Universität Stuttgart
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Item Open Access Ausbreitungsmechanismen(1993) Kull, UlrichEine Population einer Art lebt zu einem vorgegebenen Zeitpunkt in einem bestimmten Lebensgebiet, dem Areal dieser Population. Infolge einer Zunahme der Populationsgröße oder auch aus umweltbedingten Gründen wie z.B. Veränderungen klimatischer Faktoren, Zerstörung von Lebensraum, kann es zu einer Ausbreitung oder Wanderung kommen. Der Ausbreitung dienen verschiedene Ausbreitungsmechanismen, die insbesondere bei festsitzenden Lebewesen von großer Bedeutung sind.Item Open Access Specific DNMT3C flanking sequence preferences facilitate methylation of young murine retrotransposons(2024) Dossmann, Leonie; Emperle, Max; Dukatz, Michael; de Mendoza, Alex; Bashtrykov, Pavel; Jeltsch, AlbertThe DNA methyltransferase DNMT3C appeared as a duplication of the DNMT3B gene in muroids and is required for silencing of young retrotransposons in the male germline. Using specialized assay systems, we investigate the flanking sequence preferences of DNMT3C and observe characteristic preferences for cytosine at the -2 and -1 flank that are unique among DNMT3 enzymes. We identify two amino acids in the catalytic domain of DNMT3C (C543 and V547) that are responsible for the DNMT3C-specific flanking sequence preferences and evolutionary conserved in muroids. Reanalysis of published data shows that DNMT3C flanking preferences are consistent with genome-wide methylation patterns in mouse ES cells only expressing DNMT3C. Strikingly, we show that CpG sites with the preferred flanking sequences of DNMT3C are enriched in murine retrotransposons that were previously identified as DNMT3C targets. Finally, we demonstrate experimentally that DNMT3C has elevated methylation activity on substrates derived from these biological targets. Our data show that DNMT3C flanking sequence preferences match the sequences of young murine retrotransposons which facilitates their methylation. By this, our data provide mechanistic insights into the molecular co-evolution of repeat elements and (epi)genetic defense systems dedicated to maintain genomic stability in mammals.Item Open Access Item Open Access Identifizierung neuer Proteine des Polyphosphat Granulumkomplexes von Ralstonia eutropha H16(2017) Tumlirsch, Tony; Jendrossek, Dieter (Prof. Dr.)Item Open Access The natural breakup length of a steady capillary jet : application to serial femtosecond crystallography(2021) Gañán-Calvo, Alfonso M.; Chapman, Henry N.; Heymann, Michael; Wiedorn, Max O.; Knoska, Juraj; Gañán-Riesco, Braulio; López-Herrera, José M.; Cruz-Mazo, Francisco; Herrada, Miguel A.; Montanero, José M.; Bajt, SašaOne of the most successful ways to introduce samples in Serial Femtosecond Crystallography has been the use of microscopic capillary liquid jets produced by gas flow focusing, whose length-to-diameter ratio and velocity are essential to fulfill the requirements of the high pulse rates of current XFELs. In this work, we demonstrate the validity of a classical scaling law with two universal constants to calculate that length as a function of the liquid properties and operating conditions. These constants are determined by fitting the scaling law to a large set of experimental and numerical measurements, including previously published data. Both the experimental and numerical jet lengths conform remarkably well to the proposed scaling law. We show that, while a capillary jet is a globally unstable system to linear perturbations above a critical length, its actual and shorter long-term average intact length is determined by the nonlinear perturbations coming from the jet breakup itself. Therefore, this length is determined solely by the properties of the liquid, the average velocity of the liquid and the flow rate expelled. This confirms the very early observations from Smith and Moss 1917, Proc R Soc Lond A Math Phys Eng, 93, 373, to McCarthy and Molloy 1974, Chem Eng J, 7, 1, among others, while it contrasts with the classical conception of temporal stability that attributes the natural breakup length to the jet birth conditions in the ejector or small interactions with the environment.Item Open Access Microarray and molecular genetic analysis of aberrant splicing in human drug metabolizing cytochromes P450 CYP2D6 and CYP2B6(2008) Hofmann, Marco Hans; Schmid, Rolf (Prof. Dr.)This study was devoted to the detection of alternative splicing within the Cytochrome P450 enzymes 2D6 and 2B6, mapping of the most common splice variants and to draw connections to certain single nucleotide polymorphisms (SNPs) and alleles. For both enzymes a splicing sensitive microarray was developed. The microarray was produced and optimized in all steps including the oligonucleotide probe design, microarray processing and target preparation, optimization of hybridization conditions and the development of a new data quantification method for the used probe design. For the developed splicing platform a design was chosen based on 5 different probes. Within the CYP2D6 gene it was known that the SNP 2988G>A (allele *41) in intron 6 shifts splicing towards a variant lacking exon 6, what explains the intermediate phenotype within allele *41. The splicing platform verified this splicing aberration in allele *41. Using the microarry specific splicing patterns were monitored in human liver tissue within the most common alleles of CYP2D6 *1, *2, *4 and *41. It could be observed that within mRNA from allele *41 carriers additionally to the known transcript variant, which is lacking exon 6, total or partial retention of intron 5 and 6 was enhanced. Transcript patterns of CYP2D6*1 and *2 were similar with 5 times higher amount of the full functional transcript (NP), including all nine exons, compared to allele *41. The splicing array showed to be a valuable tool not only for detection of splicing variants in human liver tissue but additionally for detection for allele specific splicing patterns. The existence of highly homologous Cytochrome P450 pseudogenes, which in some cases, as in CYP2D7 also express alternative splicing variants, results in a major problem of interpreting the data from splicing arrays. The developed splicing platform is the first existing array with which gene and pseudogene specific transcript patterns can be monitored individually. The microarray platform can be easily transferred to other genes as shown for the second gene CYP2B6. Alternative splicing in this gene was so far only reported descriptive. CYP2B6 is a polymorphic human drug metabolizing cytochrome P450 with clinical relevance for several drug substrates including cyclophosphamide, bupropion and efavirenz. The common allele CYP2B6*6 [c. 516G>T, Q172H and c.785A>G, K262R] has previously been associated with lower expression in human liver and with increased plasma levels of efavirenz in HIV patients, but the molecular mechanism has remained unclear. With the developed splicing array for CYP2B6 allele specific splicing patterns were observed comparing CYP2B6*6 and CYP2B6*1. This lead to the idea that alternative splicing might play an important role in allele *6. This was investigated in more detail using RNA originating from well-documented human liver tissue. Analysis of mRNA in this tissue demonstrated that additional unknown splicing variants exist (SV8, SV7, SV9). Investigations in human liver tissue using RT-PCR and sequencing showed that the most common transcript in CYP2B6*6 was not the normal transcript (NP) but an alternative splicing transcript lacking exons 4 to 6 (SV1). SV1 was tightly associated with the allele*6 and apparently also with the rare variant c.777C>A (CYP2B6*3). The observations lead to the assumptions that alternative splicing might explain the decreased function observed in allele CYP2B6*6. Further investigations in this direction were performed by cloning CYP2B6 minigene constructs including all nine exons and additional intronic regions. Minigenes carrying the single c.785A>G polymorphism or the rare c.777C>A variant resulted in normal and intermediate expression phenotypes, respectively. In conclusion, the mechanism of the common allele*6 involves predominantly a pretranslational mechanism resulting in decreased enzyme expression. Aberrant splicing is leading to reduce functional mRNA, protein and activity. These results establish the SNP c.516G>T, a nonsynonymous exonic mutation, as the causal sequence variation for severely decreased expression and function associated with CYP2B6*6. This work emphasizes the role of SNPs in non-consensus splicing elements such as exonic and intronic splicing enhancers as well as the clinical relevance of alternative splicing in context of adverse drug reactions. In both investigated genes CYP2D6 as well as in CYP2B6 there exists a common allele (CYP2D6*41 and CYP2B6*6, respectively) in which aberrant splicing results in reduced amounts of functional transcript, reduced amount of protein and enzyme activity. The findings establishes the SNP c.516G>T as the causal sequence variation that can now be reliably used in pharmacogenetic studies in various clinical settings including prediction of drug plasma concentration, toxicity, drug effectiveness and dose adjustment.Item Open Access Mechanistic insights into the allosteric regulation of the Clr4 protein lysine methyltransferase by autoinhibition and automethylation(2020) Khella, Mina S.; Bröhm, Alexander; Weirich, Sara; Jeltsch, AlbertClr4 is a histone H3 lysine 9 methyltransferase in Schizosaccharomyces pombe that is essential for heterochromatin formation. Previous biochemical and structural studies have shown that Clr4 is in an autoinhibited state in which an autoregulatory loop (ARL) blocks the active site. Automethylation of lysine residues in the ARL relieves autoinhibition. To investigate the mechanism of Clr4 regulation by autoinhibition and automethylation, we exchanged residues in the ARL by site-directed mutagenesis leading to stimulation or inhibition of automethylation and corresponding changes in Clr4 catalytic activity. Furthermore, we demonstrate that Clr4 prefers monomethylated (H3K9me1) over unmodified (H3K9me0) histone peptide substrates, similar to related human enzymes and, accordingly, H3K9me1 is more efficient in overcoming autoinhibition. Due to enzyme activation by automethylation, we observed a sigmoidal dependence of Clr4 activity on the AdoMet concentration, with stimulation at high AdoMet levels. In contrast, an automethylation-deficient mutant showed a hyperbolic Michaelis–Menten type relationship. These data suggest that automethylation of the ARL could act as a sensor for AdoMet levels in cells and regulate the generation and maintenance of heterochromatin accordingly. This process could connect epigenome modifications with the metabolic state of cells. As other human protein lysine methyltransferases (for example, PRC2) also use automethylation/autoinhibition mechanisms, our results may provide a model to describe their regulation as well.Item Open Access Die HECT-Ligase Hul5, eine neue Komponente der ER-assoziierten Proteindegradation(2007) Kohlmann, Sonja; Wolf, Dieter H. (Prof. Dr.)Die meisten sekretorischen Proteine der eukaryontischen Zellen erreichen durch das endoplasmatische Retikulum (ER) den sekretorischen Signalweg. Sie gelangen vom Zytoplasma durch einen Kanal in der ER-Membran in das ER, wo sie ihre native Konformation erhalten. Das ER enthält ein strenges Qualitätskontrollsystem, welches fehlgefaltete Proteine erkennt, im ER zurückhält und letztendlich der ER-assoziierten Degradation (ERAD) zuführt. Die ER-Qualitätskontrolle und die ER-assoziierte Degradation sind eng miteinander verknüpft, und werden unter der Bezeichnung ER-Qualitätskontrolle und assoziierte Degradation (ERQD) zusammengefasst. Die ERQD ist von der Hefe bis hin zum Menschen ein hoch konservierter Prozess. Aus diesem Grund wird die Hefe Saccharomyces cerevisiae als Modellorganismus zur Erforschung solcher sogenannter „housekeeping“ Prozesse genutzt. In dieser Arbeit wurden durch einen genomweiten Screen neue Komponenten der ER-assoziierten Degradation identifiziert. Für diesen Screen wurden die EUROSCARF Hefe-Deletionsbank und das Screeningsubstrat Sec61-2L verwendet. Die Deletionsbank besteht aus etwa 5000 diploiden S. cerevisiae Stämmen mit je einer homozygoten Einfachdeletion. Bei dem Screeningsubstrat Sec61-2L handelt es sich um das nicht glykosylierte, mutierte Translokonprotein Sec61-2 und einer C-terminalen zytosolischen Fusion mit der 3-Isopropylmalat-Dehydrogenase (Leu2). Das für Sec61-2L kodierende Plasmid wurde in die leu2-auxotrophen Deletionsstämme transformiert und der Wachstumsphänotyp bei 38° auf Leucin-defizientem Medium getestet. Aufgrund der Punktmutation faltet sich Sec61-2 bei 38°C in einer Art und Weise, dass es der ER-Degradation unterliegt. Nur wenn Sec61-2L stabil vorliegt, also in Deletionsstämmen mit einem Defekt in der Erkennung oder der Degradation des fehlgefalteten Sec61-2L, ist ein Wachstum auf Leucin-defizientem Medium möglich. Auf diese Weise konnten über 40 bisher unbekannte, potentielle Komponenten der ER-Qualitätskontrolle und ER-assoziierten Degradation identifiziert werden. Unter anderem wurde durch diesen genomischen Screen die E4-Ligase Hul5 als Komponente des ERAD für dieses nicht glykosylierte Substrat gefunden. Des Weiteren war bereits durch einen entsprechenden Screen mit dem Substrat CTL* bekannt, dass Hul5 auch am Abbau dieses glykosylierten ERAD-Substrats beteiligt ist. In der vorliegenden Arbeit wurde nachgewiesen, dass für den vollständigen Abbau der ERAD-Substrate Sec61-2Lmyc und CTL*myc die katalytische Funktion der E4-Ligase Hul5 benötigt wird. Außerdem wurde gezeigt, dass der Abbau der Substrate Sec61-2Lmyc und CTL*myc im Wildtypstamm sowie in der HUL5 Deletionsmutante am N-Terminus einsetzt und über definierte Zwischenprodukte verläuft. Im Wildtypstamm kann auf diese Weise der Abbau der Substrate vollständig verlaufen. Im Gegensatz dazu erfolgt in der HUL5 Deletionsmutante ein Abbruch der Degradation am Proteasom, was zu einer Akkumulation der C-terminalen Abbaufragmente truncSec61-2Lmyc und truncCTL*myc führt. Des Weiteren wurde gezeigt, dass für den Abbau des N-terminalen Anteils von CTL*myc keine Extraktion des Proteins aus der ER-Membran notwendig ist. Demzufolge muß der N-Terminus von CTL*myc durch die ER-Membran in das Zytosol der Zelle ragen, wo die Ubiquitinierung und die Degradation des Substrats einsetzen. Außerdem wurde gefunden, dass auch das Proteasom an der Extraktion von CTL*myc aus dem ER beteiligt ist. Es ist bekannt, dass die E4-Ligase Hul5 gemeinsam mit dem deubiquitinierenden Enzym Ubp6 und dem Ubiquitin-konjugierenden Enzym Ubc4 den Abbau anderer proteasomaler Substrate regulieren kann. In dieser Arbeit wurde gezeigt, dass die Degradation des ERAD-Substrats CTL*myc durch Hul5, jedoch nicht durch Ubp6 und Ubc4 beeinflusst wird. Dieses Ergebnis gibt Hinweise auf weitere mit Hul5 agierende deubiquitinierende und Ubiquitin-konjugierende Enzyme.Item Open Access Arachidonovaja kislota obratimo blokiruet vysokopronicaemye mežkletočnye kontakty(1994) Hülser, Dieter F.; Zempel, Günther; Reuss, Bernhard; Suhr, Dierk; Sarovskaja, Julija J.; Murav'eva, O. V.; Dunina-Barkovskaja, Antonina; Margolis, Leonid B.The effect of arachidonic on intercellular coupling via gap junctions has been studied in BICR/M1R k cells - a mammary tumor cell line of the Marshall ratt. Arachidonic acid is shown to reversibly block both ionic and dye coupling in a dose-dependent manner. The cells recoupled after the washout with either serum- or albumin (essentially fatty acid-free)-containing solution. The intercellular pH decreased from 7,2 to 7,0 after arachidonic acid treatment; the same pH shift in the absence of arachidonic acid, however, had no effect on the junctional permeability. Flow cytometric measurments revealed an arachidonic acid-induced increase of the cytoplasmic free Ca 2+ concentration which was also reversible upon albumin treatment. Intracellular Ca 2+ or H+ are unlikely to be involved in the mechanism of the arachidonic acid effect on intercellular coupling: high resolution measurments using double whole-cell technique also show reversible blockage of the junctional conductance in the presence of arachidonic acid while the pipette solution was buffered with 10 mM HEPES and 10 mM EGTA to clamp intracellular calcium and proton concentrations. We suggest that arachiconic acid directly affects the gap junction channels, probably interfering with the lipid-protein interactions.Item Open Access Characterization of novel proteins involved in catabolite degradation of fructose-1,6-bisphosphatase in saccharomyces cerevisiae(2006) Pfirrmann, Thorsten; Wolf, Dieter (Prof. Dr.)Glycolysis and gluconeogenesis are reciprocally controlled central metabolic pathways in cells. Catabolite degradation of fructose-1,6-bisphosphatase (FBPase) is a key regulatory step, when Saccharomyces cerevisiae cells switch from anabolic gluconeogenesis to catabolic glycolysis. Addition of glucose to cells growing on a non-fermentable carbon source causes FBPase phosphorylation resulting in a decrease of enzymatic activity. This is followed by a proteolytic breakdown of the enzyme via the ubiquitin-proteasome system with a half-life of 20-30 min. In a genome wide screen nine so called gid mutants (glucose induced degradation deficient) defective in proteasome-dependent catabolite degradation of FBPase were identified. Analysis of Gid2 revealed that this protein is a part of a soluble, cytosolic protein complex with a molecular mass of at least 600kDa (Regelmann et al., 2003). The work of this thesis focuses on the analysis of the novel Gid proteins and their possible role in a higher molecular mass protein complex. To be able to detect Gid proteins immunologically, functional chromosomally HA eptitope tagged versions of Gid5, Gid6, Gid7, Gid8 and Gid9 proteins were generated. Using step glycerol gradient centrifugation it could be shown that Gid5/Vid28, Gid7, Gid8 and Gid9 are also components of a higher molecular mass complex of about 600kDa. Gid1/Vid30, Gid/Ubc8 and Gid4/Vid24 exhibit a sedimentation profile of lower molecular mass slightly overlapping with 600kDa aminopeptidase I. Gid6/Ubp14 is only present in its monomeric form. Use of Gid7 as a bait protein in a co-immunoprecipitation experiment, led to the identification of Gid1/Vid30, Gid2, Gid4/Vid24, Gid5/Vid28, Gid7, Gid8 and Gid9 as interacting components. The protein Gid6/Ubp14 is not part of this protein complex. The direct interaction of Gid4 with Gid5 could be shown via the two hybrid method. Expression profiles on ethanol or glucose of Gid1, Gid2, Gid5, Gid6, Gid7, Gid8 and Gid9 were similar. Gid4/Vid24 was not expressed on ethanol but appears when cells are treated with glucose. As found for Gid3/Ubc8 (Schüle et al., 2000), Gid4/Vid24 seems to disappear during incubation on glucose in a time-dependent fashion. Fructose-1,6-bisphosphatase was found to interact with Gid1 and Gid7 protein. As shown for GID2 (Regelmann et al., 2003) deletion of GID1 and GID7 leads to a block in fructose-1,6-bisphosphatase polyubiquitination. This shows that Gid proteins are directly involved in the ubiquitination process which preceeds proteasome degradation. Two discovered short RING domains in Gid2 and Gid9 (ShRING domains) as well as the discovery of 5 WD40 domains within Gid7 suggest a role of the Gid complex as a novel E3 ubiquitin ligase. The targeted mutation of conserved cysteine residues within the shRING domain of Gid2 could support this theory. Biochemical and molecular methods were used to identify the localization of Gid1, Gid6, Gid7 and Gid8. Interestingly all four Gid proteins were found to be localized in the nucleus. The direct interaction of FBPase with these Gid proteins raised the question of whether FBPase itself had a function in the nucleus of the cell or not. To investigate this question GFP-fusions with FBPase were constructed and localisation studies were performed. An increasing signal of FBPase within the nucleus after onset of catabolite degradation gave proof of the existence of this enzyme in the nucleus as well. Several mutants known to have a defect in nuclear import were tested for the catabolite degradation of FBPase. The protein kinaseA pathway was shown to be the signal transduction pathway triggering FBPase degradation. This led to the discovery of novel putative phosphorylation sites within FBPase by bioinformatics.