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A peptide nucleic acid (PNA) encoded 1296 member peptide library was synthesised and incubated with a variety of cell types. Library members entering cells were extracted, hybridised onto DNA microarrays and the peptide identity was determined via deconvolution. Global consensus analysis highlighted the tetrapepide, Glu-Llp- Glu-Glu (Llp is 6-hexamine-N-aminoacetic acid), a surprise in view of the basic residues typically observed in cell penetrating peptides. When evaluated, Glu-Llp- Glu-Glu revealed cellular uptake comparable to a known basic peptide (tetraLlp). In depth delineation via clustering analysis allowed assessment of differential cellular uptake, with the identified peptides showing clear cellular specificity. This was verified by peptide synthesis and cellular uptake analysis by flow-cytometry, and in all cases an endocytic uptake mechanism was confirmed. This approach establishes a strategy for the identification of short peptides as tools for selective delivery into specific cell types. The incubation of a 10,000 member PNA-encoded peptide library with D54 and HEK293T transfected with CCR6 cells followed by microarray analysis allowed detailed information on the interaction between peptide-ligands and cell surface receptors to be extracted. This allowed the identification of new ligands for integrins and G-protein coupled receptors and offers a novel approach to ligand discovery allowing the comparative analysis of different cell types for the identification of differences in surface-receptor ligands and/or receptor expression between various cell types. In addition, this work included the development of a novel method for the indirect amplification of a PNA library by amplification of a complementary DNA library hybridised to the PNA. The generation of 10,000 defined pieces of DNA would have a myriad of applications, not least in the area of defined or directed sequencing and synthetic biology, but also in applications associated with encoding and tagging. By this approach DNA microarrays were used to allow the linear amplification of immobilised DNA sequences on an array followed by PCR amplification. Arrays of increasing sophistication (1; 10; 3875; 10,000 defined oligonucleotides) were used to validate the process, with sequences verified by selective hybridisation to a complementary DNA microarray with DNA sequencing demonstrating error rates of ca ≈ 0.2%. This technique offers an economical and efficient way of producing hundreds to thousands of specific DNA primers, while the DNA-arrays can be used as “factories” allowing specific DNA oligonucleotide pools to be generated with or without masking. This study also demonstrated a significant variance observed between the sequence frequencies found via Solexa sequencing compared to microarray analysis.

Caenorhabditis elegans has been studied as a model organism in various areas of biomedical research because it shares many conserved functions at molecular and genetic levels with humans. Specifically, it is an ideal organism to study heterogeneous metabolic syndromes such as Type 2 Diabetes Mellitus (T2DM) as C. elegans can be used to delineate molecular pathways that are at the core of its problems. A growing number of populations worldwide are faced with chronic T2DM, which also manifests several complications, such as blindness, neuropathy and cardiovascular diseases. Currently, metformin is the first-line drug of choice administered to treat T2DM. While the mechanism by which it alleviates the symptoms of diabetes is unknown, it has been found to reduce metabolic rate by partially inhibiting the mitochondrial complex I in mammals. Using C. elegans as a genetic model organism, we show that metformin reduces the mitochondrial activity through endosomal Na+/H+ exchanger, which a previous lab member has found to be a potential target of metformin. Furthermore, we show that high glucose diet−known to reduce the worm’s lifespan−alter the endosomal-lysosomal system and autophagy, providing insights to using C. elegans as a diabetic model. Based on these results, we propose that C. elegans can serve as a model organism to study T2DM as well as provide new ways to further investigate the pathophysiology of this disease.

Vital cellular processes such as nutrient uptake, receptor signaling, and cell migration are controlled by a balance between cell surface receptor internalization and recycling. Clathrin-mediated endocytosis is the major mechanism of receptor internalization in which cargo-enriched endocytic vesicles form at, and are released from, the plasma membrane before maturing into early endosomes. The receptors can then be sorted into fast and slow recycling pathways that replenish receptor levels at the cell surface. A major fast recycling pathway is controlled by the small GTPase Rab4a, which plays a central role in cell migration and cancer cell invasion through regulation of integrin αvβ3 recycling. Recent studies have discovered a family of clathrin-coated vesicle proteins, known as adaptin-ear-binding coat-associated proteins (NECAPs), that consists of two family members, NECAP1 and NECAP2. NECAP1 functions in endocytosis and cooperates with the clathrin adaptor AP-2 to control endocytic vesicle size, number and cargo. Importantly, NECAP2 did not rescue the knock-down phenotype of NECAP1, revealing that NECAPs are not functionally redundant. The studies described in this dissertation show that NECAP2 controls the fast recycling of epidermal growth factor receptor and transferrin receptor. Furthermore, NECAP2 specifically functions in Rab4a-mediated fast recycling together with the clathrin adaptor AP-1. In contrast, NECAP2 has no effect on AP-1-mediated transport from the Golgi or on other Rab4a-dependent sorting events that utilize additional clathrin adaptors and effector proteins. Thus, NECAP2 regulates a sub-route within the Rab4a recycling pathway and, in fact, is the first protein known to date to show this level of specificity. NECAP2 knock-down revealed that this sub-route controls cell migration and cancer cell invasion. Specifically, NECAP2 knock-down impaired the recycling of integrin αvβ3 to the cell surface, leading to decreased Rac1 activation and integrin αvβ3-dependent persistent cell migration. NECAP2 depletion also alleviated the inhibitory effect on integrin α5β1 recycling, switching cells to integrin α5β1-dependent cell migration. Notably, loss of NECAP2 function in breast cancer cells inhibited invasive migration in a 3D invasion model system. Therefore, the NECAP2 pathway may provide a therapeutic target, in particular for the 25% of breast cancers with amplification of Rab4a.

<p>Neurons, with their enormous membrane contents, depend heavily on regulated membrane trafficking processes to maintain their morphology and function. The phosphatidylinositol 3-kinase class III, or PIK3C3, plays a critical role in various membrane trafficking processes including both the endocytic and autophagic pathways. The functions of PIK3C3 in the nervous system in vivo are un-characterized. We reasoned that studying PIK3C3 in neurons would provide us an entry point into understanding the regulations and functions of the neuronal membrane trafficking processes and their roles in neuronal morphogenesis and homeostasis. </p><p>We generated a conditional allele of Pik3c3 and first deleted it specifically in the peripheral sensory neurons. Mutant large-diameter myelinated sensory neurons accumulated numerous enlarged vacuoles and ubiquitin-positive aggregates and underwent rapid degeneration. By contrast, Pik3c3-deficient small-diameter unmyelinated neurons accumulated excessive numbers of lysosome-like organelles and degenerated slower than large-diameter neurons. These differential degenerative phenotypes are unlikely caused by a disruption of the autophagy pathway, because inhibiting autophagy alone by conditional deletion of Atg7 results in a completely distinct subcellular phenotypes and very slow degenerations of all sensory neurons. More surprisingly, a noncanonical PIK3C3-independent LC3-positive autophagosome formation pathway was activated in Pik3c3-deficient small-diameter neurons. This work uncovered unexpected differences of the endo-lysosomal systems in different types of neurons and discovered a novel autophagy initiation pathway in vivo in neurons. </p><p>To examine the role of PIK3C3 in the central nervous system (CNS), we next deleted Pik3c3 in CNS neural progenitor cells using the Nestin-Cre transgenic line. The resulting conditional knockout mice displayed a severe cortical lamination abnormality caused by defective cortical neuron migration. This finding uncovered a previously under-appreciated role of endocytic trafficking in neural migration, which was further confirmed by electron microscopic analyses of the developing cortex. Moreover, overexpressing the dominant negative forms of Dynamin2 or Rab5, two regulators of endocytosis, caused similar migration defects as Pik3c3-deletion. Mechanistically, Pik3c3-deficient cortical neurons drastically reduced surface Reelin binding sites, and showed significantly decreased levels of Dab1 phosphorylation, despite expressing normal total amount of Reelin receptor ApoER2. This work suggests endocytosis and recycling of Reelin receptors are likely to play an important role in cortical migration regulated by the Reelin signaling pathway. </p><p>These studies represent the first in vivo characterization of PIK3C3 functions in mammals, and provide insight into the complexity and functional importance of neuronal endo-lysosomal and autophagic pathways.</p> / Dissertation

L’auto-incompatibilité est une barrière génétique qui permet à une plante de reconnaître et rejeter son propre pollen tout en acceptant le pollen d’individus moins apparentés d’un point de vue génétique. Chez les Brassicacées, l’auto-incompatibilité est contrôlée par un locus hautement polymorphe appelé le locus S, qui contient les déterminants mâle et femelle. Le stigmate exprime le déterminant femelle de l’auto-incompatibilité, S-LOCUS RECEPTOR KINASE (SRK). Chez Brassica oleracea, la localisation subcellulaire d’SRK est unique en son genre : le récepteur est localisé principalement au niveau des endosomes et dans une moindre mesure à la membrane plasmique.Nous avons étudié la fonction de la localisation endosomale de SRK chez Arabidopsis thaliana. Premièrement, nous avons réintroduit l’auto-incompatibilité chez Arabidopsis thaliana grâce à l’expression d’un allèle fonctionnel de SRK en provenance d’Arabidopsis lyrata (une espèce auto-incompatible). Deuxièmement, nous avons montré qu’un mutant perte de fonction de DYNAMIN-RELATED PROTEIN1A, une protéine requise pour l’endocytose, abolissait l’auto-incompatibilité. Nos résultats suggèrent que l’endocytose est requise pour l’auto-incompatibilité, et que SRK pourrait activer sa voie de signalisation depuis les endosomes. / Self-incompatibility is a genetic barrier by which a plant recognizes and rejects its own pollen while allowing pollen from more distantly related plants to germinate. In the Brassicacea family, it is controlled by a highly polymorphic locus called the S-locus, which contains the male and female determinants of self-incompatibility. The stigma expresses the female determinant of self-incompatibility, the plant receptor kinase (PRK) S-LOCUS RECEPTOR KINASE (SRK). In Brassica oleracea, SRK has a unique subcellular localization among PRK: the receptor is mostly localized in endosomes and to a lesser extent at the plasma membrane.We investigated the function of the endosomal localization of SRK in Arabidopsis thaliana. Firstly, we reintroduced self-incompatibility in Arabidopsis thaliana by expression of a functional SRK allele from Arabidopsis lyrata (a self-incompatible species). Secondly, we showed that a loss-of-function mutant of DYNAMIN-RELATED PROTEIN1A, a protein required for endocytosis, abolished self-incompatibility. Our results suggest that endocytosis is required for self-incompatibility, and that SRK may be signaling from endosomal compartments.

Nhx1 est un antiport vacuolaire de Na+/H+ chez la levure Saccharomyces cerevisiae. Nhx1 joue un rôle important dans le maintien de l’homéostasie ionique du cytoplasme de la cellule. En effet, la mutation du gène NHX1 chez la levure nhx1Δ entraîne une perte de l’homéostasie cellulaire quand les cellules sont cultivées dans un milieu de faible osmolarité. Ce travail rapporte pour la première fois, et contrairement à la cellule parentale, que la mutation du gène NHX1 a pour effet une sensibilité du mutant nhx1Δ à une variété des drogues et des agents cationiques et anioniques lorsque les cellules sont cultivées dans un milieu riche. En outre, dans ces conditions de culture, aucune sensibilité n’a été observée chez le mutant nhx1Δ quand les cellules sont traitées avec différentes concentrations de sel. Nous avons aussi démontré que la sensibilité du mutant nhx1Δ aux différents agents ainsi que la sécrétion de l’enzyme carboxypeptidase Y observé chez ce mutant n’ont pas été restauré lorsque les cellules sont cultivées dans des milieux avec différents pH ou avec différentes concentrations de sel. Enfin, une analyse génétique a révélé que le mutant nhx1Δ montre un phénotype distinct d’autres mutants qui ont un défaut dans le trafic entre le compartiment pré-vacuolaire et l’appareil de Golgi quand ces cellules sont traitées avec différents agents. Cette analyse prouve que la sensibilité de nhx1Δ aux différents agents n’est pas liée au trafic entre le compartiment pré-vacuolaire et l’appareil de Golgi. / Nhx1 is an intracellular Na+/H+ exchanger localized to the late endosome in Saccharomyces cerevisiae. It is believed that Nhx1 plays a major role in pH-mediated vesicle trafficking, as nhx1Δ mutant is defective in maintaining the intracellular pH in the vacuoles and cytoplasm when grown in low osmolarity media. In this work, we reported novel drug sensitivities of the nhx1Δ mutant to a range of cationic and anionic agents when cells are grown in rich media. Unlike the low osmolarity media, the nhx1Δ mutant showed no sensitivity to salt. Furthermore, we showed that the drug phenotypes of the nhx1Δ mutant, as well as the secretion of the vacuolar protein carboxypeptidase Y, were not rescued by either altering the pH or salt concentration. Although, amino acid substitution of the phylogenetically conserved residue Glu355 for Ala (E355A) in Nhx1 resulted in sensitivity to genotoxic drug bleomycin, it was not observed for the non-conserved residue Glu371Ala (E371A). Moreover, genetic analysis revealed that the nhx1Δ mutant displayed distinct drug phenotypes in comparison to mutants that are defective in retrograde trafficking from the prevacuole to the late Golgi, excluding the possibility that the drug sensitivity of the nhx1Δ mutant is related to retrograde trafficking.

Nhx1 est un antiport vacuolaire de Na+/H+ chez la levure Saccharomyces cerevisiae. Nhx1 joue un rôle important dans le maintien de l’homéostasie ionique du cytoplasme de la cellule. En effet, la mutation du gène NHX1 chez la levure nhx1Δ entraîne une perte de l’homéostasie cellulaire quand les cellules sont cultivées dans un milieu de faible osmolarité. Ce travail rapporte pour la première fois, et contrairement à la cellule parentale, que la mutation du gène NHX1 a pour effet une sensibilité du mutant nhx1Δ à une variété des drogues et des agents cationiques et anioniques lorsque les cellules sont cultivées dans un milieu riche. En outre, dans ces conditions de culture, aucune sensibilité n’a été observée chez le mutant nhx1Δ quand les cellules sont traitées avec différentes concentrations de sel. Nous avons aussi démontré que la sensibilité du mutant nhx1Δ aux différents agents ainsi que la sécrétion de l’enzyme carboxypeptidase Y observé chez ce mutant n’ont pas été restauré lorsque les cellules sont cultivées dans des milieux avec différents pH ou avec différentes concentrations de sel. Enfin, une analyse génétique a révélé que le mutant nhx1Δ montre un phénotype distinct d’autres mutants qui ont un défaut dans le trafic entre le compartiment pré-vacuolaire et l’appareil de Golgi quand ces cellules sont traitées avec différents agents. Cette analyse prouve que la sensibilité de nhx1Δ aux différents agents n’est pas liée au trafic entre le compartiment pré-vacuolaire et l’appareil de Golgi. / Nhx1 is an intracellular Na+/H+ exchanger localized to the late endosome in Saccharomyces cerevisiae. It is believed that Nhx1 plays a major role in pH-mediated vesicle trafficking, as nhx1Δ mutant is defective in maintaining the intracellular pH in the vacuoles and cytoplasm when grown in low osmolarity media. In this work, we reported novel drug sensitivities of the nhx1Δ mutant to a range of cationic and anionic agents when cells are grown in rich media. Unlike the low osmolarity media, the nhx1Δ mutant showed no sensitivity to salt. Furthermore, we showed that the drug phenotypes of the nhx1Δ mutant, as well as the secretion of the vacuolar protein carboxypeptidase Y, were not rescued by either altering the pH or salt concentration. Although, amino acid substitution of the phylogenetically conserved residue Glu355 for Ala (E355A) in Nhx1 resulted in sensitivity to genotoxic drug bleomycin, it was not observed for the non-conserved residue Glu371Ala (E371A). Moreover, genetic analysis revealed that the nhx1Δ mutant displayed distinct drug phenotypes in comparison to mutants that are defective in retrograde trafficking from the prevacuole to the late Golgi, excluding the possibility that the drug sensitivity of the nhx1Δ mutant is related to retrograde trafficking.

Self-incompatibility is a genetic barrier by which a plant recognizes and rejects its own pollen while allowing pollen from more distantly related plants to germinate. In the Brassicacea family, it is controlled by a highly polymorphic locus called the S-locus, which contains the male and female determinants of self-incompatibility. The stigma expresses the female determinant of self-incompatibility, the plant receptor kinase (PRK) S-LOCUS RECEPTOR KINASE (SRK). In Brassica oleracea, SRK has a unique subcellular localization among PRK: the receptor is mostly localized in endosomes and to a lesser extent at the plasma membrane.We investigated the function of the endosomal localization of SRK in Arabidopsis thaliana. Firstly, we reintroduced self-incompatibility in Arabidopsis thaliana by expression of a functional SRK allele from Arabidopsis lyrata (a self-incompatible species). Secondly, we showed that a loss-of-function mutant of DYNAMIN-RELATED PROTEIN1A, a protein required for endocytosis, abolished self-incompatibility. Our results suggest that endocytosis is required for self-incompatibility, and that SRK may be signaling from endosomal compartments.