@unpublished{LoefflerMayerTrujilloVieraetal.2018, author = {L{\"o}ffler, Mona C. and Mayer, Alexander E. and Trujillo Viera, Jonathan and Loza Valdes, Angel and El-Merahib, Rabih and Ade, Carsten P. and Karwen, Till and Schmitz, Werner and Slotta, Anja and Erk, Manuela and Janaki-Raman, Sudha and Matesanz, Nuria and Torres, Jorge L. and Marcos, Miguel and Sabio, Guadalupe and Eilers, Martin and Schulze, Almut and Sumara, Grzegorz}, title = {Protein kinase D1 deletion in adipocytes enhances energy dissipation and protects against adiposity}, series = {The EMBO Journal}, journal = {The EMBO Journal}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-176093}, year = {2018}, abstract = {Nutrient overload in combination with decreased energy dissipation promotes obesity and diabetes. Obesity results in a hormonal imbalance, which among others, activates G-protein coupled receptors utilizing diacylglycerol (DAG) as secondary messenger. Protein kinase D1 (PKD1) is a DAG effector which integrates multiple nutritional and hormonal inputs, but its physiological role in adipocytes is unknown. Here, we show that PKD1 promotes lipogenesis and suppresses mitochondrial fragmentation, biogenesis, respiration, and energy dissipation in an AMP-activated protein kinase (AMPK)-dependent manner. Moreover, mice lacking PKD1 in adipocytes are resistant to diet-induced obesity due to elevated energy expenditure. Beiging of adipocytes promotes energy expenditure and counteracts obesity. Consistently, deletion of PKD1 promotes expression of the β3-adrenergic receptor (ADRB3) in a CCAAT/enhancerbinding protein (C/EBP)-α and δ-dependent manner, which leads to the elevated expression of beige markers in adipocytes and subcutaneous adipose tissue. Finally, deletion of PKD1 in adipocytes improves insulin sensitivity and ameliorates liver steatosis. Thus, loss of PKD1 in adipocytes increases energy dissipation by several complementary mechanisms and might represent an attractive strategy to treat obesity and its related complications.}, language = {en} } @phdthesis{Spieler2021, author = {Spieler, Valerie}, title = {Bioinspired drug delivery of interleukin-4}, doi = {10.25972/OPUS-19359}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-193590}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Chronic inflammatory diseases such as rheumatoid arthritis, type 2 diabetes and cardiovascular diseases, are associated with the homeostatic imbalance of one of several physiological systems combined with the lack of spontaneous remission, which causes the disease to persevere throughout patients' lives. The inflammatory response relies mainly on tissue-resident, pro-inflammatory M1 type macrophages and, consequently, a chance for therapeutic intervention lies in driving macrophage polarization towards the anti-inflammatory M2 phenotype. Therefore, anti-inflammatory cytokines that promote M2 polarization, including interleukin-4 (IL4), have promising therapeutic potential. Unfortunately, their systemic use is hampered by a short serum half-life and dose-limiting toxicity. On the way towards cytokine therapies with superior safety and efficacy, this thesis is focused on designing bioresponsive delivery systems for the anti-inflammatory cytokine IL4. Chapter 1 describes how anti-inflammatory cytokines are tightly regulated in chronic, systemic inflammation as in rheumatoid arthritis but also in acute, local inflammation as in myocardial infarction. Both diseases show a characteristic progression during which anti-inflammatory cytokine delivery is of variable benefit. A conventional, passive drug delivery system is unlikely to release the cytokines such that the delivery matches the dynamic course of the (patho-)physiological progress. This chapter presents a blueprint for active drug delivery systems equipped with a 24/7 inflammation detector that continuously senses for matrix metalloproteinases (MMP) as surrogate markers of the disease progress and responds by releasing cytokines into the affected tissues at the right time and place. Because they are silent during phases of low disease activity, bioresponsive depots could be used to treat patients in asymptomatic states, as a preventive measure. The drug delivery system only gets activated during flares of inflammation, which are then immediately suppressed by the released cytokine drug and could prevent the steady damage of subclinical chronic inflammation, and therefore reduce hospitalization rates. In a first proof of concept study on controlled cytokine delivery (chapter 2), we developed IL4-decorated particles aiming at sustained and localized cytokine activity. Genetic code expansion was deployed to generate muteins with the IL4's lysine 42 replaced by two different unnatural amino acids bearing a side chain suitable for click chemistry modification. The new IL4 muteins were thoroughly characterized to ensure proper folding and full bioactivity. Both muteins showed cell-stimulating ability and binding affinity to IL4 receptor alpha similar to those of wild type IL4. Copper-catalyzed (CuAAC) and strain-promoted (SPAAC) azide-alkyne cycloadditions were used to site-selectively anchor IL4 to agarose particles. These particles had sustained IL4 activity, as demonstrated by the induction of TF-1 cell proliferation and anti-inflammatory M2 polarization of M-CSF-generated human macrophages. This approach of site-directed IL4 anchoring on particles demonstrates that cytokine-functionalized particles can provide sustained and spatially controlled immune-modulating stimuli. The idea of a 24/7 sensing, MMP driven cytokine delivery system, as described in the introductory chapter, was applied in chapter 3. There, we simulated the natural process of cytokine storage in the extracellular matrix (ECM) by using an injectable solution of IL4 for depot formation by enzyme-catalyzed covalent attachment to ECM components such as fibronectin. The immobilized construct is meant to be cleaved from the ECM by matrix-metalloproteinases (MMPs) which are upregulated during flares of inflammation. These two functionalities are facilitated by a peptide containing two sequences: a protease-sensitive peptide linker (PSL) for MMP cleavage and a sequence for covalent attachment by activated human transglutaminase FXIIIa (TGase) included in the injection mix for co-administration. This peptide was site-selectively conjugated to the unnatural amino acid at IL4 position 42 allowing to preserve wild type bioactivity of IL4. In vitro experiments confirmed the anticipated MMP response towards the PSL and TGase-mediated construct attachment to fibronectin of the ECM. Furthermore, the IL4-peptide conjugates were able to reduce inflammation and protect non-load bearing cartilage along with the anterior cruciate ligament from degradation in an osteoarthritis model in rabbits. This represents the first step towards a minimally invasive treatment option using bioresponsive cytokine depots with potential clinical value for inflammatory conditions. One of the challenges with this approach was the production of the cytokine conjugate, with incorporation of the unnatural amino acid into IL4 being the main bottleneck. Therefore, in chapter 4, we designed a simplified version of this depot system by genetically fusing the bifunctional peptide via a flexible peptide spacer to murine IL4. While human IL4 loses its activity upon C-terminal elongation, murine IL4 is not affected by this modification. The produced murine IL4 fusion protein could be effectively bound to in vitro grown extracellular matrix in presence of TGase. Moreover, the protease-sensitive linker was selectively recognized and cleaved by MMPs, liberating intact and active IL4, although at a slower rate than expected. Murine IL4 offers the advantage to evaluate the bioresponsive cytokine depot in many available mouse models, which was so far not possible with human IL4 due to species selectivity. For murine IL4, the approach was further extended to systemic delivery in chapter 5. To increase the half-life and specifically target disease sites, we engineered a murine IL4 variant conjugated with a folate-bearing PEG chain for targeting of activated macrophages. The bioactive IL4 conjugate had a high serum stability and the PEGylation increased the half-life to 4 h in vivo. Surprisingly, the folate moiety did not improve targeting in an antigen-induced arthritis (AIA) mouse model. IL4-PEG performed better in targeting the inflamed joint, while IL4-PEG-folate showed stronger accumulation in the liver. Fortunately, the modular nature of the IL4 conjugate facilitates convenient adaption of PEG chain length and the targeting moiety to further improve the half-life and localization of the cytokine. In summary, this thesis describes a platform technology for the controlled release of cytokines in response to inflammation. By restricting the release of the therapeutic to the site of inflammation, the benefit-risk ratio of this potent class of biologics can be positively influenced. Future research will help to deepen our understanding of how to perfectly combine cytokine, protease-sensitive linker and immobilization tag or targeting moiety to tackle different diseases.}, subject = {Targeted drug delivery}, language = {en} } @phdthesis{Fackler2014, author = {Fackler, Marc}, title = {Biochemical characterization of GAS2L3, a target gene of the DREAM complex}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-103394}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2014}, abstract = {GAS2L3 was identified recently as a target gene of the DREAM complex (Reichert et al., 2010; Wolter et al., 2012). It was shown that GAS2L3 is expressed in a cell cycle specific manner and that depletion of the protein leads to defects in cytokinesis and genomic instability (Wolter et al., 2012). Major aim of this thesis was, to further characterize the biochemical properties and physiological function of GAS2L3. By in vitro co-sedimentation and bundling assays, GAS2L3 was identified as a cytoskeleton associated protein which bundles, binds and crosslinks F-actin and MTs. GST pulldown assays and co-immunoprecipitation experiments revealed that GAS2L3 interacts in vitro and in vivo with the chromosomal passenger complex (CPC), a very important regulator of mitosis and cytokinesis, and that the interaction is mediated by the GAR domain of GAS2L3 and the C-terminal part of Borealin and the N-terminal part of Survivin. Kinase assays showed that GAS2L3 is not a substrate of the CPC but is strongly phosphorylated by CDK1 in vitro. Depletion of GAS2L3 by shRNA influenced protein stability and activity of the CPC. However pharmacological studies showed that the decreased CPC activity is not responsible for the observed cytokinesis defects upon GAS2L3 depletion. Immunofluorescence experiments revealed that GAS2L3 is localized to the constriction zone by the CPC in a GAR dependent manner and that the GAR domain is important for proper protein function. New interacting proteins of GAS2L3 were identified by stable isotope labelling by amino acids in cell culture (SILAC) in combination with tandem affinity purification and subsequent mass spectrometrical analysis. Co-immunoprecipitation experiments further confirmed the obtained mass spectrometrical data. To address the physiological function of GAS2L3 in vivo, a conditional and a non-conditional knockout mouse strain was established. The non-conditional mouse strain showed a highly increased mortality rate before weaning age probably due to heart failure. The physiological function of GAS2L3 in vivo as well as the exact reason for the observed heart phenotype is not known at the moment.}, subject = {Zellzyklus}, language = {en} } @phdthesis{Sowik2014, author = {Sowik, Thomas}, title = {Assessment of the surface functionalization of SPION and DND nanomaterials for cellular uptake and fluorescence imaging}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-103709}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2014}, abstract = {The aim of this work was to synthesize and functionalize different bio-relevant nanomaterials like silica-coated superparamagnetic iron oxide nanoparticles (SPIONs) as contrast agents for T2 magnetic resonance imaging (MRI) and detonation nanodiamond (DND) with the neurohormone peptide allatostatin 1 (ALST1) and a fluorescent dye. Analytical techniques for the determination and quantification of surface functional groups like amines, azides, and peptides were also developed and established. Thus, in the first part of the work, a TGF-1 binding peptide and allatostatin 1 (ALST1), both supposed to act as active tumour targeting vectors, were synthesized by solid-phase peptide synthesis (SPPS) and characterized by high pressure liquid chromatography (HPLC) and mass spectrometry. Then, azide-functionalized silica nanoparticles were synthesized by the St{\"o}ber process and characterized by transmission electron microscopy (TEM) and infrared spectroscopy (IR). The surface loading of amine and azide groups was determined by a new protocol. The azide groups were reduced with sodium boronhydride to amine and then functionalized with Fmoc-Rink Amide linker according to a standard SPPS protocol. Upon cleavage of Fmoc by piperidine, the resulting dibenzofulvene and its piperidine adduct were quantified by UV/Vis spectroscopy and used to determine the amount of amine groups on the nanoparticle surface. Then, ALST1 and related tyrosine- and phenylalanine substituted model peptides were conjugated to the azide-functionalized silica nanoparticles by copper(I)-catalyzed azide-alkyne dipolar cycloaddition (CuAAC). The successful peptide conjugation was demonstrated by the Pauly reaction, which however is only sensitive to histidine- and tyrosine-containing peptides. As a more general alternative, the acid hydrolysis of the peptides to their individual amino acid building blocks followed by derivatization with phenyl isothiocyanate (PITC) allowed the separation, determination, and quantification of the constituent amino acids by HPLC. In the second part of the work, amine- and azide-functionalized silica-coated superparamagnetic iron oxide nanoparticles (SPIONs) were synthesized by co-precipitation and subsequent silica-coated based on the St{\"o}ber process and characterized by TEM and IR. The amine surface loading was determined by the method already established for the pure silica systems. The azide surface loading could also be quantified by reduction with sodium boronhydride to amine groups and then conjugation to Fmoc-Rink amide linker. Upon cleavage of Fmoc with piperidine, the total amine surface loading was obtained. The amount of azide surface groups was then determined from the difference of the total amine surface loading and the amine surface loading. Thus, it was possible to quantify both amine and azide surface groups on a single nanoparticle system. Superparamagnetic iron oxide nanoparticles (SPIONs) are potent T2 contrast agents for magnetic resonance imaging (MRI). Due to their natural metabolism after injection into the blood stream, SPIONs mostly end up inside macrophages, liver, spleen or kidneys. To generate a potential target-specific SPION-based T2 contrast agent for MRI, the neurohormone peptide ALST1 was conjugated by CuAAC to the azide- and amine functionalized superparamagnetic iron oxide nanoparticles, since ALST1 is supposed to target difficult-to-treat neuroendocrinic tumours due to its analogy to galanin and somastatin receptor ligands. The organic fluorescent dye cyanine 5 (Cy5) was also conjugated to the silica-coated superparamagnetic iron oxide nanoparticles (SPIONs) via a NHS-ester to the amines to enable cell uptake studies by fluorescence microscopy. These constructs were characterized by TEM, dynamic light scattering (DLS), and IR. The amino acids of the conjugated ALST1 were determined by the HPLC method as described before for peptide-modified silica nanoparticle surfaces. Then, the relaxivity r2 was measured at 7 T. However, a r2 value of 27 L/mmolFe·s for the dual ALST1-/Cy5-functionalized silica-coated SPIONs was not comparable to T2 contrast agents in clinical use, since their relaxivity is commonly determined at 1.5 T, and no such instrument was available. However, it can be assumed that the synthesized dual ALST1-/Cy5-functionalized silica-coated SPION would show a lower r2 at 1.5 T than at 7T. Commercial T2 MRI contrast agents like VSOP-C184 from Ferropharm show at r2 values of about 30 L/mmolFe·s at 1.5 T. Still, the relaxivity of the new material has some potential for application as a T2 contrast agent. Then, the material was used in cell uptake studies by fluorescence microscopy with the conjugated Cy5 dye as a probe. The dual ALST1-/Cy5-functionalized silica-coated SPION showed a high degree of agglomeration with no cellular uptake unlike described for ALST1-functionalized nanoparticles in literature. It is assumed that upon agglomeration of the particles, constructs form which are unable to be internalized by the cellular endocytotic pathways anymore. As a future perspective, the tendency of the particle to agglomerate should be reduced by changing the coating material to polyethylene glycol (PEG) or chitosan, which are known to be bio-compatible, bio-degradable and prevent agglomeration. In the third part of the work, the rhenium compound [ReBr(CO)3(L)] with L = 2-phenyl-1H-imidazo[4,5-f][1,10]phenanthroline and its manganese analogue were synthesized by heating the ligand and rhenium pentacarbonyl bromide or and manganese pentacarbonyl bromide respectively, in toluene. However, [MnBr(CO)3(L)] was unstable upon illumination by UV light at 365 nm. Thus, it was dismissed for further application. The photophysical properties of [ReBr(CO)3(L)] were explored, by determination of the excited-state life time by the time-correlated single-photon counting (TCSPC) method and the quantum yield by a fluorescence spectrometer equipped with an integration sphere. A value of  = 455 ns, a Stokes shift of 197 nm and a rather low quantum yield =were found. Metal complexes are supposed to have superior properties compared to organic dyes due to their large Stokes shifts, long excited-state life times, and high quantum yields. Thus, amine- and azide-functionalized detonation nanodiamond (DND) as an alternative biological inert carrier system was functionalized with ALST1 to enhance its cell uptake properties. A luminescent probe for cell uptake studies using fluorescence microscopy was also attached, either based on the new rhenium complex or the commercially available organic dye Cy5, respectively. The aldehyde-functionalized rhenium complex was conjugated to the DND via oxime ligation, which is known to be a mild and catalyst-free conjugation method. The amount of peptide ALST1 on the DND was analyzed and quantified after acid hydrolysis and PITC derivatization by HPLC as described before. Then, the ALST1-/luminescent probe-functionalized DND was investigated for its photophysical properties by fluorescence spectroscopy. The Cy5-functionalized material showed a slightly lower fluorescence performance in aqueous solution than reported in literature and commercial suppliers with a life time  < 0.4 ns and quantum yields not determinable by integration sphere due to the week signal intensity. The rhenium complex-functionalized material had a very low signal intensity in only aqueous medium, and thus determination of life times and quantum yield by fluorescence spectroscopy was not possible. After incubation with MDA-MB 231 cells, the Cy5-functionalized DND could easily be detected due to its red fluorescence. However, it was not possible to visualize the rhenium complex-functionalized DND with fluorescence microscopy due to the low fluorescence intensity of the complex in aqueous medium and the lack of proper filters for the fluorescence microscope. Cy5-functionalized DND did not show any cellular uptake in fluorescence microscopy after conjugation with ALST1. Since the nanodiamond surface is known to strongly adsorb peptides and proteins, it is assumed that the peptide chain is oriented perpendicular to the nanoparticle surface and thus not able to interact with cell membrane receptors to promote cell uptake of the particles. As a future perspective, the ALST1-promoted cellular uptake of the DND should be improved by using different linker systems for peptide conjugation to prevent adsorption of the peptide chain on the particle surface. The new analytical methods for amino-, azide-, and peptide-functionalized nanoparticles have great potential to assist in the quantification of nanoparticle surface modifications by UV/Vis spectroscopy and HPLC. The determination of surface amine and azide groups based on the cleavage of conjugated Fmoc-Rink amide linker and detected by UV/Vis spectroscopy is applicable to all amine-/azide-functionalized nanomaterials. However, particles which form very stable suspension with the cleavage mixture can cause quantification problems due to scattering, making an accurate quantification of dibenzofulvene and its piperidine adduct impossible. The detection of tyrosine- and histidine-containing peptides based on the Pauly reaction is well-suited as a fast and easy-to-perform qualitative demonstration of successful peptide surface conjugation. However, its major drawback as a colourimetric approach is that coloured particles cannot be evaluated by this method. The amino acid analysis based on HPLC after acid hydrolysis of peptides conjugated to nanoparticle surfaces to its individual building blocks and subsequent derivatization with PITC, can be used on all nanomaterials with peptide or protein surface modification. It allows detection of amino acids down to picomolar concentrations and even enables analysis of very small peptide surface loadings. However, the resulting HPLC traces are difficult to analyze. Three new analytical methods based on UV/Vis and HPLC techniques have been developed and established. They assisted in the characterization of the synthesized DND and SPIONs with dual functionalization by ALST1 and Cy5 or [ReBr(CO)3(L)], respectively. However, the nanomaterials showed no cellular uptake due to a high tendency to agglomerate. The cellular uptake should be improved and the tendency to agglomerate of the SPIONs should be reduced by changing the surface coating from silica to either PEG or chitosan. Furthermore, different linker systems for connecting peptides to DND surfaces should be synthesized and evaluated to reduce potential peptide chain adsorption.}, subject = {Nanopartikel}, language = {en} } @article{MuellerWindhofMaximovetal.2013, author = {M{\"u}ller, Sara and Windhof, Indra M. and Maximov, Vladimir and Jurkowski, Tomasz and Jeltsch, Albert and F{\"o}rstner, Konrad U. and Sharma, Cynthia M. and Gr{\"a}f, Ralph and Nellen, Wolfgang}, title = {Target recognition, RNA methylation activity and transcriptional regulation of the Dictyostelium discoideum Dnmt2-homologue (DnmA)}, series = {Nucleic Acids Research}, volume = {41}, journal = {Nucleic Acids Research}, number = {18}, issn = {1362-4962}, doi = {10.1093/nar/gkt634}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-123149}, pages = {8615-8627}, year = {2013}, abstract = {Although the DNA methyltransferase 2 family is highly conserved during evolution and recent reports suggested a dual specificity with stronger activity on transfer RNA (tRNA) than DNA substrates, the biological function is still obscure. We show that the Dictyostelium discoideum Dnmt2-homologue DnmA is an active tRNA methyltransferase that modifies C38 in \(tRNA^{Asp(GUC)}\) in vitro and in vivo. By an ultraviolet-crosslinking and immunoprecipitation approach, we identified further DnmA targets. This revealed specific tRNA fragments bound by the enzyme and identified \(tRNA^{Glu(CUC/UUC)}\) and \(tRNA^{Gly(GCC)}\) as new but weaker substrates for both human Dnmt2 and DnmA in vitro but apparently not in vivo. Dnmt2 enzymes form transient covalent complexes with their substrates. The dynamics of complex formation and complex resolution reflect methylation efficiency in vitro. Quantitative PCR analyses revealed alterations in dnmA expression during development, cell cycle and in response to temperature stress. However, dnmA expression only partially correlated with tRNA methylation in vivo. Strikingly, dnmA expression in the laboratory strain AX2 was significantly lower than in the NC4 parent strain. As expression levels and binding of DnmA to a target in vivo are apparently not necessarily accompanied by methylation, we propose an additional biological function of DnmA apart from methylation.}, language = {en} } @article{BonnSchmittAsan2012, author = {Bonn, Maria and Schmitt, Angelika and Asan, Esther}, title = {Double and triple in situ hybridization for coexpression studies: combined fluorescent and chromogenic detection of neuropeptide Y (NPY) and serotonin receptor subtype mRNAs expressed at different abundance levels}, series = {Histochemistry and Cell Biology}, volume = {137}, journal = {Histochemistry and Cell Biology}, number = {1}, doi = {10.1007/s00418-011-0882-3}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-127080}, pages = {11-24}, year = {2012}, abstract = {Multiple fluorescence in situ hybridization is the method of choice for studies aimed at determining simultaneous production of signal transduction molecules and neuromodulators in neurons. In our analyses of the monoamine receptor mRNA expression of peptidergic neurons in the rat telencephalon, double tyramide-signal-amplified fluorescence in situ hybridization delivered satisfactory results for coexpression analysis of neuropeptide Y (NPY) and serotonin receptor 2C (5-HT2C) mRNA, a receptor subtype expressed at high-to-moderate abundance in the regions analyzed. However, expression of 5-HT1A mRNA, which is expressed at comparatively low abundance in many telencephalic areas, could not be unequivocally identified in NPY mRNA-reactive neurons due to high background and poor signal-to-noise ratio in fluorescent receptor mRNA detections. Parallel chromogenic in situ hybridization provided clear labeling for 5-HT1A mRNA and additionally offered the possibility to monitor the chromogen deposition at regular time intervals to determine the optimal signal-to-noise ratio. We first developed a double labeling protocol combining fluorescence and chromogenic in situ hybridization and subsequently expanded this variation to combine double fluorescence and chromogenic in situ hybridization for triple labelings. With this method, we documented expression of 5-HT2C and/or 5-HT1A in subpopulations of telencephalic NPY-producing neurons. The method developed in the present study appears suitable for conventional light and fluorescence microscopy, combines advantages of fluorescence and chromogenic in situ hybridization protocols and thus provides a reliable non-radioactive alternative to previously published multiple labeling methods for coexpression analyses in which one mRNA species requires highly sensitive detection.}, language = {en} } @article{WilmsOverloeperNowrousianetal.2012, author = {Wilms, Ina and Overl{\"o}per, Aaron and Nowrousian, Minou and Sharma, Cynthia M. and Narberhaus, Franz}, title = {Deep sequencing uncovers numerous small RNAs on all four replicons of the plant pathogen Agrobacterium tumefaciens}, series = {RNA Biology}, volume = {9}, journal = {RNA Biology}, number = {446-457}, doi = {10.4161/rna.17212}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-127101}, pages = {4}, year = {2012}, abstract = {Agrobacterium species are capable of interkingdom gene transfer between bacteria and plants. The genome of Agrobacterium tumefaciens consists of a circular and a linear chromosome, the At-plasmid and the Ti-plasmid, which harbors bacterial virulence genes required for tumor formation in plants. Little is known about promoter sequences and the small RNA (sRNA) repertoire of this and other α-proteobacteria. We used a differential RNA sequencing (dRNA-seq) approach to map transcriptional start sites of 388 annotated genes and operons. In addition, a total number of 228 sRNAs was revealed from all four Agrobacterium replicons. Twenty-two of these were confirmed by independent RNA gel blot analysis and several sRNAs were differentially expressed in response to growth media, growth phase, temperature or pH. One sRNA from the Ti-plasmid was massively induced under virulence conditions. The presence of 76 cis-antisense sRNAs, two of them on the reverse strand of virulence genes, suggests considerable antisense transcription in Agrobacterium. The information gained from this study provides a valuable reservoir for an in-depth understanding of sRNA-mediated regulation of the complex physiology and infection process of Agrobacterium.}, language = {en} } @phdthesis{Schmitt2017, author = {Schmitt, Dominik}, title = {Structural Characterization of the TFIIH Subunits p34 and p44 from C. thermophilum}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-104851}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2017}, abstract = {Several important cellular processes, including transcription, nucleotide excision repair and cell cycle control are mediated by the multifaceted interplay of subunits within the general transcription factor II H (TFIIH). A better understanding of the molecular structure of TFIIH is the key to unravel the mechanism of action of this versatile protein complex within these pathways. This becomes especially important in the context of severe diseases like xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy, that arise from single point mutations in some of the TFIIH subunits. In an attempt to structurally characterize the TFIIH complex, we harnessed the qualities of the eukaryotic thermophile Chaetomium thermophilum, a remarkable fungus, which has only recently been recognized as a novel model organism. Homologues of TFIIH from C. thermophilum were expressed in E. coli, purified to homogeneity and subsequently utilized for crystallization trials and biochemical studies. The results of the present work include the first crystal structure of the p34 subunit of TFIIH, comprising the N-terminal domain of the protein. The structure revealed a von Willebrand Factor A (vWA) like fold, which is generally known to be involved in a multitude of protein-protein interactions. Structural comparison allowed to delineate similarities as well as differences to already known vWA domains, providing insight into the role of p34 within TFIIH. These results indicate that p34 assumes the role of a structural scaffold for other TFIIH subunits via its vWA domain, while likely serving additional functions, which are mediated through its C-terminal zinc binding domain and are so far unknown. Within TFIIH p34 interacts strongly with the p44 subunit, a positive regulator of the XPD helicase, which is required for regulation of RNA Polymerase II mediated transcription and essential for eukaryotic nucleotide excision repair. Based on the p34 vWA structure putative protein-protein interfaces were analyzed and binding sites for the p34 p44 interaction suggested. Continuous crystallization efforts then led to the first structure of a p34 p44 minimal complex, comprising the N-terminal vWA domain of p34 and the C-terminal C4C4 RING domain of p44. The structure of the p34 p44 minimal complex verified the previous hypothesis regarding the involved binding sites. In addition, careful analysis of the complex interface allowed to identify critical residues, which were subsequently mutated and analyzed with respect to their significance in mediating the p34 p44 interaction, by analytical size exclusion chromatography, electrophoretic mobility shift assays and isothermal titration calorimetry. The structure of the p34 p44 complex also revealed a binding mode of the p44 C4C4 RING domain, which differed from that of other known RING domains in several aspects, supporting the hypothesis that p44 contains a novel variation of this domain.}, subject = {DNA-Reparatur}, language = {en} } @phdthesis{Stoll2015, author = {Stoll, Georg}, title = {Identification of the mRNA-associated TOP3β- TDRD3-FMRP (TTF) -complex and its implication for neurological disorders}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-111440}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2015}, abstract = {The propagation of the genetic information into proteins is mediated by messenger- RNA (mRNA) intermediates. In eukaryotes mRNAs are synthesized by RNA- Polymerase II and subjected to translation after various processing steps. Earlier it was suspected that the regulation of gene expression occurs primarily on the level of transcription. In the meantime it became evident that the contribution of post- transcriptional events is at least equally important. Apart from non-coding RNAs and metabolites, this process is in particular controlled by RNA-binding proteins, which assemble on mRNAs in various combinations to establish the so-called "mRNP- code". In this thesis a so far unknown component of the mRNP-code was identified and characterized. It constitutes a hetero-trimeric complex composed of the Tudor domain-containing protein 3 (TDRD3), the fragile X mental retardation protein (FMRP) and the Topoisomerase III beta (TOP3β) and was termed TTF (TOP3β-TDRD3-FMRP) -complex according to its composition. The presented results also demonstrate that all components of the TTF-complex shuttle between the nucleus and the cytoplasm, but are predominantly located in the latter compartment under steady state conditions. Apart from that, an association of the TTF-complex with fully processed mRNAs, not yet engaged in productive translation, was detected. Hence, the TTF-complex is a component of „early" mRNPs. The defined recruitment of the TTF-complex to these mRNPs is not based on binding to distinct mRNA sequence-elements in cis, but rather on an interaction with the so-called exon junction complex (EJC), which is loaded onto the mRNA during the process of pre-mRNA splicing. In this context TDRD3 functions as an adapter, linking EJC, FMRP and TOP3β on the mRNP. Moreover, preliminary results suggest that epigenetic marks within gene promoter regions predetermine the transfer of the TTF-complex onto its target mRNAs. Besides, the observation that TOP3β is able to catalytically convert RNA-substrates disclosed potential activities of the TTF-complex in mRNA metabolism. In combination with the already known functions of FMRP, this finding primarily suggests that the TTF-complex controls the translation of bound mRNAs. In addition to its role in mRNA metabolism, the TTF-complex is interesting from a human genetics perspective as well. It was demonstrated in collaboration with researchers from Finland and the US that apart from FMRP, which was previously linked to neurocognitive diseases, also TOP3β is associated with neurodevelopmental disorders. Understanding the function of the TTF-complex in mRNA metabolism might hence provide important insight into the etiology of these diseases.}, subject = {Messenger-RNS}, language = {en} } @article{BerghoffKonzerManketal.2013, author = {Berghoff, Bork A. and Konzer, Anne and Mank, Nils N. and Looso, Mario and Rische, Tom and F{\"o}rstner, Konrad U. and Kr{\"u}ger, Marcus and Klug, Gabriele}, title = {Integrative "Omics"-Approach Discovers Dynamic and Regulatory Features of Bacterial Stress Responses}, series = {PLOS Genetics}, volume = {9}, journal = {PLOS Genetics}, number = {6}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1003576}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-127587}, pages = {e1003576}, year = {2013}, abstract = {Bacteria constantly face stress conditions and therefore mount specific responses to ensure adaptation and survival. Stress responses were believed to be predominantly regulated at the transcriptional level. In the phototrophic bacterium Rhodobacter sphaeroides the response to singlet oxygen is initiated by alternative sigma factors. Further adaptive mechanisms include post-transcriptional and post-translational events, which have to be considered to gain a deeper understanding of how sophisticated regulation networks operate. To address this issue, we integrated three layers of regulation: (1) total mRNA levels at different time-points revealed dynamics of the transcriptome, (2) mRNAs in polysome fractions reported on translational regulation (translatome), and (3) SILAC-based mass spectrometry was used to quantify protein abundances (proteome). The singlet oxygen stress response exhibited highly dynamic features regarding short-term effects and late adaptation, which could in part be assigned to the sigma factors RpoE and RpoH2 generating distinct expression kinetics of corresponding regulons. The occurrence of polar expression patterns of genes within stress-inducible operons pointed to an alternative of dynamic fine-tuning upon stress. In addition to transcriptional activation, we observed significant induction of genes at the post-transcriptional level (translatome), which identified new putative regulators and assigned genes of quorum sensing to the singlet oxygen stress response. Intriguingly, the SILAC approach explored the stress-dependent decline of photosynthetic proteins, but also identified 19 new open reading frames, which were partly validated by RNA-seq. We propose that comparative approaches as presented here will help to create multi-layered expression maps on the system level ("expressome"). Finally, intense mass spectrometry combined with RNA-seq might be the future tool of choice to re-annotate genomes in various organisms and will help to understand how they adapt to alternating conditions.}, language = {en} }