TY - THES A1 - Horvat, Aleksandra T1 - Untersuchungen zur Signalwahrnehmung der Sensorkinase BvgS des BvgAS-Zwei-Komponentensystems aus Bordetella bronchiseptica und Struktur-Funktionsanalyse des Response Regulator-Proteins BvgA aus Bordetella holmesii T1 - Characterisation of signal perception of the BvgS sensorkinase of Bordetella bronchiseptica and molecular characterisation of the BvgA response regulator of Bordetella holmesii N2 - Die Histidin-Kinase BvgS des BvgAS-Zwei-Komponentensystems gehört zu den unorthodoxen Histidin-Kinasen, die im Gegensatz zu den klassischen Sensorkinasen durch eine komplexere Domänen-Struktur gekennzeichnet ist. Schon seit längerem ist bekannt, dass BvgS durch niedrige Temperaturen oder die Anwesenheit von chemischen Substanzen, wie Sulfationen oder Nikotinsäure inaktiviert wird. Zudem konnte in vitro gezeigt werden, dass die Autophosphorylierungs-Aktivität der BvgS Histidin-Kinase nach Inkubation mit oxidiertem Ubichinon inhibiert wird (Bock & Gross, 2002). Bislang ist weitgehend unklar, welche Bedeutung die zusätzlichen Domänen, wie die periplasmatische-, PAS- bzw. HPt-Domäne für die Signalwahrnehmung besitzen. Im Rahmen dieser Arbeit wurde deshalb nach Erstellung einer B. bronchiseptica spezifischen Genbank mit Hilfe des GAL4-Yeast Two-Hybrid (YTH) Systems nach Interaktionspartnern der einzelnen BvgS-Domänen gesucht. Nach dem Ausschluss von falsch-positiven Klonen und dem Durchlauf entsprechender Kontrollen konnten im YTH-System für die periplasmatische und die PAS-Domäne von BvgS insgesamt vier Interaktionspartner identifiziert werden. Für die HPt-Domäne konnte mit Hilfe des YTH-Systems kein möglicher Interaktionspartner gefunden werden. Als ein putativer Interaktionspartner der BvgS-PAS-Domäne wurde das BB0602-Protein identifiziert, das ein ATP-Bindeprotein darstellt, welches als Bestandteil eines ABC-Transport-System für den Transport von verzweigten Aminosäuren verantwortlich gemacht wird. Diese Interaktion konnte mittels eines GST-Pulldownassays bestätigt werden. Der biochemische Nachweis der übrigen identifizierten Protein-Interaktionen konnte im Rahmen dieser Arbeit nicht erbracht werden. Die Ergebnisse des YTH-Screenings deuten darauf hin, dass die Aktivität der BvgS Histidin-Kinase und damit die Virulenzgenexpression durch die An- bzw. Abwesenheit von verzweigten Aminosäuren beeinflusst werden könnte. Im Rahmen dieser Arbeit konnte die Relevanz der Interaktion zwischen der PAS-Domäne und dem ATP-Bindeprotein BB0602 nicht näher charakterisiert werden, so dass in Zukunft unter anderem die Konstruktion einer B. bronschiseptica bb0602-Deletionsmutante geplant ist, um somit mögliche Auswirkungen auf die Expression von bvg-abhängigen Genen zu beobachten. Ein weiteres Ziel dieser Arbeit lag in der Struktur-Funktionsanalyse des Response Regulators BvgA aus B. holmesii (BvgABH). Kürzlich konnte gezeigt werden, dass trotz der umfangreichen Sequenzkonservierung der BvgA-Proteine aus B. holmesii und B. pertussis, eine B. pertussis bvgA-Mutante nicht durch den bvgA-Lokus aus B. holmesii komplementiert werden konnte (Gerlach et al., 2004). Im Rahmen dieser Arbeit wurde ein hybrider Response Regulator BvgAfus konstruiert, der aus der Receiver- und Linker-Domäne des BvgABH-Proteins und der Output-Domäne von BvgABP zusammengesetzt ist. Voraussetzung hierfür war die Kenntnis der einzelnen Domänengrenzen und die Sequenz des Linker-Bereiches des Response Regulators BvgA aus B. pertussis (BvgABP), welche durch limitierte Proteolyse und massenspektrometrische Methoden identifiziert wurden (Bantscheff et al., 2000). Im Falle des hybriden Proteins konnte im Gegensatz zu BvgABH eine Bindung an BvgABP-abhängige Promotorsequenzen beobachtet werden. Zudem war BvgAfus in der Lage, die Expression BvgABP-abhängiger Gene in vivo zu induzieren. Allerdings war es in seiner Phosphorylierungseffizienz im Vergleich zum wildtypischen Response Regulator-Protein aus B. holmesii eingeschränkt. Die Ergebnisse deuten darauf hin, dass die wenigen Abweichungen zwischen den Aminosäuresequenzen der Output-Domänen dafür verantwortlich sind, dass das BvgABH-Protein die Funktion von BvgABP in vivo und in vitro nicht übernehmen kann. So unterscheiden sich die Output-Domänen der Response Regulatoren aus B. pertussis und B. holmesii in zehn Aminosäureaustauschen, wobei davon vier Aminosäuren innerhalb des Helix-Turn-Helix-Motives verändert sind. Um zu untersuchen, ob die unterschiedlichen DNA-Binde- und transkriptionsaktivierenden Eigenschaften von BvgABH im Besonderen auf diese Aminosäureunterschiede zurückzuführen sind, wurden mittels ortspezifischer Mutagenese die Aminosäuresequenz innerhalb des Helix-Turn-Helix-Motives an die Sequenz aus B. pertussis angeglichen. Das resultierende Protein BvgABH* zeigte eine dem wildtypischen BvgABH-Protein ähnliche Phosphorylierungseffizienz, war aber nicht in der Lage, BvgABP-abhängige Zielsequenzen spezifisch zu erkennen bzw. die Funktion des BvgABP-Proteins in vivo zu ersetzen. Dieses Ergebnis lässt vermuten, dass die wenigen Aminosäureunterschiede der Output-Domäne außerhalb der DNA-Binderegion zwar nicht im Zusammenhang mit der Phosphorylierungseffizienz stehen, jedoch die DNA-Bindeeigenschaften beeinflussen. N2 - The BvgS protein of the BvgAS two-component system belongs to the family of unorthodox histidine-kinases, which are characterized by a more complex domain-structure compared to the classical sensor proteins. Since a long time it is known that the activity of BvgS can be modulated by several external stimuli. At low temperature or in the presence of nicotinic acid or sulfate, the protein is inactivated in vivo and therefore the respective system is switched off under these conditions. Moreover, it has been shown that the incubation of BvgS with oxidized ubichinone had an inhibitory effect on the autophosphorylation activity of the kinase (Bock & Gross, 2002). So far, the relevance for the signal perception of the additional BvgS-domains, like the periplasmic, the PAS- or the HPt-domain is still unclear. Therefore in this work a self-constructed Bordetella bronchiseptica specific gene bank was screened with the periplasmic, the PAS- and the HPt-Domain of BvgS for protein-interactions in the GAL4-yeast two-hybrid (YTH) system. All together four putative protein-interactions were found in the case of the periplasmic and the PAS domain after exclusion of false-positive clones and after going through corresponding controls, while on the other hand no protein interaction could be detected for the HPt domain. Among the detected putative protein interactions of the PAS domain the protein BB0602 was identified as an ATP binding protein of an ABC transport system for branched chain amino acids. This interaction could also be verified by GST-pull down assay. The biochemical proof for the other protein interactions still remains to be done. The results of the YTH screening indicate that the activity of BvgS and therefore the virulence gene expression might be influenced by the presence or absence of branched chain amino acids. Among others characterization of a B. bronchiseptica bb0602 deletion mutant with respect to the possible effect on the expression of bvg-dependent genes will further elucidate the relevance of the detected protein interaction between the BvgS-PAS domain and the BB0602 protein. Another aim of this work was the structural and functional characterization of the response regulator BvgA of B. holmesii (BvgABH). Recently, it was shown that despite extensive sequence conservation between the response regulator BvgA of B. holmesii and BvgA of B. pertussis (BvgABP), the BvgABH protein is not able to replace the function of the BvgABP protein in vitro and in vivo (Gerlach et al., 2004). Therefore in this work a hybrid response regulator protein BvgAfus was constructed, which contains the receiver and the linker domain of BvgABH and the output domain of BvgABP. A Prerequisite for this experiment was the knowledge of domain borders and linker sequences of BvgABP, which have been identified by means of limited proteolysis in combination with mass spectrometric methods (Bantscheff et al., 2000). In contrast to the BvgABH protein, the hybrid response regulator BvgAfus showed binding to BvgABP-dependent promoter sequences. Additionally, BvgAfus was able to induce the expression of BvgABP-dependent genes in vivo. But compared to the wild-type protein BvgABH the hybrid response regulator BvgAfus was limited in its phosphorylation efficiency. These results indicate that the inability of BvgABH to complement BvgABP in B. pertussis is due to the small number of sequence variations present in its output domain. The output domains of BvgABH and BvgABP differ in ten amino acids of which four amino acid substitutions are located in the helix-turn-helix motif (HTH). To investigate whether the different binding and transcription activating properties of BvgABH are due to the sequence variations in the HTH, the sequence was adjusted as compared to BvgABP by means of site directed mutagenesis. The resulting protein BvgABH* showed similar phosphorylation efficiency compared to the wild-type protein BvgABH but no specific binding to BvgABP-dependent promoter sequences and was not able to replace BvgABP functionally in vivo. This result indicates that the few additional amino acid differences outside of the HTH present in the output domain of BvgABH which do not interfere much with the phosphorylation efficiency of the protein influence its DNA binding properties. The identification of further BvgABH regulated genes of B. holmesii and the characterization of BvgABH binding sites will help to further clarify the functional differences between the orthologous BvgA proteins of B. holmesii and B. pertussis. KW - Bordetella KW - Genregulation KW - Bordetella KW - Genregulation KW - Bordetella KW - gene regulation Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-21991 ER - TY - JOUR A1 - Klein-Hessling, Stefan A1 - Muhammad, Khalid A1 - Klein, Matthias A1 - Pusch, Tobias A1 - Rudolf, Ronald A1 - Flöter, Jessica A1 - Qureischi, Musga A1 - Beilhack, Andreas A1 - Vaeth, Martin A1 - Kummerow, Carsten A1 - Backes, Christian A1 - Schoppmeyer, Rouven A1 - Hahn, Ulrike A1 - Hoth, Markus A1 - Bopp, Tobias A1 - Berberich-Siebelt, Friederike A1 - Patra, Amiya A1 - Avots, Andris A1 - Müller, Nora A1 - Schulze, Almut A1 - Serfling, Edgar T1 - NFATc1 controls the cytotoxicity of CD8\(^{+}\) T cells JF - Nature Communications N2 - Cytotoxic T lymphocytes are effector CD8\(^{+}\) T cells that eradicate infected and malignant cells. Here we show that the transcription factor NFATc1 controls the cytotoxicity of mouse cytotoxic T lymphocytes. Activation of Nfatc1\(^{-/-}\) cytotoxic T lymphocytes showed a defective cytoskeleton organization and recruitment of cytosolic organelles to immunological synapses. These cells have reduced cytotoxicity against tumor cells, and mice with NFATc1-deficient T cells are defective in controlling Listeria infection. Transcriptome analysis shows diminished RNA levels of numerous genes in Nfatc1\(^{-/-}\) CD8\(^{+}\) T cells, including Tbx21, Gzmb and genes encoding cytokines and chemokines, and genes controlling glycolysis. Nfatc1\(^{-/-}\), but not Nfatc2\(^{-/-}\) CD8\(^{+}\) T cells have an impaired metabolic switch to glycolysis, which can be restored by IL-2. Genome-wide ChIP-seq shows that NFATc1 binds many genes that control cytotoxic T lymphocyte activity. Together these data indicate that NFATc1 is an important regulator of cytotoxic T lymphocyte effector functions. KW - cytotoxic T cells KW - lymphocyte activation KW - signal transduction KW - gene regulation KW - immune cells KW - NFATc1 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-170353 VL - 8 IS - 511 ER - TY - JOUR A1 - Gaubatz, Stefan A1 - Esterlechner, Jasmina A1 - Reichert, Nina A1 - Iltzsche, Fabian A1 - Krause, Michael A1 - Finkernagel, Florian T1 - LIN9, a Subunit of the DREAM Complex, Regulates Mitotic Gene Expression and Proliferation of Embryonic Stem Cells JF - PLoS ONE N2 - The DREAM complex plays an important role in regulation of gene expression during the cell cycle. We have previously shown that the DREAM subunit LIN9 is required for early embryonic development and for the maintenance of the inner cell mass in vitro. In this study we examined the effect of knocking down LIN9 on ESCs. We demonstrate that depletion of LIN9 alters the cell cycle distribution of ESCs and results in an accumulation of cells in G2 and M and in an increase of polyploid cells. Genome-wide expression studies showed that the depletion of LIN9 results in downregulation of mitotic genes and in upregulation of differentiation-specific genes. ChIP-on chip experiments showed that mitotic genes are direct targets of LIN9 while lineage specific markers are regulated indirectly. Importantly, depletion of LIN9 does not alter the expression of pluripotency markers SOX2, OCT4 and Nanog and LIN9 depleted ESCs retain alkaline phosphatase activity. We conclude that LIN9 is essential for proliferation and genome stability of ESCs by activating genes with important functions in mitosis and cytokinesis. KW - cell cycle KW - cell division KW - cell differentation KW - DNA-binding proteins KW - gene expression KW - gene regulation KW - gene targeting KW - microarrays KW - pluripotency Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-96922 ER - TY - JOUR A1 - Rohmer, Carina A1 - Dobritz, Ronja A1 - Tuncbilek-Dere, Dilek A1 - Lehmann, Esther A1 - Gerlach, David A1 - George, Shilpa Elizabeth A1 - Bae, Taeok A1 - Nieselt, Kay A1 - Wolz, Christiane T1 - Influence of Staphylococcus aureus strain background on Sa3int phage life cycle switches JF - Viruses N2 - Staphylococcus aureus asymptomatically colonizes the nasal cavity of mammals, but it is also a leading cause of life-threatening infections. Most human nasal isolates carry Sa3 phages, which integrate into the bacterial hlb gene encoding a sphingomyelinase. The virulence factor-encoding genes carried by the Sa3-phages are highly human-specific, and most animal strains are Sa3 negative. Thus, both insertion and excision of the prophage could potentially confer a fitness advantage to S. aureus. Here, we analyzed the phage life cycle of two Sa3 phages, Φ13 and ΦN315, in different phage-cured S. aureus strains. Based on phage transfer experiments, strains could be classified into low (8325-4, SH1000, and USA300c) and high (MW2c and Newman-c) transfer strains. High-transfer strains promoted the replication of phages, whereas phage adsorption, integration, excision, or recA transcription was not significantly different between strains. RNASeq analyses of replication-deficient lysogens revealed no strain-specific differences in the CI/Mor regulatory switch. However, lytic genes were significantly upregulated in the high transfer strain MW2c Φ13 compared to strain 8325-4 Φ13. By transcriptional start site prediction, new promoter regions within the lytic modules were identified, which are likely targeted by specific host factors. Such host-phage interaction probably accounts for the strain-specific differences in phage replication and transfer frequency. Thus, the genetic makeup of the host strains may determine the rate of phage mobilization, a feature that might impact the speed at which certain strains can achieve host adaptation. KW - phage KW - virulence KW - induction KW - gene regulation KW - Staphylococcus KW - hemolysin Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-297209 SN - 1999-4915 VL - 14 IS - 11 ER - TY - JOUR A1 - Morton, Charles Oliver A1 - Fliesser, Mirjam A1 - Dittrich, Marcus A1 - Müller, Tobias A1 - Bauer, Ruth A1 - Kneitz, Susanne A1 - Hope, William A1 - Rogers, Thomas Richard A1 - Einsele, Hermann A1 - Löffler, Jürgen T1 - Gene Expression Profiles of Human Dendritic Cells Interacting with Aspergillus fumigatus in a Bilayer Model of the Alveolar Epithelium/Endothelium Interface N2 - The initial stages of the interaction between the host and Aspergillus fumigatus at the alveolar surface of the human lung are critical in the establishment of aspergillosis. Using an in vitro bilayer model of the alveolus, including both the epithelium (human lung adenocarcinoma epithelial cell line, A549) and endothelium (human pulmonary artery epithelial cells, HPAEC) on transwell membranes, it was possible to closely replicate the in vivo conditions. Two distinct sub-groups of dendritic cells (DC), monocyte-derived DC (moDC) and myeloid DC (mDC), were included in the model to examine immune responses to fungal infection at the alveolar surface. RNA in high quantity and quality was extracted from the cell layers on the transwell membrane to allow gene expression analysis using tailored custom-made microarrays, containing probes for 117 immune-relevant genes. This microarray data indicated minimal induction of immune gene expression in A549 alveolar epithelial cells in response to germ tubes of A. fumigatus. In contrast, the addition of DC to the system greatly increased the number of differentially expressed immune genes. moDC exhibited increased expression of genes including CLEC7A, CD209 and CCL18 in the absence of A. fumigatus compared to mDC. In the presence of A. fumigatus, both DC subgroups exhibited up-regulation of genes identified in previous studies as being associated with the exposure of DC to A. fumigatus and exhibiting chemotactic properties for neutrophils, including CXCL2, CXCL5, CCL20, and IL1B. This model closely approximated the human alveolus allowing for an analysis of the host pathogen interface that complements existing animal models of IA. KW - aspergillus fumigatus KW - gene expression KW - immune receptors KW - immune response KW - denritic cells KW - B cell receptors KW - gene regulation KW - RNA extraction Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-112893 ER - TY - JOUR A1 - Riedel, Alice A1 - Mofolo, Boitumelo A1 - Avota, Elita A1 - Schneider-Schaulies, Sibylle A1 - Meintjes, Ayton A1 - Mulder, Nicola A1 - Kneitz, Susanne T1 - Accumulation of Splice Variants and Transcripts in Response to PI3K Inhibition in T Cells JF - PLoS ONE N2 - Background Measles virus (MV) causes T cell suppression by interference with phosphatidylinositol-3-kinase (PI3K) activation. We previously found that this interference affected the activity of splice regulatory proteins and a T cell inhibitory protein isoform was produced from an alternatively spliced pre-mRNA. Hypothesis Differentially regulated and alternatively splice variant transcripts accumulating in response to PI3K abrogation in T cells potentially encode proteins involved in T cell silencing. Methods To test this hypothesis at the cellular level, we performed a Human Exon 1.0 ST Array on RNAs isolated from T cells stimulated only or stimulated after PI3K inhibition. We developed a simple algorithm based on a splicing index to detect genes that undergo alternative splicing (AS) or are differentially regulated (RG) upon T cell suppression. Results Applying our algorithm to the data, 9% of the genes were assigned as AS, while only 3% were attributed to RG. Though there are overlaps, AS and RG genes differed with regard to functional regulation, and were found to be enriched in different functional groups. AS genes targeted extracellular matrix (ECM)-receptor interaction and focal adhesion pathways, while RG genes were mainly enriched in cytokine-receptor interaction and Jak-STAT. When combined, AS/RG dependent alterations targeted pathways essential for T cell receptor signaling, cytoskeletal dynamics and cell cycle entry. Conclusions PI3K abrogation interferes with key T cell activation processes through both differential expression and alternative splicing, which together actively contribute to T cell suppression. KW - T cells KW - gene regulation KW - alternative splicing KW - measles virus KW - T cell receptors KW - reverse transcriptase-polymerase chain reaction KW - cell cycle and cell division KW - TCR signaling cascade Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-130335 VL - 8 IS - 2 ER -