Indiana University-Purdue University Indianapolis (IUPUI) / Knowledge of the molecular and cellular mechanisms of ischemic injury is necessary for understanding acute kidney injury and devising optimal treatment regimens. The cortical actin cytoskeleton in the proximal tubule epithelial cells of the kidney nephron, playing an important role in both the establishment and maintenance of cell polarity, is drastically disrupted by the onset of ischemia. We found that in LLC-PK cells (a porcine kidney proximal tubule epithelial cell line), cortactin, an important regulator of actin assembly and organization, translocated from the cell cortex to the cytoplasmic regions upon ischemia/ATP-depletion. Meanwhile both the tyrosine phosphorylation level of cortactin and cortactin’s interaction with either F-actin or the actin nucleator Arp2/3 complex were down-regulated upon ischemia/ATP-depletion or inhibition of Src kinase activity. These results suggest that tyrosine phosphorylation plays an important role in regulating cortactin’s cellular function and localization in the scenario of kidney ischemia. The Rho GTPase signaling pathways is also a critical mediator of the effects of ATP depletion and ischemia on the actin cytoskeleton, but the mechanism by which ATP depletion leads to altered RhoA and Rac1 activity is unknown. We propose that ischemia and ATP depletion result in activation of AMP-activated protein kinase (AMPK) and that this affects Rho GTPase activity and cytoskeletal organization (possibly via TSC1/2 complex and/or mTOR complex). We found that AMPK was rapidly activated (≤5 minutes) by ATP depletion in S3 epithelial cells derived from the proximal tubule in mouse kidney, and there was a corresponding decrease in RhoA and Rac1 activity. During graded ATP-depletion, we found intermediate levels of AMPK activity at the intermediate ATP levels, and that the activity of RhoA and Rac1 activity correlated inversely with the activity of AMPK. Activation of AMPK using two different drugs suppressed RhoA activity, and also led to morphological changes of stress fibers. In addition, the inhibition of AMPK activation partially rescued the disruption of stress fibers caused by ATP-depletion. This evidence supports our hypothesis that the activation of AMPK is upstream of the signaling pathways that eventually lead to RhoA inactivation and cytoskeletal dysregulation during ATP-depletion.

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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.

Le transport intracellulaire du cholestérol et sa distribution correcte au niveau des différentes membranes sont essentiels pour assurer de nombreuses fonctions cellulaires. Malgré l’importance de ce transport les mécanismes de sa régulation restent encore mal connus. L’objectif de cette thèse était de mieux caractériser les acteurs du transport intracellulaire du cholestérol. Dans ce contexte, nous nous sommes intéressés à deux acteurs de ce transport : la dynamine et les Rab GTPases. Dans la première partie de la thèse nous avons utilisé le dynasore, un inhibiteur pharmacologique de la dynamine pour étudier le rôle de la dynamine dans le contrôle du transport endolysosomal dans les cellules HeLa et les macrophages humains. Nous avons ainsi confirmé le rôle de la dynamine dans la sortie du compartiment endolysosomal et la régulation de l’homéostasie du cholestérol. Dans la deuxième partie de la thèse, nous avons étudié le rôle de Rab7 et de Rab9 dans le transport du cholestérol en utilisant la technique d’ARN interférence ainsi que l’expression de mutants dominant négatifs. Nous avons montré qu’en plus de son rôle classique dans les étapes tardives du transport du cholestérol, Rab7 contrôle les étapes précoces du transport endosomal. Enfin, nous avons évalué le rôle de Rab7 dans notre modèle de macrophages humains surchargés. Nous avons mis en évidence un effet limité de l’inactivation de Rab7 sur le contrôle de l’homéostasie du cholestérol mais à l’inverse un effet majeur pour l’efflux du cholestérol vers l’apo AI. En conclusion, notre étude a permis de mieux caractériser le transport vésiculaire du cholestérol et de démontrer son importance dans la régulation de l’homéostasie intracellulaire en cholestérol. Nos résultats permettent également d’établir le rôle critique de Rab7 dans le trafic des LDL au niveau des endosomes précoces. / Intracellular transport of cholesterol and its distribution within cellular membranes are essential to maintain correct cellular functions. Despite the importance of this transport, mechanisms that regulate cholesterol transport still poorly defined. The objectives of this thesis were to better characterize the actors of intracellular cholesterol trafficking. In this context, we focused our interest on two known actors of intracellular transport : dynamin and Rab GTPases. In the first part of this thesis, we used dynasore, a pharmacological dynamin inhibitor, to study the role of dynamin in the control of endolysosomal transport in HeLa cells and human macrophages. We confirmed the role of dynamin in endolysosomal sorting and cholesterol homeostasis regulation. In the second part of this thesis, we studied the role of Rab7 and Rab9 in the regulation of cholesterol transport using RNA interference and dominant negative mutants. We showed that in addition to it classical role in late steps of cholesterol transport, Rab7 controls also early steps of endosomal trafficking. Finally, we evaluated the role of Rab7 in our model of loaded human macrophages. We showed a weak impact of Rab7 inactivation on cholesterol homeostasis but a major effect on cholesterol efflux to apo AI. In conclusion, in this study we have better characterized the vesicular transport of cholesterol and demonstrated its importance in cholesterol intracellular homeostasis. Our results also establish that Rab7 plays a critical role in the sorting of LDL at the early endosome.

Clathrin-mediated endocytosis is a process by which cells can internalise diverse molecules such as nutrients, antigens and signalling-surface receptors. The creation of clathrin-coated vesicles demands interplay between the plasma membrane lipids, cargo molecules and the proteins that build up the coat. This thesis deals with the identification and characterisation of sorting nexin 9 (SNX9) as a novel component of the endocytic machinery. SNX9 belongs to a large family of proteins based on the presence of a PX domain. In addition, SNX9 harbours an SH3 domain followed by a region with predicted low-complexity and a C-terminal BAR homology domain. Binding studies demonstrated that SNX9 interacted with the endocytic core components clathrin and AP-2 and dynamin-2, a GTPase known to be crucial for vesicle scission. The C-terminal region bound to phosphatidylinositols and targeted SNX9 to artificial liposomes and cellular membranes. Consistent with a role in endocytosis, a large portion of SNX9 co-localised with AP-2 and dynamin-2 but not with markers for early endosomes, Golgi. Over-expression of truncated variants of SNX9 in K562 and HeLa cells interfered with the uptake of transferrin. SNX9 recycles between a membrane-bound and a cytosolic pool. In cytosol, SNX9 formed a resting complex together with dynamin-2 and the metabolic enzyme aldolase. Activation for membrane binding involved ATP hydrolysis and correlated with phosphorylation of SNX9 and the release of aldolase. Aldolase bound to a tryptophan-containing acidic region near the clathrin and AP-2 motifs and blocked lipid binding of purified SNX9 derivatives. SNX9 was required for membrane targeting of dynamin2 in vitro and knockdown of SNX9 in HeLa cells by RNAi resulted in impaired membrane localisation. Together these results argue strongly for a role of SNX9 in recruiting and linking of dynamin-2 to sites of vesicle creation.

Proteins are essential parts of living organisms that initiate and control almost all cellular processes. Despite the widely accepted belief that all functional proteins fold into stable and well-defined three-dimensional (3D) structures mandatory for protein activity, the existence of biologically functional disordered proteins has been increasingly recognized during past two decades. Proteins with inherent structural disorder, commonly known as intrinsically disordered proteins (IDPs), play many roles in a biological context. However, in contrast to their folded counterparts, they are dynamically unstructured and typically fluctuate among many conformations even while performing biological functions. In fact, it is this dynamical structural heterogeneity that that allows for IDPs to interact with other biological macromolecules in unique ways. Moreover, while a majority of proteins in eukaryotic proteomes have been found to have intrinsically disordered regions (IDR), the mechanisms by which protein disorder fives rise to biological functionality is still not well understood. Through a series of simulation studies on specific systems, this thesis probes several aspects of the emerging structure-function paradygm of IDPs, namely the mechanics, intermolecular assembly, and structural transitions occurring in these proteins. The lack of well-defined 3D structure in IDPs gives rise to distinct mechanical properties, the subject of the first study in the thesis on the elasticity of a elastomeric gluten-mimetic polypeptide with an intrinsically disordered character. This disordered polypeptide was shown to exhibit distinctively variable elastic response to a wide range of tensions, which a classical worm-like chain model failed to accurately describe, thus requiring a molecular-level analysis. IDPs frequently are frequently involved in protein-protein interactions, the focus of the second study on the propensity of an IDR, the B domain in dynamin-related protein 1 (Dpr1), to self-assemble into dimer structures while remaining disordered in all solution conditions. Despite a hypothesized auto-inhibitory role for this domain in Dpr1 that was assumed to be triggered by an disordered-to-order transition, the B domains in solution showed no tendency to form ordered structures even in the presence of order promoting osmolytes. Instead, self-association in the presence of osmolyte was found to occur by favorable intermolecular intereactions between specific region on the surface of the B-domains. Other IDPs do undergo a disorder-to-order transition in response to environmental cues, in ways that are unique disordered proteins, the focus of the last study on intermolecular ordering transitions in silk-like proteins. Factors such as protein sequence and physical tension were investigated, and results suggested that tyrosine residues in the key silk sequence motifs promote templating of beta structure from disordered precursors and that elongational stresses preferentialy stabilize antiparallel beta-sheet order. Together, these three computational studies provide insight into the nature of the structure-function mechanisms of IDPs.

The mechanisms that order cellular packing geometry are critical for the functioning of many tissues, but are poorly understood. Here we investigate this problem in the developing wing of Drosophila. The surface of the wing is decorated by hexagonally packed hairs that are uniformly oriented towards the distal wing tip. They are constructed by a hexagonal array of wing epithelial cells. We find that wing epithelial cells are irregularly arranged throughout most of development but become hexagonally packed shortly before hair formation. During the process, individual cell junctions grow and shrink, resulting in local neighbor exchanges. These dynamic changes mediate hexagonal packing and require the efficient delivery of E-cadherin to remodeling junctions; a process that depends on both the large GTPase Dynamin and the function of Rab11 recycling endosomes. We suggest that E-cadherin is actively internalized and recycled as wing epithelial cells pack into a regular hexagonal array. Hexagonal packing furthermore depends on the activity of the Planar Cell Polarity proteins. The Planar Cell Polarity group of proteins coordinates complex and polarized cell behavior in many contexts. No common cell biological mechanism has yet been identified to explain their functions in different tissues. A genetic interaction between Dynamin and the Planar Cell Polarity mutants suggests that the planar cell polarity proteins may modulate Dynamin-dependent trafficking of E-cadherin to enable the dynamic remodeling of junctions. We furthermore show that the Planar Cell Polarity protein Flamingo can recruit the exocyst component Sec5. Sec5 vesicles also co-localizes with E-cadherin and Flamingo. Based on these observations we propose that during the hexagonal repacking of the wing epithelium these proteins polarize the trafficking of E-cadherin-containing exocyst vesicles to remodeling junctions. The work presented in this thesis shows that one of the basic cellular functions of planar cell polarity signaling may be the regulation of dynamic cell adhesion. In doing so, the planar cell polarity pathway mediates the acquisition of a regular packing geometry of Drosophila wing epithelial cells. We identify polarized exocyst-dependent membrane traffic as the first basic cellular mechanism that can explain the role of PCP proteins in different developmental systems.

The mechanisms that order cellular packing geometry are critical for the functioning of many tissues, but are poorly understood. Here we investigate this problem in the developing wing of Drosophila. The surface of the wing is decorated by hexagonally packed hairs that are uniformly oriented towards the distal wing tip. They are constructed by a hexagonal array of wing epithelial cells. We find that wing epithelial cells are irregularly arranged throughout most of development but become hexagonally packed shortly before hair formation. During the process, individual cell junctions grow and shrink, resulting in local neighbor exchanges. These dynamic changes mediate hexagonal packing and require the efficient delivery of E-cadherin to remodeling junctions; a process that depends on both the large GTPase Dynamin and the function of Rab11 recycling endosomes. We suggest that E-cadherin is actively internalized and recycled as wing epithelial cells pack into a regular hexagonal array. Hexagonal packing furthermore depends on the activity of the Planar Cell Polarity proteins. The Planar Cell Polarity group of proteins coordinates complex and polarized cell behavior in many contexts. No common cell biological mechanism has yet been identified to explain their functions in different tissues. A genetic interaction between Dynamin and the Planar Cell Polarity mutants suggests that the planar cell polarity proteins may modulate Dynamin-dependent trafficking of E-cadherin to enable the dynamic remodeling of junctions. We furthermore show that the Planar Cell Polarity protein Flamingo can recruit the exocyst component Sec5. Sec5 vesicles also co-localizes with E-cadherin and Flamingo. Based on these observations we propose that during the hexagonal repacking of the wing epithelium these proteins polarize the trafficking of E-cadherin-containing exocyst vesicles to remodeling junctions. The work presented in this thesis shows that one of the basic cellular functions of planar cell polarity signaling may be the regulation of dynamic cell adhesion. In doing so, the planar cell polarity pathway mediates the acquisition of a regular packing geometry of Drosophila wing epithelial cells. We identify polarized exocyst-dependent membrane traffic as the first basic cellular mechanism that can explain the role of PCP proteins in different developmental systems.

La myopathie centronucléaire autosomique dominante (MCN-AD) est une maladie congénitale rare liée à des mutations principalement retrouvées dans le gène dynamine-2. La majorité des patients atteints de MCN-AD présente une évolution lentement progressive, avec une perte de masse et de force musculaire. A ce jour, aucune thérapie n’est disponible pour la MCN-AD. Des interventions thérapeutiques visant à limiter la progression et la sévérité de l’atteinte musculaire ainsi qu’à améliorer la qualité de vie des patients, sont donc nécessaires. Nous faisons l’hypothèse qu’une hypertrophie induite par l’invalidation de la myostatine (mstn), régulateur négatif majeur de la masse musculaire, pourrait être bénéfique pour la souris modèle de cette pathologie (KI-Dnm2R465W/+), permettant notamment le maintien de la masse et de la force musculaire. Nous avons généré un modèle doublement muté résultant du croisement de souris KI-Dnm2R465W/+ myopathe avec des souris KO-mstn hypermusclées. Notre étude démontre que l'inactivation du gène mstn permet une amélioration de la masse et du volume musculaire, limite la perte de force et de motricité. Nos données suggèrent également que cette amélioration est majoritairement due à une diminution du niveau d’expression de certains acteurs impliqués dans le système catabolique ubiquitine-protéasome. De plus, nous montrons une accélèration de la diminution de la fréquence des anomalies histologiques caractéristiques de la myopathie chez les souris KI-Dnm2R465W/+. Nous proposons que ces anomalies pourraient être dues à une altération de la structure et/ou de la fonction mitochondriale. / Autosomal dominant centronuclear myopathy (AD-CNM) is a rare congenital muscle disease caused by mutations predominantly found in the dynamin 2 gene (DNM2). The clinical features generally reported are progressive muscle atrophy and weakness. To date, no treatment is available. The mouse model for AD-CNM harboring a mutation of the dynamin-2 gene (KI-Dnm2R465W/+) reproduces some of the human clinical features, notably muscle atrophy and weakness. Mstn, is a master negative regulator of skeletal muscle mass. We hypothesized that inactivation of mstn could limit muscle atrophy and weakness reported in the AD-CNM mouse model (KI-dnm2R465W/+). To test this hypothesis, we intercrossed KI-Dnm2R465W/+ mice with mice inactivated for mstn (KO-mstn) to generate a double mutated lineage (KIKO). The present study demonstrates that mstn gene inactivation allows for an improvement of muscle weight and volume, prevents muscle weakness and motor skill alterations. Our data also reveal that inactivation of mstn essentially downregulates some actors implicated in the catabolic ubiquitin-proteasome system. Furthermore, we show that inactivation of mstn decreases the frequency of of histological abnormalities characteristical in KI mice. We hypothesize that these abnormalities could be due to an alteration of mitochondrial function and network. The perspective to this work is to verify this hypothesis in the mouse model, which will contribute to a better understanding of the physiopathological mechanisms and can open new insight in the therapeutical approach to AD-CNM.