Flavonoids are secondary metabolites that are important in plant defense, protection, and human health. Most naturally-occurring flavonoids are found in glucosylated form. Glucosyltransferases (GTs) are enzymes that catalyze the transfer of glucose from a high energy sugar donor to an acceptor molecule. At this time, it is not possible to accurately predict putative GT activity from sequence alone; biochemical characterization is critical. A flavonol-specific 3-O-GT enzyme has been identified and cloned from the leaf tissues of grapefruit. The enzyme shows rigid substrate specificity and regiospecificity. F3GTs from grape and grapefruit were modeled against F7GTs from Crocus sativus and Scrutellaria biacalensis, and several non-conservative amino acid differences were identified that may impact regioselectivity. This research is designed to test the hypothesis that specific amino acid residues impart the regiospecificity of the grapefruit enzyme. Site-directed mutagenesis was performed on three potentially key amino acid residues within the grapefruit F3-GT that were identified through homology modeling. Enzyme activity of the mutant F3-GT proteins will be analyzed for a possible change in glucosylation pattern. Other flavonoid classes will also be tested with the mutant enzymes to test for change in substrate specificity.

Flavonoids are secondary metabolites that are important in plant defense, protection, and human health. Most naturally-occurring flavonoids are found in glucosylated form. Glucosyltransferases (GTs) are enzymes that catalyze the transfer of glucose from a high energy sugar donor to an acceptor molecule. At this time, it is not possible to accurately predict putative GT activity from sequence alone; biochemical characterization is critical. A flavonol-specific 3-O-GT enzyme has been identified and cloned from the leaf tissues of grapefruit. The enzyme shows rigid substrate specificity as well as regiospecificity. Several F3GT's characterized from other plants also had the ability to glucosylate anthocyanidins, however the grapefruit F3GT did not. This research is designed to test the hypothesis that specific amino acid residues impart the substrate specificity and regiospecificity of the grapefruit enzyme. Site-directed mutagenesis was performed on three potentially key amino acid residues within the grapefruit F3-GT that were identified through homology modelling. Enzyme activity of the mutant F3-GT proteins will be tested with flavonols for a possible change in glucosylation pattern. Other flavonoid classes will also be tested with the mutant F3-GT enzyme to test for change in substrate specificity. The result from this study will add to our knowledge of GTs.

Darmkrebs ist die zweithäufigste malignombedingte Todesursache in den westlichen Industrieländern. Durch eine frühzeitige Diagnose besteht jedoch eine hohe Chance auf Heilung. Der Goldstandard zur Darmkrebsfrüherkennung ist gegenwärtig die Koloskopie. Eine Darmspiegelung ist jedoch invasiv und mit Unannehmlichkeiten für den Patienten verbunden. Die Akzeptanz in der Bevölkerung ist daher gering. Ziel des BMBF- Projektes „Entwicklung eines nichtinvasiven Nachweissystems zur Früherkennung von humanem Darmkrebs“, in dessen Rahmen diese Arbeit entstand, ist die Bereitstellung eines nichtinvasiven Nachweisverfahrens zur Darmkrebsfrüherkennung. Der Nachweis soll über die Detektion von aus neoplastischen Zellen stammender DNA in Stuhl erfolgen. Die Entartung dieser Zellen beruht auf Veränderungen im Erbgut, welches unter anderem Mutationen sind. Im ersten Teil des BMBF-Projektes wurde ein Set von Mutationen zusammengestellt, welches eine hohe Sensitivität für Vorstufen von Darmkrebs aufweist. Ziel dieser Arbeit war es, eine Nachweismethode für die zuvor identifizierten Punktmutationen zu entwickeln. Das Nachweisverfahren musste dabei unempfindlich gegen einen hohen Hintergrund nichtmutierter DNA sein, da im Stuhl geringe Mengen DNA aus neoplastischen Zellen bei einem hohen Hintergrund von DNA aus gesunden Zellen vorliegen. Hierzu wurden Plasmidmodellsysteme für die aus dem Marker-Set stammenden Genfragmente BRAF und dessen Mutante V600E, CTNNB1 und T41I, T41A, S45P und K-ras G12C hergestellt. Mit Hilfe dieser Plasmidmodellsysteme wurde dann das Nachweissystem entwickelt. Der entscheidende Schritt für die Detektion von Punktmutationen bei hohem Wildtypüberschuss ist eine vorhergehende Anreicherung. In der vorliegenden Arbeit wurde dazu die Methode der LNA-clamp-PCR (locked nucleic acid) etabliert. Die Bewertung der erzielten Anreicherung erfolgte über das relative Detektionslimit. Zur Bestimmung des Detektionslimits wurde die Schmelzkurvenanalyse von Hybridisierungssonden eingesetzt; diese wurde im Rahmen dieser Arbeit für die drei oben genannten Genfragmente und ihre Mutanten entwickelt. Die LNA-clamp-PCR wird in Anwesenheit eines LNA-Blockers durchgeführt. Das Nukleotidanalogon LNA weist im Vergleich zu DNA eine erhöhte Affinität zu komplementären DNA-Strängen auf. Gleichzeitig kommt es bei Anwesenheit einer Basenfehlpaarung zu einer größeren Destabilisierung der Bindung. Als Blocker werden kurze LNA-DNA-Hybridoligonukleotide eingesetzt, die den mutierten Sequenzbereich überspannen und selbst der Wildtypsequenz entsprechen. Durch Bindung an die Wildtypsequenz wird deren Amplifikation während der PCR verhindert (clamp = arretieren, festklemmen). Der Blocker selbst wird dabei nicht verlängert. Der Blocker bindet unter optimalen Bedingungen jedoch nicht an die mutierte Sequenz. Die Mutante wird daher ungehindert amplifiziert und somit gegenüber dem Wildtyp-Fragment angereichert. Die Position des Blockers kann im Bindungsbereich eines der Primer sein und hier dessen Hybridisierung an dem Wildtyp-Fragment verhindern oder zwischen den beiden Primern liegen und so die Synthese durch die Polymerase inhibieren. Die Anwendbarkeit beider Systeme wurde in dieser Arbeit gezeigt. Die LNA-clamp-PCR mit Primerblocker wurde für BRAF etabliert. Es wurde ein Detektionslimit von mindestens 1:100 erzielt. Die LNA-clamp-PCR mit Amplifikationsblocker wurde erfolgreich für BRAF, K-ras und CTNNB1: T41I, T41A mit einem Detektionslimit von 1:1000 bis 1:10 000 entwickelt. In Stuhlproben liegt DNA aus neoplastischen Zellen nach Literaturangaben zu einem Anteil von 1% bis 0,1% vor. Die LNA-clamp-PCR weist also mit Amplifikationsblockern ein ausreichend hohes Detektionslimit für die Analyse von Stuhlproben auf. Durch die erfolgreiche Etablierung der Methode auf drei verschiedenen Genfragmenten und vier unterschiedlichen Punktmutationen konnte deren universelle Einsetzbarkeit gezeigt werden. Für die Ausweitung der LNA-clamp-PCR auf die übrigen Mutationen des Marker-Sets wurden Richtlinien ausgearbeitet und die Blockereffizienz als Kennzahl eingeführt. Die LNA-clamp-PCR ist ein schnelles, kostengünstiges Verfahren, welches einen geringen Arbeitsaufwand erfordert und wenig fehleranfällig ist. Sie ist somit ein geeignetes Anreicherungsverfahren für Punktmutationen in einem diagnostischen System zur Darmkrebsfrüherkennung. Darüber hinaus kann die LNA-clamp-PCR auch in anderen Bereichen, in denen die Detektion von Punktmutationen in einem hohen Wildtyphintergrund erforderlich ist, eingesetzt werden. / Colon cancer is the second leading cause of cancer related deaths in the western world. However if diagnosed early there is a great chance curing the disease. Coloscopy is the gold standard for early detection of colorectal cancer today. Its greatest disadvantage is the fact that it is an invasive technique and provides some discomfort for the patients. Therefore, the compliance to undergo such a procedure is extremely low. This work was generated in the context of the BMBF-project „Development of a non-invasive assay for the early detection of preneoplastic and neoplastic lesions in the human colon“. The aim of the work described here is the development of a non-invasive assay for the early detection of colon cancer. The assay should detect DNA from neoplastic cells in feces samples. The transformation of these cells is based on alterations in the genome predominantly mutations. In the first part of the BMBF-project a mutation panel with high sensitivity for preneoplastic lesions of colon cancer was determined. The aim of this work was to develop a detection method for the point mutations of the determined mutation panel. The rare mutant DNA needs to be detected in the presence of a great amount of wild-type DNA shed from healthy tissue. The assay system needs to be insensitive to this high background of healthy DNA. Therefore a model system of plasmid DNA containing gene fragments of BRAF and its mutation V600E, CTNNB1 and T41I, T41A, S45P and K-ras G12C obtained from the marker panel was established. Using these plasmid system the detection method was developed. The most critical parameter for the detection of rare point mutations is an enrichment of these rare DNA molecules. In this work LNA-clamp-PCR (locked nucleic acid) technology was used to enrich the mutant DNA.. For the estimation of the achieved enrichment the relative detection limit was used. The detection limit was determined by melting curve analysis of hybridization probes. These assays were established in the present work for the three above mentioned gene fragments. LNA-clamp-PCR is performed in the presence of an LNA blocker. LNA is a synthetic DNA analog. LNA nucleotide analog bind to complementary DNA strands with higher affinity. In addition a single mismatch in the LNA-DNA duplex causes a much greater destabilization compared to a DNA-DNA duplex. Short LNA-DNA-hybrids were used as clamp, which cover the mutated region and represent the wild-type sequence. Within an appropriate temperature range, LNA can specifically bind to wild type template and can inhibit its amplification. The clamp itself will not be elongated. Under optimal conditions the LNA clamp will not interfere with the amplification of the mismatched template. Therefore the mutated gene fragment will be enriched in comparison to the wild-type. The position of the LNA clamp can either be at the primer binding site inhibiting primer hybridization on the wild-type fragment or the LNA clamp is positioned between the two primer binding sites inhibiting chain elongation of the perfectly matched template. In the present work both systems were applied. For the gene fragment BRAF the LNA was used at the primer binding site. The achieved detection limit was at least 1:100. The LNA-clamp-PCR with LNA inhibiting the chain elongation were developed successfully for BRAF, K-ras and CTNNB1: T41I, T41A achieving a detection limit of 1:1000 to 1:10 000. According to the literature 1% to 0.1% of the DNA in feces derives from neoplastic cells. Therefore the detection limit achieved by LNA-clamp-PCR with LNA inhibiting chain elongation would be sufficient for analyzing feces samples. LNA-clamp-PCR protocols were established for three different gene fragments and four diverse point mutations indicating that the technology can generally be used for high sensitive detection of DNA mutations. For the development of LNA-clamp-PCR protocols for the other mutations of the marker panel development guidelines were established. Clamp efficiency was identified as a quantitative parameter for protocol optimization. The LNA-clamp-PCR is a robust, fast and cost-saving technique which needs low labor input. Therefore the method is adequate for enriching point mutated gene fragments in a diagnostic assay for the detection of early colon cancer stages. In addition LNA-clamp-PCR can be applied in other fields where rare sequence variations need to be detected in the presence of high wild-type DNA background.

A síndrome de McCune Albrigth (SMA) é uma doença genética não hereditária, com incidência estimada entre 1/100.000 e 1/1.000.000 casos/ano. A SMA caracteriza-se clinicamente pela tríade: displasia óssea fibrosa (FD), manchas cutâneas café-com-leite e hiperfunção endócrina tais como: síndrome de Cushing, pseudo-puberdade precoce, hipertiroidismo, acromegalia. O diagnóstico da SMA clássica é usualmente baseado no quadro clínico associado a dosagens hormonais e exames de imagem, principalmente cintilografia do esqueleto. No entanto, quadros atípicos e formas parciais muitas vezes dificultam o diagnóstico preciso da síndrome. O objetivo deste estudo foi padronizar dentre as técnicas de PNA (peptide nucleic acid) e PCT em Tempo Real, para a detecção de polimorfismos de base única (SNPs), a técnica mais sensível para a discriminação das mutações ativadoras da subunidade da proteína G. Para este estudo foram selecionados 32 pacientes, 1 masculino e 31 femininos, com SMA, todos em seguimento no Hospital das Clínicas da Faculdade de Medicina da USP. Como resultado positivo, apresentamos nesse trabalho pela primeira vez o uso do RT-PCR genotipagem na detecção das mutações ativadoras da proteína G, em DNA extraído de tecidos afetados e em leucócitos de sangue periférico, sendo a técnica considerada sensível o suficiente para discriminar de forma simples e rápida as mutações ativadoras da PGs. Sugerimos nesse estudo o uso da técnica de discriminação alélica pelo sistema Taqman. Essa técnica possibilita a detecção destas mutações gsp no sangue periférico mesmo numa baixa porcentagem, uma vez que nem sempre o tecido afetado (gônada, osso, hipófise) é disponível. / The McCune-Albright Syndrome (MAS) is a genetic disease, with incidence estimated at 1/100.000 and 1/1000000 cases per year. MAS is clinically characterized by the triad: bone fibrous dysplasia (FD) café-au-lait skin spots and endocrine hyperfunction, such as: precocious puberty (PP), Cushing's syndrome, hyperthyroidism and acromegaly. The diagnosis of MAS is originally based on clinical characteristics associated with hormonal and imaging studies. However, atypical and partial forms often hamper the accurate diagnosis of the syndrome. For this study we selected 32 patients, 1male and 31 females, all being treated in Hospital das Clínicas, School of Medicine, University of São Paulo. As a positive result, we showed for the first time the use of Real Time PCR/genotyping for the detection of activating mutations of the stimulatory G protein, using blood leucocytes DNA. This technique was sensible and can bring fast results for the patient and the physician, making the diagnosis easier. Our study proposes the use of allelic discrimination by Taqman system, which can be used as a probe that allows the identification of specific genotypes. These techniques could help detect these mutations in peripheral blood when the affected tissue is not available.

This diploma thesis provides an overview of gene conversion, its role in the pathogenesis of human diseases and the use of methods based on next-generation sequencing (NGS) for detection rare variants of DNA sequence. Labeling of target DNA molecules by random nucleotides in primer and NGS were used for detection point mutations arising de novo in the β-glucocerebrosidase gene by gene conversion between it and its pseudogene in meiotic and mitotic cells of control subjects. Primers specific for the active gene were used to selectively amplify the ninth and tenth exon of the gene where "recombinant" variants occur most frequently. Sequences generated from 20 genomic DNA samples on Illumina MiSeq platform were quality filtered, sorted by unique labels and consensus sequences were created from alignments of sequences carrying the same DNA tag. The number of potential point mutations in the samples ranged between 12 and 48. The mutations were manually re-evaluated from the alignments. The number of alignments with unique labeling was in the range of 7-15 thousand per sample. Only three samples carried possible recombinant mutations, suggesting a lower frequency of conversion in the region than reported by other techniques. Analysis of unique sequences in primer indicated possible ways to improve the...

The transient receptor potential ankyrin 1 (TRPA1) ion channel is expressed in a subset of primary afferent neurones where it is activated by a variety of pungent and chemically reactive compounds such as allyl isothiocyanate or cinnamaldehyde. This voltage- dependent channel is activated through covalent modification of cytoplasmic cysteines and, from the cytoplasmic side, is also critically regulated by calcium ions. Both, amino (N-) and carboxyl (C-) termini have been shown to be involved in these processes. Using electrophysiological and molecular-biology techniques, we explored the role of specific cytoplasmic domains in the activation of TRPA1. By measuring chemically-, voltage-, and calcium-activated membrane TRPA1-mediated currents, we identified highly conserved serine and threonine residues along the N-terminal ankyrin repeat domain, mutation of which strongly affected responses of the channel. In addition, using C-terminally truncated construct previously reported to be involved in calcium regulation, we present a new finding that the distal C-terminal tail contributes to voltage-dependent activation of TRPA1.

Evolution is the single cohesive logical framework in which all biological processes may exist simultaneously. Incremental changes in phenotype over imperceptibly large timescales have given rise to the enormous diversity of life we witness on earth both presently and through the natural record. The basic unit of evolution is mutation, and by perturbing biological processes, mutations may alter the fitness of an individual. However, the fitness effect of a mutation is difficult to infer from historical record, and complex to obtain experimentally in an efficient and accurate manner. We have recently developed a high throughput method to iteratively mutagenize regions of essential genes in yeast and subsequently analyze individual mutant fitness termed Exceedingly Methodical and Parallel Investigation of Randomized Individual Codons (EMPIRIC). Utilizing this technique as exemplified in Chapters II and III, it is possible to determine the fitness effects of all possible point mutations in parallel through growth competition followed by a high throughput sequencing readout. We have employed this technique to determine the distribution of fitness effects in a nine amino acid region of the Hsp90 gene of S. cerevisiae under elevated temperature, and found the bimodal distribution of fitness effects to be remarkably consistent with near-neutral theory. Comparing the measured fitness effects of mutants to the natural record, phylogenetic alignments appear to be a poor predictor of experimental fitness. In Chapter IV, to further interrogate the properties of this region, library competition under conditions of elevated temperature and salinity were performed to study the potential of protein adaptation. Strikingly, whereas both optimal and elevated temperatures produced no statistically significant beneficial mutations, under conditions of elevated salinity, adaptive mutations appear with fitness advantages up to 8% greater than wild type. Of particular interest, mutations conferring fitness benefits under conditions of elevated salinity almost always experience a fitness defect in other experimental conditions, indicating these mutations are environmentally specialized. Applying the experimental fitness measurements to long standing theoretical predictions of adaptation, our results are remarkably consistent with Fisher’s Geometric Model of protein evolution. Epistasis between mutations can have profound effects on evolutionary trajectories. Although the importance of epistasis has been realized since the early 1900s, the interdependence of mutations is difficult to study in vivo due to the stochastic and constant nature of background mutations. In Chapter V, utilizing the EMPIRIC methodology allows us to study the distribution of fitness effects in the context of mutant genetic backgrounds with minimal influence from unintended background mutations. By analyzing intragenic epistatic interactions, we uncovered a complex interplay between solvent shielded structural residues and solvent exposed hydrophobic surface in the amino acid 582-590 region of Hsp90. Additionally, negative epistasis appears to be negatively correlated with mutational promiscuity while additive interactions are positively correlated, indicating potential avenues for proteins to navigate fitness ‘valleys’. In summary, the work presented in this dissertation is focused on applying experimental context to the theory-rich field of evolutionary biology. The development and implementation of a novel methodology for the rapid and accurate assessment of organismal fitness has allowed us to address some of the most basic processes of evolution including adaptation and protein expression level. Through the work presented here and by investigators across the world, the application of experimental data to evolutionary theory has the potential to improve drug design and human health in general, as well as allow for predictive medicine in the coming era of personalized medicine.

The primary amino acid sequence of a protein governs its specific cellular functions. Since the cracking of the genetic code in the late 1950’s, it has been possible to predict the amino acid sequence of a given protein from the DNA sequence of a gene. Nevertheless, the ability to predict a protein’s function from its primary sequence remains a great challenge in biology. In order to address this problem, we combined recent advances in next generation sequencing technologies with systematic mutagenesis strategies to assess the function of thousands of protein variants in a single experiment. Using this strategy, my dissertation describes the effects of most possible single point mutants in the multifunctional Ubiquitin protein in yeast. The effects of these mutants on the essential activation of ubiquitin by the ubiquitin activating protein (E1, Uba1p) as well as their effects on overall yeast growth were measured. Ubiquitin mutants defective for E1 activation were found to correlate with growth defects, although in a non-linear fashion. Further examination of select point mutants indicated that E1 activation deficiencies predict downstream defects in Ubiquitin function, resulting in the observed growth phenotypes. These results indicate that there may be selective pressure for the activity of the E1enzyme to selectively activate ubiquitin protein variants that do not result in functional downstream defects. Additionally, I will describe the use of similar techniques to discover drug resistant mutants of the oncogenic protein BRAFV600E in human melanoma cell lines as an example of the widespread applicability of our strategy for addressing the relationship between protein function and biological fitness.

Viruses constitute the vast majority of all biological entities in the biosphere and represent one of the biggest reservoirs of undetected genetic diversity on Earth. Of all the viral particles inhabiting the ocean, phages are the most abundant and can affect the overall microbial composition of marine ecosystems and the dynamics of global biogeochemical cycles. The interaction between prokaryotic cells and their phages is among the oldest and most intertwined host-parasite relationships on the planet. It has been extensively studied by culture, molecular biology, and experimental evolution. However, due to the difficulties of culture with environmental samples, only a few studies have analyzed the mechanisms of phage-host interaction in the marine environment. Here, we have studied the genes involved in viral host recognition and their evolutionary dynamics by focusing on two species of the marine copiotrophic bacterium Alteromonas and several phages infecting them. We described the genomic and morphological characterization of the first Alteromonas phage belonging to the Myoviridae family (Alteromonas myovirus V22) that was isolated in coastal waters of the Mediterranean Sea, and we identified its receptor-binding protein (RBP) used for host recognition by combining fluorescence microscopy and spectrometry. In addition, using size-exclusion chromatography, we showed how this protein required co-expression with a downstream protein to be functional, which later was identified as a new type of intermolecular chaperone crucial for RBP maturation. We also identified a conserved host recognition module in V22 and other unrelated alterophages belonging to different viral families and with completely different morphologies, suggesting horizontal gene transfer between the ancestors of these phages. Furthermore, we described the first coevolution study of a host-parasite system performed with Alteromonas using a metagenomics-like approach. Finally, we analyzed the micro- and macrodiversity of an alterophage population that was able to survive over a long period of time and showed remarkable genomic stability, indicating stable interactions over time between phage-host recognition structures. Overall, this study has contributed to extend the knowledge of known phage-host recognition mechanisms present in the marine ecosystem and has provided a first glimpse of the evolutionary dynamics in phages infecting Alteromonas.

No / Trafficking motifs present in the intracellular regions of ion channels affect their subcellular location within neurons. The mechanisms that control trafficking to dendrites of central neurons have been identified, but it is not fully understood how channels are localized to the soma. We have now identified a motif within the calcium-activated potassium channel K(Ca)2.1 (SK1) that results in somatic localization. Transfection of hippocampal neurons with K(Ca)2.1 subunits causes expression of functional channels in only the soma and proximal processes. By contrast, expressed K(Ca)2.3 subunits are located throughout the processes of transfected neurons. Point mutation of K(Ca)2.1 within this novel motif to mimic a sequence present in the C-terminus of K(Ca)2.3 causes expression of K(Ca)2.1 subunits throughout the processes. We also demonstrate that blocking of clathrin-mediated endocytosis causes K(Ca)2.1 subunit expression to mimic that of the mutated subunit. The role of this novel motif is therefore not to directly target trafficking of the channel to subcellular compartments, but to regulate channel location by subjecting it to rapid clathrin-mediated endocytosis.