The evolutionary options of a population are strongly influenced by the avail- ability of adaptive mutants. In this thesis, I use the concept of neutral networks to show that neutral drift can actually increase the accessibility of adaptive mu- tants, and therefore facilitate adaptive evolutionary change. Neutral networks are groups of unique genotypes which all code for the same phenotype, and are connected by simple point mutations. I calculate the size and shape of the networks in a small but exhaustively enumerated space of RNA genotypes by mapping the sequences to RNA secondary structure phenotypes. The qual- itative results are similar to those seen in many other genotype–phenotype map models, despite some significant methodological differences. I show that the boundary of each network has single point–mutation connections to many more phenotypes than the average individual genotype within that network. This means that paths involving a series of neutral point–mutation steps across a network can allow evolution to adaptive phenotypes which would otherwise be extremely unlikely to arise spontaneously. This can be likened to walking along a flat ridge in an adaptive landscape, rather than traversing or jumping across a lower fitness valley. Within this model, when a genotype is made up of just 10 bases, the mean neutral path length is 1.88 point mutations. Furthermore, the map includes some networks that are so convoluted that the path through the network is longer than the direct route between two sequences. A minimum length adaptive walk across the genotype space usually takes as many neutral steps as adaptive ones on its way to the optimum phenotype. Finally I show that the shape of a network can have a very important affect on the number of generations it takes a population to drift across it, and that the more routes between two sequences, the fewer generations required for a population to find an advantageous sequence. My conclusion is that, within the RNA map at least, the size, shape and connectivity of neutral networks all have a profound effect on the way that sequences change and populations evolve, and by not considering them, we risk missing an important evolutionary mechanism.

Protein (mis)folding into highly ordered, fibrillar structures, amyloid fibrils, is a hallmark of several, mainly neurodegenerative, disorders. The mechanism of this supra-molecular self-assembly reaction, as well as its relationship to protein folding are not well understood. In particular, the molecular origin of the metastability of the soluble state of proteins with respect to the aggregated states has not been clearly established. In this dissertation, it is demonstrated, that highly accurate kinetic experiments, using a novel biosensing method, can yield fundamental insight into the dynamics of proteins in the region of the free energy landscape corresponding to protein aggregation. First, a section on Method development describes the extension and elaboration of the previously established kinetic assay relying on quartz crystal microbalance measurements for the study of amyloid fibril elongation (Chapter 3). This methodology is then applied in order to study in great detail the origin of the various contributions to the free energy barriers separating the soluble state of a protein from its aggregated state. In particular, the relative importance of residual structure, hydrophobicity (Chapter 4) and electrostatic interactions (Chapter 5) for the total free energy of activation are discussed. In the last part of this thesis (Chapter 6), it is demonstrated that this biosensing method can also be used to study the binding of small molecules to amyloid fibrils, a very useful feature in the framework of the quest for potential inhibitors of amyloid formation. In addition, it is shown that Thioflavin T, to-date the most frequently employed fluorescent label molecule for bulk solution kinetic studies, can in the presence of potential amyloid inhibitor candidates be highly unreliable as a means to quantify the effect of the inhibitor on amyloid formation kinetics. In summary, the work in this thesis contributes to both the fundamental and the applied aspects of the field of protein aggregation.

Hepatocellular carcinoma (HCC) is a common malignancy of the liver that is one of the most frequent causes of cancer-related death in the world. Surgical resection and liver transplantation are the only curative options for HCC, and tumor invasion and metastasis render many patients ineligible for these treatments. Identification of the mechanisms that contribute to invasive and metastatic disease may enlighten therapeutic strategies for those not eligible for surgical treatments. In this dissertation, I describe two sets of experiments to elucidate mechanisms underlying HCC dissemination, involving the activities of Krüppel-like factor 6 and a particular p53 point mutation, R172H. Gene expression profiling of migratory HCC subpopulations demonstrated reduced expression of Krüppel-like factor 6 (KLF6) in invasive HCC cells. Knockdown of KLF6 in HCC cells increased cell transformation and migration. Single-copy deletion of Klf6 in a HCC mouse model results in increased tumor formation, increased metastasis to the lungs, and decreased survival, indicating that KLF6 suppresses both tumor formation and metastasis in HCC. To elucidate the mechanism of KLF6-mediated tumor and metastasis suppression, we performed gene expression profiling and ChIP-sequencing to identify direct transcriptional targets of KLF6 in HCC cells. This analysis revealed novel transcriptional targets of KLF6 in HCC including CDC42EP3 and VAV3, both of which are positive regulators of Rho family GTPases. Concordantly, KLF6 knockdown cells demonstrate increased activity of the Rho family GTPases RAC1 and CDC42, and RAC1 is required for migration induced following KLF6 knockdown. Moreover, VAV3 and CDC42EP3 are also required for enhanced cell migration in HCC cells with KLF6 knockdown. Together, this work describes a novel signaling axis through which KLF6-mediated repression of VAV3 and CDC42EP3 inhibits RAC1Gmediated HCC cell migration in culture, and potentially HCC metastasis in vivo. TP53 gene mutations are commonly found in HCC and are associated with poor prognosis. Prior studies have suggested that p53 mutants can display gain-of- function properties in other tumor types. Therefore, I sought to determine if a particular hotspot p53 mutation, p53R172H, provided enhanced, gain-of-function properties compared to p53 loss in HCC. In vitro, soft agar colony formation and cell migration is reduced upon knockdown of p53R172H, indicating that this mutation is required for transformation-associated phenotypes in these cells. However, p53R172H-expressing mice did not have enhanced tumor formation or metastasis compared to p53-null mice. These data suggest that p53R172H and p53 deletion are functionally equivalent in vivo, and that p53R172H is not a gain-of-function mutant in HCC. Inhibition of the related transcription factors p63 and p73 has been suggested as a potential mechanism by which mutant p53 exerts its gain-of-function effects. Analysis of p63 and p73 target genes demonstrated that they are similarly suppressed in p53-null and p53R172H-expressing HCC cell lines, suggesting a potential explanation for the phenotypes I observed in vivo and in vitro. Together, the studies described in this dissertation increase our understanding of the mechanisms underlying HCC progression and metastasis. Specifically, we find and characterize KLF6 as a novel suppressor of HCC metastasis, and determine the contribution of a common p53 point mutation in HCC. This work contributes to ongoing efforts to improve treatment options for HCC patients.

No description available.

Zahlreiche pathogene „missense“-Mutation, die verhindern, dass Proteine korrekt gefaltet werden, befinden sich in geordneten Regionen von Proteinen. Andere krankheitsrelevante Mutationen befinden sich in ungeordneten Regionen und beeinflussen somit nur begrenzt die Funktionalität, zum Beispiel durch Veränderungen kurzer linearer Sequenzmotive, die Protein-Protein Interaktionen vermitteln. In dieser Arbeit wird ein peptidbasierter Interaktionsscreen präsentiert mit dem sich Veränderungen im Interaktom identifizieren lassen. Synthetische Peptide von wild-typ und zugehörigen mutierten Proteinregionen ermöglichen die gleichzeitige Untersuchung von mehr als hundert Mutationen mittels Massenspektrometrie. Mehr als ein Drittel aller getesteten Mutationen hatten veränderte Interaktionen zur Folge. Darunter befanden sich auch drei Prolin zu Leucin Mutationen in zytosolischen Regionen von Transmembranproteinen, die zusammen mit dem benachbarten Leucin einem Dileucinmotiv ergeben und dadurch verstärkt mit Clathrin interagieren. Dieses Motiv wurde bereits mit Clathrin-vermittelter Endozytose in Verbindung gebracht. Die hinzugewonnene Endozytose könnte Krankheitsmechanismen erklären, da die Mislokalisation der betroffenen Transmembranproteine zum effektiven Verlust derer Funktion führen würde. Diese Hypothese wurde hier von verschiedenen in vitro und in vivo Experimenten bezüglich der P485L Mutation im Glukose Transporter-1 (GLUT1), die das GLUT1-Defizit-Syndrom hervorruft, bestätigt. Weitere Evidenz wurde außerdem für die Funktionalität anderer mutationsbedingter Dileucinmotive gewonnen. Die systematische Analyse von pathogenen Mutationen hat gezeigt, dass Dileucinmotive signifikant und spezifisch in ungeordneten zytosolischen Regionen von Transmembranproteinen überrepräsentiert sind. Dieser Peptidescreen macht das Potenzial unvoreingenommener Analysen zur Aufklärung von Krankheitsmechanismen deutlich, die von Veränderungen in Protein-Protein Interaktionen hervorgerufen werden. / Many disease-associated missense mutations prevent proteins from folding correctly and lead to loss-of-function. These mutations are often found in ordered regions of proteins. Another class of disease-related missense mutations can be found in disordered regions. These are thought to impair only specific parts of a protein’s functions. Those mutations could modify short linear motifs that mediate protein-protein interactions. Here, we designed a peptide-based interaction screen to identify interactions that are affected by mutations in disordered regions. We used synthetic peptides corresponding to the wild type and mutated protein regions spotted on cellulose membrane to pull-down interaction partners. This setup allows for the screening of more than hundred mutations at a time via mass spectrometry. Here, we focused on mutations implicated in neurological diseases. More than one-third of tested variant pairs show differential interactions. Three disease-related proline to leucine mutations in cytosolic tails of transmembrane proteins lead to gain of a dileucine sequence. Several dileucine-containing peptide motifs are involved in clathrin-mediated endocytosis (CME). Also in the presented screen, the newly created motifs mediate interaction with the CME machinery. This could explain the disease mechanisms since mislocalization of the affected transmembrane proteins would lead to their loss of function. This hypothesis has been corroborated for glucose transporter-1 (GLUT1) P485L, causing GLUT1 deficiency syndrome. We were able to provide functional evidence also for additional gained dileucine motifs. A systematic analysis of pathogenic mutations revealed dileucine motifs to be overrepresented in structurally disordered cytosolic regions of transmembrane proteins. The data gained with the peptide screen highlights the power of differential interactome mapping as a generic approach to unravel disease mechanisms caused by changes in protein-protein interactions.

No / The ability of neurons to modulate synaptic strength underpins synaptic plasticity, learning and memory, and adaptation to sensory experience. Despite the importance of synaptic adaptation in directing, reinforcing, and revising the behavioral response to environmental influences, the cellular and molecular mechanisms underlying synaptic adaptation are far from clear. Brain-derived neurotrophic factor (BDNF) is a prime initiator of structural and functional synaptic adaptation. However, the signaling cascade activated by BDNF to initiate these adaptive changes has not been elucidated. We have previously shown that BDNF activates mitogen- and stress-activated kinase 1 (MSK1), which regulates gene transcription via the phosphorylation of both CREB and histone H3. Using mice with a kinase-dead knock-in mutation of MSK1, we now show that MSK1 is necessary for the upregulation of synaptic strength in response to environmental enrichment in vivo. Furthermore, neurons from MSK1 kinase-dead mice failed to show scaling of synaptic transmission in response to activity deprivation in vitro, a deficit that could be rescued by reintroduction of wild-type MSK1. We also show that MSK1 forms part of a BDNF- and MAPK-dependent signaling cascade required for homeostatic synaptic scaling, which likely resides in the ability of MSK1 to regulate cell surface GluA1 expression via the induction of Arc/Arg3.1. These results demonstrate that MSK1 is an integral part of a signaling pathway that underlies the adaptive response to synaptic and environmental experience. MSK1 may thus act as a key homeostat in the activity- and experience-dependent regulation of synaptic strength.