter Protein-Protein Interaktion.rn

Funktion der C 4-Dicarboxylat-Transporter DctA und DcuB als Co-Sensoren von DcuS in Escherichia coli

Escherichia coli kann C4-Dicarboxylate sowohl unter aeroben als auch unter anaeroben Bedingungen zur Energiekonservierung nutzen. Die Synthese der beteiligten Transporter und Enzyme wird auf der Transkriptionsebene durch das Zweikomponentensystem DcuSR reguliert. DcuS ist der Sensor für C4-Dicarboxylate. Der Antwortregulator DcuR wird von DcuS aktiviert und induziert die Expression des C4-Dicarboxylat-Transporters DctA unter aeroben Verhältnissen. Anaerob verstärkt DcuSR die Expression des Fumarat/Succinat-Antiporters DcuB, der Fumarase B und der Fumaratreduktase FrdABCD. DctA und DcuB agieren als Co-Sensoren von DcuS und üben einen negativen Effekt auf die Genexpression von dctA bzw. dcuB aus.rnIn dieser Arbeit wurde die Funktion von DctA und DcuB als Co-Sensoren von DcuS untersucht. Sowohl für DcuB als auch für DctA wurde eine direkte Protein-Protein-Interaktion mit DcuS über ein bakterielles Two-Hybrid System nachgewiesen. DcuS bildete ein Transporter-Sensor-Cluster mit DctA und DcuB. C-terminale Verkürzung und die Mutagenese einzelner Aminosäuren der C-terminalen Helix 8b von DctA führten zu einem Verlust der Interaktion mit DcuS. Mit dieser Interaktion gingen sowohl die regulatorische Funktion als auch die Transportfunktion der Punktmutante DctA-L414A verloren. Ein Verlust der Interaktion wurde ebenfalls zwischen einer konstitutiv aktiven DcuS-Mutante und wildtypischem DctA beobachtet. Ebenso zeigte sich eine partielle Reduktion der Interaktion von DcuS mit DctA, wenn DcuS nach der zweiten Transmembranhelix verkürzt wurde. Die Interaktion zwischen DcuS und DctA wurde durch den Effektor Fumarat modifiziert, ging aber nicht komplett verloren.rnDctA konnte in verschiedenen Plasmidsystemen überproduziert werden und bildete Homotrimere. Die Topologie von DctA wurde mit experimentellen und in silico Methoden aufgeklärt. DctA ähnelt der Struktur und Topologie des Aminosäuretransporters Glt aus Pyrococcus horikoshii. DctA besitzt acht Transmembranhelices mit einem cytosolischen N- und C-Terminus sowie zwei Haarnadelschleifen. Die Substratbindung findet höchstwahrscheinlich in den Haarnadelschleifen statt und der Transport erfolgt nach dem „alternating access“ Modell.rnAußerdem wurde die Funktion des Transporters YfcC untersucht. Das Gen yfcC wurde mit Schlüsselgenen des Acetatstoffwechsels co-transkribiert. In yfcC-Deletionsstämmen zeigte sich ein stammspezifischer Defekt bei Wachstum mit Acetat und Transport von Acetat.