Thesis (Ph. D.)--University of Virginia, 2008. / Title from title page. Includes bibliographical references. Also available online through Digital Dissertations.

Thesis (Ph. D.)--University of Virginia, 2009. / Title from title page. Includes bibliographical references. Also available online through Digital Dissertations.

Thesis (Ph.D. in Cell Biology, Stem Cells, and Development) -- University of Colorado Denver, 2008. / Typescript. Includes bibliographical references (leaves 105-116).

As critical regulators of vesicular trafficking, Rab proteins comprise the largest GTPase family, with thirty-eight functionally distinct members and another twenty isoforms in the human genome. Activated Rab GTPases interact with effector proteins involved in vesicle formation, transport, tethering, docking and fusion. The specificity of Rab interactions with effectors and regulatory factors plays a central role with respect to the fidelity of membrane trafficking. Rab recognition determinants and the mechanisms underlying interactions with structurally diverse regulatory factors and effectors are complex and poorly understood. Using Rab5 mediated endocytic transport as a model system, the work described in this thesis provides insight into the structural basis underlying the interaction of effectors and regulatory factors with Rab GTPases. In addition, structural and biochemical approaches have been used to define how specific Rab5 interacting proteins function in the endocytic and recycling pathways. These results establish novel structural and functional concepts that can be tested using family wide analyses of Rab GTPase recognition determinants and regulatory roles in the cell.

The membrane system of a eukaryotic cell is a large and complex system handling the transport, exchange and degradation of many kinds of material. Recent research shows that double-stranded RNA (dsRNA) mediated gene silencing (RNA interference) is a membrane related process. After long dsRNA is processed to small interfering RNA (siRNA) by Dicer, the guide strand and passenger strand are separated in the RNA induced silencing complex (RISC) by Argonaute. The process of loading siRNA into RISC has been suggested to occur at the rough Endoplasmic Reticulum (rER).The components of RISC also associate with late endosomes/multivesicular bodies (MVBs). Furthermore, disturbing the balance between late endosomes/MVBs and lysosomes has been shown to affect the efficiency of silencing. We use the nematode Caenorhabditis elegans as our model organism to study two questions: how does membrane transport affect RNAi and spreading of RNAi from the recipient cells to other tissues (systemic RNAi); and how does RNA transport contribute to the multigenerational silencing induced by dsRNA (RNAi inheritance)? Using SID-5, a protein required for efficient systemic RNAi, as bait in a yeast two-hybrid (Y2H) screen, we got 32 SID-5 interacting candidate proteins. Two of these are the SNARE protein SEC-22 and the putative RNA binding protein C12D8.1. In two additional Y2H screens, we found that SID-5 interacts with multiple syntaxin SNAREs, including SYX-6, whereas SEC-22 only interacts with SYX-6. SNAREs usually function in vesicle fusion processes. We found the two SNARE proteins SEC-22 and SYX-6 to be negative regulators of RNAi and to localize to late endosomes/MVBs. In addition, loss of sid-5 leads to an endosome maturation defect. Finally, we found that the putative RNA binding protein C12D8.1 negatively regulates RNAi inheritance and that C12D8.1 mutant animals show impaired RNAi upon targeting a new gene. Taken together, the results presented in this thesis provide us with more evidence for the connection of the membrane transport system and RNAi. The identification of a putative negative regulator of RNAi inheritance further enriches this research field.

Le diagnostic de la maladie d’Alzheimer (MA) s’appuie sur des critères clinico-biologiques combinant un déficit de la mémoire épisodique et un marqueur biologique (dosage dans le liquide céphalorachidien, imagerie nucléaire) indicateur des changements qui signent le début de la maladie. Un phénomène biologique précoce de la maladie est la production de dépôts du peptide amyloïde dont le principal site de production à partir de son précurseur, l’APP, est le compartiment endosomal. L’apparition dans le cerveau d’endosomes élargis précède celle des dépôts amyloïdes.Nous avons analysé deux marqueurs biologiques. D’abord la charge amyloïde cérébrale par fixation du ligand [PiB] en tomographie d’émission de positrons (TEP) dans le cerveau des malades atteints d’une atrophie corticale postérieure (ACP). Puis nous avons étudié les endosomes dans les cellules périphériques (leucocytes mononucléaires et fibroblastes) de patients MA, et dans des lignées lymphoblastoïdes (LCL) d’individus porteurs d’une trisomie 21 dont 45% développent une MA à l’âge de 60 ans (contre 3 % dans la population générale), principalement en raison de la présence d’une troisième copie du gène codant l’APP, localisé sur le chromosome 21. Nos travaux montrent des profils de marquage [PiB] similaires entre la MA et l’atrophie corticale postérieure (ACP) aussi bien en intensité qu’en topographie. L’étude des endosomes montre que les modifications du compartiment endosomal sont détectables en périphérie du système nerveux central et sont corrélées au marquage des dépôts amyloïdes cérébraux. Ces altérations pourraient constituer un outil de diagnostic à partir de prélèvements sanguins. / Alzheimer’s disease (AD) diagnostic is based on clinical and biological criteria, and is dependent on impairment of the episodic memory together with a marker of the underlying pathophysiologic process. One of the earliest events in AD pathology in the brain is formation of Amyloid deposits in the extracellular space. One of the main subcellular sites of amyloid-β (Aβ) production from amyloid precursor protein (APP) processing is the endosomal compartment. Appearance of endosomal abnormalities precede the formation of amyloid deposits, in the brain areas affected by disease progression in AD. In the present work we first studied brain amyloid load in patients with posterior cortical atrophy using [11C]PiB ligand retention in positron emitting tomography (PET). In a second part we studied the endosomal compartment in peripheral cells (fibroblasts and mononuclear leucocytes, PBMC) from AD patients, and in lymphoblastoid cell lines (LCL) from Down’s syndrome (DS) individuals where a third copy of amyloid-precursor-protein-coding gene located on chromosome 21 is known to initiate early Alzheimer’s pathology in most DS individuals. Our work shows similar profiles in topography and intensity of [PiB] binding in AD and posterior cortical atrophy (PCA), confirming underlying AD pathology in atypical focal presentations of AD. Analysis of endosomes yielded a significant increase in the frequency of cells with large endosomes in all analyzed cell types, and mean endosome volume correlated to [PiB] binding in PBMC. This result indicates that modifications of the endosomal compartment are seen in the periphery of central nervous system and may represent diagnostic tool from blood.

Actin polymerization facilitated by the Arp2/3 complex plays a critical role in a wide range of cellular processes such as motility, endocytosis and cargo recycling. Activation and appropriate localization of the Arp2/3 complex is mediated by an interaction with the nucleation-promoting factor (NPF). WASH complex is the major endosomal NPF which plays a crucial role in the cargo recycling back to the trans-Golgi network (TGN) or plasma membrane. It is composed of five subunits: WASH1, SWIP, FAM21, CCDC53 and strumpellin. While WASH1 and FAM21 have been extensively studied, much less is known about strumpellin, a protein causally implicated in the onset of hereditary spastic paraplegia (HSP). This work focuses on strumpellin function in the cells, showing that only full-length protein incorporates into the WASH complex. In a strumpellin knock out cell line, we demonstrated that loss of strumpellin resulted in destabilization of the other WASH complex subunits. Still, an incomplete WASH complex without strumpellin was assembled. Cells also displayed enlarged endosomal subdomains and WASH complex nucleation activity on endosomes was largely diminished as assessed by loss of the actin patches. Finally, the absence of strumpellin was also accompanied by the accumulation of glucose transporter 1 (GLUT1)...

No description available.

Transport of different organelles along the Microtubule cytoskeleton is carried out mainly by motor proteins Dynein and Kinesin. The tubulin monomers in Microtubules are organized in such a way that the generate polarity (a minus and a plus end) that is recognized by Motor proteins. Dynein usually acts with a binding partner, Dynactin, and is in charge of moving cargoes to the minus end of microtubules (mainly towards the center of the cell). There are different kinesins, the most studied is Kinesin-1, which moves cargoes towards the plus end of microtubules. In order to fulfil their function Motors usually bind to their cargoes indirectly through adaptor proteins. Chapter 1 explains the general concepts related to a group of Adaptors that recognize the small GTP-ases, Rabs, in cargoes that need to be transported under certain physiological circumstances and help recruiting the Dynein/Dynactin complexes to them so they can move in the minus end direction. This family of Adaptors is called Rab-Dynein-Dynactin (RDD) adaptors and in this project I focused on two of them: BicD2 and RILP. In chapter 2, I will focus on BicD2 and its role in Golgi morphology. BicD2 is an RDD adaptor that mediates binding of Dynein/Dynactin to Rab6-positive vesicles. Some mutations in BicD2 have been associated to Golgi apparatus morphology disruption, but the mechanism is unclear. It has been suggested that mutated BicD2 abnormally binds Dynein/Dynactin, sequestering this motor complex, producing Golgi disruption indirectly since this organelle depends heavily on minus-directed transport to maintain its localization and structure. I test this hypothesis and conclude that even when most pathological mutations disrupt the Golgi, a Dynein/Dynactin-mediated mechanisms is probably true only to some of them, proposing alternatives mechanisms such as Rab6 abnormal accumulation and non-Golgi related mechanisms of pathogenesis. In chapter 3, I will focus on RILP and its role in autophagosome movement. RILP is an RDD adaptor that mediates binding of Dynein/Dynactin to Rab7-positive vesicles such as Lysosomes. During autophagy, autophagosomes (which are LC3-positive) are formed mainly in the ER and mature to finally fuse with the Late Endosomes or Lysosomes (both acidic) in the center of the cell. It has been described by our lab that RILP can transport LC3-vesicles in axons. Nevertheless, these vesicles are acidic, which suggest these LC3-vesicles are already fused with either Lysosomes or Late endosomes. I will work under the Hypothesis that RILP can move autophagosomes in early stages (before fusion with Lysosomes or Late endosomes) in non-neuronal cells. I show that RILP can move autophagosomes to the center and FYCO1 (a Kinesin-1 adaptor) can move them to the periphery. RILP-mediated movement of autophagosomes depends on Rab7 activation status and seems to be controlled by PKA. I proposed a phosphorylation in Rab7 as a control mechanism. Finally, the discovery of 3 LC3 interacting regions (LIRs) in the RILP molecule is discussed and their contribution to autophagosome movement is analyzed. My results highlight the relevance of RDD proteins in physiological and pathological context.

La dystrophie musculaire de Duchenne (DMD) est une maladie causée par l’absence de dystrophine, qui se manifeste par une dégénérescence progressive des muscles squelettiques et cardiaque. Les garçons atteints ont une espérance de vie d’environ 20 ans. Même si la prise de certains médicaments peut ralentir la progression de la maladie, il n’existe à ce jour aucune thérapie curative. La transplantation autologue de myoblastes génétiquement corrigés peut restaurer l’expression de la dystrophine, mais les myoblastes des patients DMD ont une capacité proliférative très limitée. Leur prolifération nécessite l'immortalisation avec un oncogène viral, un processus augmentant les risques associés à la transplantation de myoblastes. Les protéines fusionnées au domaine de transduction de Tat peuvent transduire les cellules en culture et plusieurs tissus in vivo. La transduction de protéines pourrait s’avérer utile dans le développement de nouvelles approches thérapeutiques. Nos objectifs étaient de tester la capacité des protéines de fusion Tat à transduire les fibres musculaires, de mieux comprendre le mécanisme de transduction, d’optimiser le ciblage efficace des cellules en culture et de développer des outils permettant l’immortalisation transitoire des myoblastes avant leur transplantation. In vivo, nos travaux indiquent que les fibres musculaires résistent à l’internalisation des protéines de fusion Tat, qui se retrouvent en périphérie associées à la matrice extracellulaire. In vitro, la distribution intracellulaire ponctuée, la cinétique d’internalisation, la sensibilité aux basses températures et l’augmentation fonctionnelle exercée par les agents lysosomotropiques révèlent un mécanisme d’endocytose classique. Ces données suggèrent que les protéines de fusion Tat, entrent par la voie endosomale, évitent les lysosomes, et sont ensuite séquestrées en périphérie du noyau. Un trafic intracellulaire inadéquat serait le principal facteur limitant l’efficacité de l’internalisation fonctionnelle des cargos fusionnés au domaine de transduction de Tat. Cette meilleure compréhension du mécanisme d’internalisation des protéines de fusion Tat, nous permit de développer une méthode efficace pour immortaliser de façon réversible les myoblastes d'un patient DMD. En utilisant un protéine de fusion Tat-Cre, nous avons déimmortalisé des myoblastes DMD transformés par l'AgT flanqué de sites LoxP. Cette technique permet de proliférer extensivement les myoblastes DMD, tout en rendant plus sécuritaire la déimmortalisation. / Duchenne muscular dystrophy (DMD) is caused by the absence of dystrophin and leads to progressive weakness in heart and skeletal muscles. Affected boys can only hope to live for 20 years since there is still no effective therapy for DMD. Autologous transplantation of genetically modified myoblasts can restore dystrophin expression, but the rapid death, the specific immune response and limited cellular migration severely limit the efficiency of the treatment. Immortalization, although a risky procedure, is necessary to proliferate myoblasts isolated from dystrophic patients, since by age five; their myogenic cells are practically senescent. Proteins and cargos fused to the Tat protein (HIV) can be internalized in cells and living tissue. The mechanism of Tat internalization is still misunderstood and controversial. Our objectives were to test the susceptibility of muscle fibers to be transduced by Tat fusion proteins, to better understand the mechanism of entry of Tat fusions, to optimize intracellular delivery and to develop techniques allowing the immortalization reversal of myoblasts using Tat-fusion proteins. The low susceptibility of muscle fibers to be transduced and the strong interaction between Tat-fusion proteins and the extracellular matrix surrounding muscle fibers resulted in poor protein delivery. Our work shows that the nuclear localization signal comprised in Tat is not sufficient to confer nuclear delivery to eGFP. The punctuate intracellular distribution, the internalization kinetics, the inhibitory effect of low temperatures and the functional increase exerted by lysosomotropic agents are coherent with a classical endocytosis internalisation mechanism. Our data suggests that Tat-fusion proteins proceed through the endosomal pathway, avoid lysosomes and are then sequestered in the periphery of the nucleus. Hence, improper intracellular trafficking is the main factor limiting the efficiency of Tat-mediated protein internalization. With a better understanding of this internalization mechanism, we were able to optimize the delivery of a Tat-Cre fusion protein to mediate the complete and efficient removal of an oncogene necessary for the proliferation of myoblasts isolated from DMD patients. Therefore this technique should help in the design of a successful treatment based on the autologous transplantation genetically-modified cells.