Fakultät für Chemie und Pharmazie - Digitale Hochschulschriften der LMU - Teil 06/06

Ludwig-Maximilians-Universität München

Die Universitätsbibliothek (UB) verfügt über ein umfangreiches Archiv an elektronischen Medien, das von Volltextsammlungen über Zeitungsarchive, Wörterbücher und Enzyklopädien bis hin zu ausführlichen Bibliographien und mehr als 1000 Datenbanken reicht. Auf iTunes U stellt die UB unter anderem eine Auswahl an Dissertationen der Doktorandinnen und Doktoranden an der LMU bereit. (Dies ist der 6. von 6 Teilen der Sammlung 'Fakultät für Chemie und Pharmazie - Digitale Hochschulschriften der LMU'.)

  1. 10.05.2016

    High-quality, high-throughput measurement of protein-DNA binding using HiTS-FLIP

    In order to understand in more depth and on a genome wide scale the behavior of transcription factors (TFs), novel quantitative experiments with high-throughput are needed. Recently, HiTS-FLIP (High-Throughput Sequencing-Fluorescent Ligand Interaction Profiling) was invented by the Burge lab at the MIT (Nutiu et al. (2011)). Based on an Illumina GA-IIx machine for next-generation sequencing, HiTS-FLIP allows to measure the affinity of fluorescent labeled proteins to millions of DNA clusters at equilibrium in an unbiased and untargeted way examining the entire sequence space by Determination of dissociation constants (Kds) for all 12-mer DNA motifs. During my PhD I helped to improve the experimental design of this method to allow measuring the protein-DNA binding events at equilibrium omitting any washing step by utilizing the TIRF (Total Internal Reflection Fluorescence) based optics of the GA-IIx. In addition, I developed the first versions of XML based controlling software that automates the measurement procedure. Meeting the needs for processing the vast amount of data produced by each run, I developed a sophisticated, high performance software pipeline that locates DNA clusters, normalizes and extracts the fluorescent signals. Moreover, cluster contained k-mer motifs are ranked and their DNA binding affinities are quantified with high accuracy. My approach of applying phase-correlation to estimate the relative translative Offset between the observed tile images and the template images omits resequencing and thus allows to reuse the flow cell for several HiTS-FLIP experiments, which greatly reduces cost and time. Instead of using information from the sequencing images like Nutiu et al. (2011) for normalizing the cluster intensities which introduces a nucleotide specific bias, I estimate the cluster related normalization factors directly from the protein Images which captures the non-even illumination bias more accurately and leads to an improved correction for each tile image. My analysis of the ranking algorithm by Nutiu et al. (2011) has revealed that it is unable to rank all measured k-mers. Discarding all the clusters related to previously ranked k-mers has the side effect of eliminating any clusters on which k-mers could be ranked that share submotifs with previously ranked k-mers. This shortcoming affects even strong binding k-mers with only one mutation away from the top ranked k-mer. My findings show that omitting the cluster deletion step in the ranking process overcomes this limitation and allows to rank the full spectrum of all possible k-mers. In addition, the performance of the ranking algorithm is drastically reduced by my insight from a quadratic to a linear run time. The experimental improvements combined with the sophisticated processing of the data has led to a very high accuracy of the HiTS-FLIP dissociation constants (Kds) comparable to the Kds measured by the very sensitive HiP-FA assay (Jung et al. (2015)). However, experimentally HiTS-FLIP is a very challenging assay. In total, eight HiTS-FLIP experiments were performed but only one showed saturation, the others exhibited Protein aggregation occurring at the amplified DNA clusters. This biochemical issue could not be remedied. As example TF for studying the details of HiTS-FLIP, GCN4 was chosen which is a dimeric, basic leucine zipper TF and which acts as the master regulator of the amino acid starvation Response in Saccharomyces cerevisiae (Natarajan et al. (2001)). The fluorescent dye was mOrange. The HiTS-FLIP Kds for the TF GCN4 were validated by the HiP-FA assay and a Pearson correlation coefficient of R=0.99 and a relative error of delta=30.91% was achieved. Thus, a unique and comprehensive data set of utmost quantitative precision was obtained that allowed to study the complex binding behavior of GCN4 in a new way. My Downstream analyses reveal that the known 7-mer consensus motif of GCN4, which is TGACTCA, is modulated by its 2-mer neighboring flanking regions spanning an affinity range over two orders of magnitude from a Kd=1.56 nM to Kd=552.51 nM. These results suggest that the common 9-mer PWM (Position Weight Matrix) for GCN4 is insufficient to describe the binding behavior of GCN4. Rather, an additional left and right flanking nucleotide is required to extend the 9-mer to an 11-mer. My analyses regarding mutations and related delta delta G values suggest long-range interdependencies between nucleotides of the two dimeric half-sites of GCN4. Consequently, models assuming positional independence, such as a PWM, are insufficient to explain these interdependencies. Instead, the full spectrum of affinity values for all k-mers of appropriate size should be measured and applied in further analyses as proposed by Nutiu et al. (2011). Another discovery were new binding motifs of GCN4, which can only be detected with a method like HiTS-FLIP that examines the entire sequence space and allows for unbiased, de-novo motif discovery. All These new motifs contain GTGT as a submotif and the data collected suggests that GCN4 binds as monomer to these new motifs. Therefore, it might be even possible to detect different binding modes with HiTS-FLIP. My results emphasize the binding complexity of GCN4 and demonstrate the advantage of HiTS-FLIP for investigating the complexity of regulative processes.

  2. 28.04.2016

    Structural und functional characterization of Rubisco assembly chaperones

    In the present study, the structure and mechanism of two assembly chaperones of Rubisco, Raf1 and RbcX, were investigated. The role of Raf1 in Rubisco assembly was elucidated by analyzing cyanobacterial and plant Raf1 with a vast array of biochemical and biophysical techniques. Raf1 is a dimeric protein. The subunits have a two-domain structure. The crystal structures of two separate domains of Arabidopsis thaliana (At) Raf1 were solved at resolutions of 1.95 Å and 2.6–2.8 Å, respectively. The oligomeric state of Raf1 proteins was investigated by size exclusion chromatography connected to multi angle light scattering (SEC-MALS) and native mass spectrometry (MS). Both cyanobacterial and plant Raf1 are dimeric with an N-terminal domain that is connected via a flexible linker to the C-terminal dimerization domain. Both Raf1 poteins were able to promote assembly of cyanobacterial Rubisco in an in vitro reconstitution system. The homologous cyanobacterial system resulted in very high yields of active Rubisco (>90%), showing the great efficiency of Raf1 mediated Rubisco assembly. Two distinct oligomeric complex assemblies in the assembly reaction could be identified via native PAGE immunoblot analyses as well as SEC-MALS and native MS. Furthermore, a structure-guided mutational analysis of Raf1 conserved residues in both domains was performed and residues crucial for Raf1 function were identified. A new model of Raf1 mediated Rubisco-assembly could be proposed by analyzing the Raf1-Rubisco oligomeric complex with negative stain electron microscopy. The final model was validated by determining Raf1-Rubisco interaction sites using chemical crosslinking in combination with mass spectrometry. Taken together, Raf1 acts downstream of chaperonin-assisted Rubisco large subunit (RbcL) folding by stabilizing RbcL antiparallel dimers for assembly into RbcL8 complexes with four Raf1 dimers bound. Raf1 displacement by Rubisco small subunit (RbcS) results in holoenzyme formation. In the second part of this thesis, the role of eukaryotic RbcX proteins in Rubisco assembly was investigated. Eukaryots have two distinct homologs of RbcX, RbcX-I and RbcX-II. Both, plant and algal RbcX proteins were found to promote cyanobacterial Rubisco assembly in an in vitro reconstitution system. Mutation of a conserved residue important for Rubisco assembly in cyanobacterial RbcX also abolished assembly by eukaryotic RbcX, underlining functional similarities among RbcX proteins from different species. The crystal structure of Chlamydomonas reinhardtii (Cr) RbcX was solved at a resolution of 2.0 Å. RbcX forms an arc-shaped dimer with a central hydrophobic cleft for binding the C-terminal sequence of RbcL. Structural analysis of a fusion protein of CrRbcX and the C-terminal peptide of RbcL suggests that the peptide binding mode of CrRbcX may differ from that of cyanobacterial RbcX. RbcX homologs appear to have adapted to their cognate Rubisco clients as a result of co-evolution. Preliminary analysis of RbcX in Chlamydomonas indicated that the protein functions as a Rubisco assembly chaperone in vivo. Therefore, RbcX was silenced using RNAi in Chlamydomonas which resulted in a photosynthetic growth defect in several transformants when grown under light. RbcX mRNA levels were highly decreased in these transformants which resulted in a concomitant decrease of Rubisco large subunit levels. Biochemical and structural analysis from both independent studies in this thesis show that Raf1 and RbcX fulfill similar roles in Rubisco assembly, thus suggesting that functionally redundant factors ensure efficient Rubisco biogenesis.

  3. 17.03.2016

    Molecular mechanisms of PAH function in response to phenylalanine and tetrahydrobiopterin binding

    Phenylketonuria (PKU) is an autosomal recessive inborn error of metabolism (IEM) caused by mutations in the phenylalanine hydroxylase (PAH) gene. The molecular mechanism underlying deficiency of the PAH protein is, in most of the cases, loss of function due to protein misfolding. PAH mutations induce disturbed oligomerisation, decreased stability and accelerated degradation of hepatic PAH, a key enzyme in phenylalanine metabolism. Since the development of a phenylalanine-restricted diet in the 1950ies, PKU is a prototype for treatable inherited diseases. About 60 years later, the natural PAH cofactor tetrahydrobiopterin (BH4) was shown to act as a pharmacological chaperone stabilising the misfolded PAH protein. In consequence, BH4 (KUVAN®) was introduced to the pharmaceutical market as an alternative treatment for BH4-responsive PAH deficiency. Therefore, PKU is also regarded as a prototype for a pharmacologically treatable protein misfolding disease. Despite the progress in PKU therapy, knowledge on the molecular basis of PKU and the BH4 mode of action was still incomplete. Biochemical and biophysical characterisation of purified variant PAH proteins, which were derived from patient’s mutations, aimed at a better understanding of the molecular mechanisms of PAH loss of function. We showed that local side-chain replacements induce global conformational changes with negative impact on molecular motions that are essential for physiological enzyme function. The development of a continuous real-time fluorescence-based assay of PAH activity allowed for robust analysis of steady state kinetics and allosteric behaviour of recombinantly expressed PAH proteins. We identified positive cooperativity of the PAH enzyme towards BH4, where cooperativity does not rely on the presence of phenylalanine but is determined by activating conformational rearrangements. In vivo investigations on the mode-of-action of BH4 revealed differences in pharmacodynamics but not in pharmacokinetics between different strains of PAH-deficient mice (wild-type, Pahenu1/1 and Pahenu1/2). These observations pointed to a significant impact of the genotype on responsiveness to BH4. The available database information on PAH function associated with PAH mutations was based on non-standardised enzyme activity assays performed in different cellular systems and under different conditions usually focusing on single PAH mutations. These inconsistent data on PAH enzyme activity hindered robust prediction of the patient’s phenotype. Furthermore, assays on single PAH mutations do not reflect the high allelic and phenotypic heterogeneity of PKU with 89 % of patients being compound heterozygotes. In addition, the knowledge on enzyme function and regulation in the therapeutic and pathologic metabolic context was still scarce. In order to get more insight into the interplay of the PAH genotype, the phenylalanine concentration and BH4 treatment, we performed functional analyses of both, single, purified PAH variants as well as PAH full genotypes in the physiological, pathological and therapeutic context. The analysis of PAH activity as a function of phenylalanine and BH4 concentrations enabled determination of the optimal working ranges of the enzyme and visualisation of differences in the regulation of PAH activity by BH4 and phenylalanine depending on the underlying genotype. Moreover, these PAH activity landscapes allowed for setting rules for dietary regimens and pharmacological treatment based on the genotype of the patient. Taken together, precise knowledge on the mechanism of the misfolding-induced loss of function in PAH deficiency enabled a better understanding of the molecular mode of action of pharmacological rescue of enzyme function by BH4. We implemented the combination of genotype-specific functional analyses together with biochemical, clinical and therapeutic data of individual patients as a powerful tool for phenotype prediction and paved the way for personalised medicine strategies in phenylketonuria.

  4. 10.03.2016

    The role of FKBP5 in transcriptional regulation and in shaping cellular pathways of psychopharmaca action

    FK506 binding protein 5 (FKBP5) has been linked to stress related diseases and treatment response in depression (Binder et al., 2004). The corresponding protein FKBP51 was first identified as co-chaperone of HSP90 in a complex with steroid hormone receptors, where it diminishes hormone affinity and nuclear translocation efficiency of the receptors (Pratt and Toft, 1997; Wochnik et al., 2005). With FKBP5 transcription being induced by glucocorticoid signalling, an ultra-short feedback loop is provided for regulation and termination of GR activity. Dysregulation of this ultra-short feedback loop interferes with the stress hormone regulation and likely contributes to the association of FKBP5 with stress-related psychiatric disorders. Recently, important actions of FKBP51 beyond glucocorticoid signalling have been characterised in shaping the posttranslational regulation of certain molecular pathways in response to treatment with particular psychopharmaca (Gassen et al., 2014, 2015). As a contribution to elucidating the role of FKBP5 in stress related diseases, a two-sided approach was taken in this study by analysing the role of FKBP5 in regulation of transcription and in calibrating the responsiveness of these pathways to psychopharmacological treatment. To elucidate the transcriptional effects of FKBP5 in an unbiased approach, the expression profile of mice with deleted FKBP5 and their litter mates with functional FKBP5 were compared. A marked difference in glyoxalase-1 (GLO1) transcription was observed with higher GLO1 transcription in mice with deleted FKBP5, which was reflected by about two-fold more GLO1 protein in these mice. The efforts in deciphering the role of FKBP5 in elevation of GLO1 expression led to the identification of a duplication of the GLO1 gene inherent to mice with deleted FKBP5; this likely explains the enhanced GLO1 expression in these mice. This observation exemplifies the flanking gene problem and is a note of caution for interpreting data from conventionally generated knock-out mice. Overall, deletion of FKBP5 did not markedly change gene expression. In the second part of this thesis, the molecular effects of psychopharmacologic drugs were profiled for their dependency on FKBP51 function to modulate intracellular pathways relevant for treatment outcome in a cellular FKBP5 knockout model. For this purpose, psychopharmaca from the classes of SSRIs, SSNRIs, TCAs, atypical antidepressants, mood stabilisers, and NMDA receptor antagonists were analysed. In addition to GSK3β and AKT, which were reported to interact with and be targeted by FKBP51 recently (Gassen et al., 2015; Pei et al., 2009), ERK was identified as a novel kinase interacting with and being targeted by FKBP51 in this work. With GSK3β, AKT, and ERK, three major kinases were observed to be regulated by psychopharmaca. The effects were not homogeneous across all psychopharmaca and only loosely followed drug classes. Moreover, regulation of these kinases as well as their downstream targets was non-uniformly influenced by FKBP51. With FKBP51 being a stress induced gene, this transcriptional mechanism efficiently links the stress response to the regulation of the targets analysed in this work. Moreover, markers of autophagy, a cellular degradation process which has been linked to neurotransmission, were detected to be regulated by valproic acid (VPA), a mood stabiliser with HDAC inhibitory activity. VPA, as well as a second HDAC inhibitor butyric acid (BUT) enhanced the transcription of late and delayed autophagy markers controlled by FOXO3 signalling. Considering the versatile action of FKBP51 on targets analysed in this work, the list of proteins modulated by FKBP5 seems by far not complete. The diversity of effects evoked by different psychopharmaca hints to superimposed molecular effects underlying treatment outcome. Better understanding of pathway responsiveness could yield molecular markers for personalised medication that could be utilised to improve treatment outcome in stress related psychiatric diseases.

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Die Universitätsbibliothek (UB) verfügt über ein umfangreiches Archiv an elektronischen Medien, das von Volltextsammlungen über Zeitungsarchive, Wörterbücher und Enzyklopädien bis hin zu ausführlichen Bibliographien und mehr als 1000 Datenbanken reicht. Auf iTunes U stellt die UB unter anderem eine Auswahl an Dissertationen der Doktorandinnen und Doktoranden an der LMU bereit. (Dies ist der 6. von 6 Teilen der Sammlung 'Fakultät für Chemie und Pharmazie - Digitale Hochschulschriften der LMU'.)

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