Ce projet vise à cartographier la machinerie de régulation des Rho GTPases chez C. elegans afin de mieux comprendre les mécanismes d'intégration des voies de signalisation au cours du développement des organismes multicellulaires. La première partie du projet consistait à caractériser la spécificité catalytique des Rho GAP envers les Rho GTPases in silico et in vitro. En adaptant un programme de prédiction de structures tridimensionnelles, Combinatorial Extension (CE), nous avons pu faire corréler une similitude structurelle avec la spécificité catalytique des GAP. Ce prédicteur amélioré a validé des interactions GAP-GTPase connues: cinq chez les mammifères et quatre avec des GAP homologues chez C. elegans. Les résultats de conservation des interactions que nous avons obtenus, permettent de justifier l'utilisation de ce nématode comme modèle d'étude pour l'humain. Par la suite, nous avons optimisé les essais expérimentaux pour tester la spécificité catalytique des Rho GAP de C. elegans en vue de valider le prédicteur. Dans la deuxième partie nous avons étudié les interactions fonctionnelles des Rho GAP au cours du développement embryonnaire du C. elegans in vivo. Les résultats obtenus nous ont aidés à mieux comprendre le réseau de régulation de la GTPase rho-1 par les GAP rga-5, gei-1 et rga-13 au cours de l'élongation embryonnaire. De plus, nous savons désormais qu'ocrl-1 est dans une voie antagoniste à rga-5. Enfin, dans la troisième partie de notre travail, nous avons mis au point une méthode d'analyse haut débit des interactions génétiques des Rho GAP sur le cytomètre en flux pour vers (le COPAS Biosort) avec des transgéniques histone::GFP. Puis cette méthode a été adaptée pour permettre d'utiliser des souches non fluorescentes, en colorant les noyaux des cellules des embryons fixés. Ce travail a apporté un nouvel outil de prédictions et a permis de simplifier les méthodes de travail pour l'étude des machineries de régulation de GTPases Rho. La technique haut-débit que nous avons développée pourrait aussi s'adapter à l'étude d'autres régulateurs (GEF, etc). ______________________________________________________________________________ MOTS-CLÉS DE L’AUTEUR : Caenorhabditis elegans, Rho GAP, prédicteur, développement embryonnaire, haut débit

Cell polarity is the asymmetric distribution of organelles that almost all cells use to separate individual processes and perform complex functions. Although the manner in which cells are polarized is very diverse, the processes necessary to assume polarized phenotypes are similar in many cell types. Epithelial cell polarization is of particular importance, as these cells serve form linings of organs and act as barriers distinguishing different compartments. Furthermore, loss of epithelial polarization occurs in some disease states and may result in cell invasion through underlying matrix. During initial polarization, vesicle trafficking is indispensible for assembly of structures, including apical junctional complex formation. Trafficking of new membrane and associated proteins to leading edges is also necessary for cell migration. RalA and RalB are members of the Ras superfamily of GTPases and have been implicated in several processes, including vesicle trafficking. Only 5 Ral effectors have been identified, two of which are members of the Exocyst complex, a hetero-octameric complex also involved with vesicle trafficking. I hypothesized that Ral GTPases were necessary for several aspects of cell polarization, and that they engage the Exocyst complex to mediate these processes. Initial investigation of tight junction assembly found that both RalA and RalB antagonistically affect paracellular permeability. Knockdown of RalA and RalB resulted in decreased and increased incorporation of components into assembling tight junctions, respectively. Furthermore, both RalA and RalB engaged the Exocyst in order to mediate tight junction assembly. I next examined the role of RalA-Sec5 and RalA-Exo84 interactions during tumor cell migration and invasion. Both interactions were necessary for invasion and single cell migration, although disruption of each interaction affected different aspects of migration. Furthermore, significant differences in cytoskeleton organization occurred in response to disruption of RalA-Sec5 and RalA-Exo84 interactions. Finally, I investigated the effects of RalA and RalB knockdown on growth of primary cilia and cyst formation. RalA decreased primary cilia growth and reduced average cilia length, while RalB increased cilia length. Knockdown of RalA and RalB also affected lumen formation during cystogenesis, as RalA knockdown prevented lumen formation and RalB knockdown caused formation of multiple lumens. Taken together, data presented here show that Ral engages the Exocyst to mediate distinct processes during tight junction assembly and cell migration, and implicates Ral GTPases in several different aspects of cell polarity.

RhoA is a small GTPase that acts as a molecular switch to control a variety of signal transduction pathways in eukaryotes. From an initial established role in the regulation of the actin cytoskeleton, RhoA has now been implicated in a range of functions that include gene transcription and regulation of cell morphology. In earlier studies from this laboratory that employed differential display and in situ hybridisation, RhoA was indicated as being up-regulated during the stages of early heart development in the developing chick embryo. Given the important effects of RhoA on both gene expression and morphology in other systems, it was hypothesised that RhoA plays a central role in the molecular mechanisms controlling cardiogenesis. This thesis describes investigations undertaken to elucidate the role of RhoA in these processes. As an initial approach to corroborate the earlier gene expression findings and provide further evidence for a role in tissue developmental mechanisms, RhoA proteins levels in the developing chick embryo were analysed using immunocytochemistry. These experiments demonstrated that RhoA is most abundant in heart-forming regions, findings compatible with the earlier gene expression studies and the proposed role of this protein in early heart development. Preliminary studies from this laboratory had also suggested that chick RhoA is expressed as different length mRNA transcripts that vary only in the 3' untranslated region (UTR). This thesis presents additional evidence for the existence of these different RhoA transcripts from experiments using Northern hybridisation and RT-PCR analyses. These analyses also serve to demonstrate that the second shortest RhoA transcript (designated RhoA2) is the most abundant transcript in developing heart tissue, in contrast to the situation in other embryonic tissues, findings that could be taken to suggest a possible role for this 3'UTR in developmental mechanisms that is yet to be elucidated. One potentially informative approach for testing the function of a protein in a biological system is to inhibit its expression and/or activity and observe the changes induced. The effects of inhibiting RhoA in early heart development and early organogenesis in the chick embryo model were investigated using small interfering RNAs (siRNA). Reduction in RhoA expression by siRNA treatment, as confirmed by real-time PCR, resulted in loss of heart tube fusion and abnormal head development, the former result providing further direct evidence of a role for RhoA in heart developmental processes. In order to investigate the function of RhoA specifically during the process of cardiomyocyte differentiation, an inducible model of cardiomyogenesis, P19CL6 cells, was used in combination with over-expression of different forms of mouse RhoA. The striking result from these investigations was that over-expression of the dominant negative mutant of mouse RhoA (mRhoAN19) prevented the differentiation of induced P19CL6 cells to the cardiomyocyte phenotype, results consistent with an essential role for RhoA in this cellular transition. The mechanism by which RhoA mediates its different cellular functions is unclear, however some studies have implicated RhoA in the regulation of transcription factors. To investigate such a mechanism as a possible explanation for the requirement of RhoA in cardiomyocyte differentiation, the P19CL6 inducible cell system over-expressing different forms of RhoA was analysed through real-time PCR to quantify the levels of transcription of genes known to play an important role in early heart development. These investigations indicated that RhoA inhibition causes an accumulation of the cardiac transcription factors SRF and GATA4 and the early cardiac marker cardiac-cx-actin. The expression of a protein is controlled by, among other factors, regulatory proteins that control transcription. To investigate factors in heart that potentially regulate RhoA expression at the molecular level, the chick RhoA gene organisation was analysed. The gene was shown to contain three introns that interrupt the protein coding sequence and at least one intron in the 5'UTR. Comparative RhoA gene studies indicated both an almost identical organisation and coding sequence of the chick, mouse and human RhoA genes, indicative of strict conservation of this gene during evolution. The putative promoter region of RhoA was predicted by computer analyses and tested for promoter activity using luciferase reporter analyses in non-differentiated and differentiated cardiomyocytes, using the inducible P19CL6 cell system. These investigations served to define a putative core promoter region that exhibited significantly higher promoter activity in differentiated cardiomyocytes than in non-differentiated cells, and other elements upstream of this core region that appear to be required for transcriptional regulation of RhoA. The majority of the consensus transcription factor sites identified in this putative promoter have been previously implicated in either heart development and/or organogenesis. These results therefore provide further, although indirect, evidence for an important role for RhoA in the molecular mechanisms controlling both cardiogenesis and embryogenesis in general. In summary, this thesis provides novel information on the role of RhoA in the processes of cardiogenesis and provides a firm foundation for continuing investigations aimed at elucidating the molecular basis of this contribution.

GTPases are found in all domains of life and are highly conserved. In eukaryotes, they serve as signalling molecules for many cellular processes. However, the prokaryotic GTPases play a very different role and are found to be associated with ribosome function. Among the 11 conserved GTPases, Der is the most interesting in prokaryotes. It possesses a unique structure with two GTPase domains (G-Domains) tethered by a variable length acidic linker and a carboxyl terminal KH-like domain. The exact function of Der is still under investigation and most of the data suggest that it is important for 50S ribosomal assembly or stability. In order to investigate the function of Escherichia coli Der (Ec-Der), expression plasmids for wild-type and mutated proteins were created and the proteins were successfully expressed. The expression of the mutant protein that lacked G-Domain 1 was toxic to the cells and it was found that some large ribosomal proteins were missing from the ribosomes of these cells. In addition, other macromolecular complexes such as the GroEL/GroES chaperonin appeared not to be assembled under these conditions. The activities of both wild-type and mutated proteins were also tested and found to be dependent on potassium ions (K+), which enhanced nucleotide binding. Additionally, intra-molecular control over nucleotide binding and release was also observed for Ec-Der. The in vitro selection of RNA aptamers with nanomolar affinity for Ec-Der produced aptamers that contained short variable sequences. These aptamers affected the growth of the E. coli cells and caused a change in cellular morphology that had been noted previously during Ec-Der over-expression. Ec-Der showed high affinity (nM) to both selected RNA and the unselected RNA library. The activity of Ec-Der and Era was inhibited in the presence of any sequence of RNA that has the length of greater than 16 nucleotides. RNA was also cross-linked to Ec-Der in the presence of GTP, but not GDP, suggesting that RNA was a regulator of the Ec-Der GTPase cycle. Based on these results, it is speculated that Ec-Der might be involved in more than one function. It may be acting at the level of the membrane (based on cellular morphology reported here and by Hwang and Inouye 2001) and may also take part in processes related to ribosome function. Regulation of protein activity by RNA length has not been predicted or described and this may represent a novel mean of regulation of the Era subfamily of GTPases.

Le nématode Caenorhabditis elegans est un organisme polyvalent et unique pour l'étude de la biologie du développement, de la neurologie et des mécanismes complexes de signalisation des GTPases. Ce modèle animal offre une opportunité unique pour l'étude du rôle des protéines dans le développement neurologique et les maladies. Les recherches portaient sur trois gènes : pix-1, git-1 et pak-1. Chez les mammifères, GIT / PIX / PAK agissent comme une plateforme d'intégration de la signalisation des GTPases Rho et Arf dans les processus biologiques tels que : la polarité cellulaire, la migration, le trafic vésiculaire, la formation des synapses et la morphologie des épines dendritiques. Ces recherches ont amené l'utilisation des approches génétiques et microscopiques pour établir que pix-1, git-1 et pak-1 contrôlent les phases précoces et tardives de l'élongation de l'embryon par la régulation de l'activité des chaînes légères de myosine (CLM). Les résultats de recherche suggèrent un positionnement de pix-1 et pak-1 dans l'une des voies de signalisation contrôlant la phosphorylation de ces CLMs en parallèle de la voie mel-11 / let-502. MEL-11 est une phosphatase des CLMs agissant de façon antagoniste à LET-502 (une kinase effectrice des Rhos) dans l'une des deux voies de signalisation redondantes qui assurent l'étape précoce d'élongation embryonnaire. Les résultats suggèrent, de plus, l'implication de mel-11 et let-502 au cours de la phase tardive de l'allongement. Un certain nombre de résultats suggèrent aussi une implication des intégrines ina-1 dans ces processus. La caractérisation fonctionnelle de pix-1, git-1 et pak-1 chez les nématodes adultes démontre leur implication dans le contrôle du comportement de recherche de nourriture (comportement de forage). Ce comportement dépend de la neutotransmission glutamatergique et dopaminergique et implique des mécanismes cellulaires similaires à la plasticité synaptique chez les mammifères. Un lien a été établi entre l'expression des récepteurs au glutamate AMPA homologue de GLR-l et PIX-l en utilisant la microscopie quantitative, la cytométrie de flux et des tests de comportement dans des labyrinthes micro-fluidiques secs. Les résultats suggèrent que les animaux mutants pour pix-1 contrôleraient la neurotransmission glutamatergique de façon indirecte. La conservation fonctionnelle du complexe GIT / PIX / PAK chez les invertébrés permettrait d'utiliser notre modèle dans l'identification de cibles thérapeutiques et de composés actifs contre les pathologies associées à des mutations dans aPIX et PAK3. Il aidera en outre à fournir des éclaircissements sur la fonction et les mécanismes de régulation des GTPases. ______________________________________________________________________________ MOTS-CLÉS DE L’AUTEUR : GTPases monomériques, GIT/PIX/PAK., C. elegans, signalisation cellulaire, développement embryonnaire, neuro-transmission glutamatergique.

Thesis (Ph. D.)--University of Oregon, 2001. / Typescript. Includes vita and abstract. Includes bibliographical references (leaves 90-98). Also available for download via the World Wide Web; free to University of Oregon users.

Thesis (Ph. D.)--University of Hong Kong, 2010. / Includes bibliographical references (leaves 262-280). Also available in print.

Thesis (Ph. D.)--University of Hong Kong, 2010. / Includes bibliographical references (leaves 262-280). Also available online.

published_or_final_version / Anatomy / Doctoral / Doctor of Philosophy

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