L’ubiquitination est une modification post-traductionnelle qui joue un rôle majeur chez les organismes vivants. Chez Arabidopsis thaliana, le transporteur de fer racinaire IRT1 est endocyté à la suite de la monoubiquitination de deux résidus lysine situés au niveau de sa grande boucle cytosolique. Cependant, les mécanismes régissant l’endocytose médiée par l’ubiquitine ainsi que son rôle biologique restent flous. Au cours de ma Thèse, j’ai mis en évidence que la dynamique d’IRT1 était contrôlée par les métaux substrats secondaires du transporteur (à savoir le zinc, le manganèse et le cobalt). En l’absence de ces métaux, IRT1 est localisé à la membrane plasmique avec une polarité latérale le positionnant sur la face externe des cellules de l’épiderme racinaire. La présence de ces mêmes métaux à un niveau physiologique entraîne la monoubiquitination d’IRT1 et son internalisation vers les endosomes précoces. J’ai démontré que lorsque les métaux substrats secondaires d’IRT1 sont présents en excès, les modifications monoubiquitine sont alors allongées en chaînes de polyubiquitines liées par le résidu lysine-63, entrainant ainsi son adressage vers la vacuole et sa dégradation. Mes travaux ont par ailleurs permis d’élucider les mécanismes moléculaires impliquées dans la réponse des plantes à l’excès de métaux substrats d’IRT1. J’ai notamment montré que l’endocytose d’IRT1 était dépendante i) d’un motif riche en résidus histidine dans la séquence d’IRT1 qui est capable de fixer ces métaux autres que le fer, ii) de la phosphorylation d’IRT1 au niveau d’un résidu thréonine par une protéine kinase en cours d’investigation, et iii) de l’E3 ligase à domaine RING IDF1. D’un point de vue physiologique, l’endocytose d’IRT1 médiée par l’ubiquitine et dépendante des métaux protège la plante d’une suraccumulation de ces métaux autres que le fer qui sont hautement réactifs. / Ubiquitination is a post-translational modification playing a major role in living organisms. In Arabidopsis thaliana, the root iron transporter IRT1 is endocytosed following the monoubiquitination of two lysine residues located in its large cytosolic loop. However, the mechanisms driving IRT1 ubiquitin-mediated endocytosis and its biological relevance remains unclear. During my PhD, I uncovered that IRT1 dynamics is controlled by its secondary metal substrates (i.e. zinc, manganese and cobalt). In the absence of these non-iron metals, IRT1 is found at the cell-surface of root epidermal cells with an outer lateral polarity, while their presence at physiological levels triggers IRT1 monoubiquitination, internalization and accumulation in early endosomes. However, upon non-iron metal excess, monoubiquitin modifications are extended into K63 polyubiquitin chains to promote the vacuolar targeting of IRT1 and its degradation. I investigated further the molecular mechanisms driving plant responses to non-iron metal excess. I notably showed that this regulation by non-iron metals is dependent on i) a histidine-rich stretch in IRT1 that is able to directly bind to non-iron metals, ii) the subsequent recruitment of a kinase currently under investigation which phosphorylates IRT1 at a threonine residue, and iii) the RING E3 ligase IDF1. Altogether, the metal-dependent ubiquitin-mediated endocytosis of IRT1 protects the plant from overaccumulation of highly reactive non-iron metals.

Intracellular transport is fundamental to many cellular processes- from capturing and destroying pathogens to the propagation of nerve impulses. This transport is mediated by specialized enzymes that convert the free energy of ATP hydrolysis to ‘walk’ on polymeric filaments. The microtubule filament and its associated motors- dynein and kinesin - are responsible for the long-range transport of various cellular cargoes. While these two motors move in the opposite directions, they are often simultaneously present on individual cargoes leading to bidirectional motility characterized by frequency directional reversals. How this process is regulated and what determines the direction of cargo transport remains poorly understood. Addressing these questions requires a systematic analysis where the contribution of various factors in regulating/determining the transport direction of a well-defined cargo can be elucidated. This project establishes an in vitro assay where we reconstitute bidirectional motility of large unilamellar vesicles driven by purified dynein and kinesin-3 motors. Vesicles exhibit fast runs in either direction, with a subset exhibiting directional reversals. The transport features of these vesicles are remarkably similar to that of cargoes in vivo and do not require any additional regulatory proteins/complexes. The simultaneous opposing activity of dynein and kinesin-3 leads to tugs-of-war for a finite period. Finally, we use this assay to determine how microtubule-associated proteins that have differential activity towards dynein and kinesin affect the transport direction of vesicles. MAP9 biases the direction of vesicles towards the plus-end by limiting the ability of dynein to land on microtubules. Our approach can be extended to investigate the potential biasing activities of cellular factors such as posttranslational modifications of tubulin, motor-adaptors, etc. and physical factors, such as fluidity and tension of the vesicle membrane.:1 Introduction 1.1 Microtubules, dynein, kinesin, and microtubule-associated proteins (MAPs) 1.2 Bidirectional transport: In vivo observations and models 1.3 Bidirectional transport: In vitro reconstitution 1.4 Role of membranes in modulating motor activities 1.5 Aims of the thesis 2 Purification of dynein and dynactin 2.1 Purification of dynein and dynactin from adherent mammalian cell cultures 2.2 Purification of dynein and dynactin from suspension cultures using BacMam system 2.3 Validation of dynein and dynactin function using single-molecule motility assays 3 Reconstitution and characterization of bidirectional vesicle motility 3.1 DDB-KIF16B-vesicles exhibit directional reversals in vitro 3.2 Transport direction of vesicles is dependent on the relative concentration of DDB and KIF16B 3.3 Opposing motors do not affect the velocity of the driving motor 3.4 DDB and KIF16B engage in a tug-of-war before directional reversals 3.5 Discussion 4 Characterization of bidirectional motility in the presence of MAPs 4.1 Tau does not differentially affect DDB versus KIF16B at the single-molecule level 4.2 MAP9 affects landing of DDB but not KIF16B 4.3 Motor ensembles can circumnavigate the inhibitory effects of MAPs 4.4 Tau does not bias the transport direction of DDB-KIF16B-vesicles 4.5 MAP9 biases the transport direction of DDB-KIF16B-vesicles towards the plus-end 4.6 Discussion 5 Conclusion and outlook 6 Materials and Methods 6.1 Molecular Biology 6.2 Culture of Flp-In 293 cells 6.3 Protein biochemistry 6.4 In vitro motility assays 6.5 Data processing and analysis

No description available.

Herein, different polymer libraries were examined to determine the effect polymer structure has on intracellular events. The effect of different polyamine lengths in copolymers on cellular uptake, the effect of modifying end groups of trehalose-containing polymers on transfection efficiency, and the effect of different linker lengths between galactose and a hepatocyte-targeted polymer on transfection efficiency were studied. Furthermore, it was demonstrated that polymers with terbium chelated in their repeat units could potentially be used for Förster resonance energy transfer (FRET) studies to monitor pDNA release from the polymer. Much of the work in this dissertation focuses on elucidating the intracellular mechanisms of linear poly(ethylenimine) (PEI) and how it compares to poly(L-tartaramidopentaethylenetetramine) (T4) and poly(galactaramidopentaethylenetetramine) (G4), two poly(glycoamidoamine)s synthesized by our group. The long-term goal of this project is to develop structure-function relationships between polymers and pDNA delivery efficacy that will result in the rational design of safe, efficient vehicles for therapeutic nucleic acid delivery. Many polymers used as DNA delivery vehicles display high cytotoxicity. Often, the polymers with the highest transfection efficiency are the most toxic, as demonstrated herein by PEI and T4 with varying polymer lengths. Therefore, it was of interest to study how polymer structure influences mechanisms of cytotoxicity. To this end, studies on several mechanisms of cytotoxicity, including nuclear envelope permeabilization, were conducted. Longer polymers induced more cytotoxic responses than shorter ones, and it appears that hydroxyl groups in the repeat unit of polymers play a role in polyplex formation. This research has also led us to a potential link between transfection efficiency and cytotoxicity; the polymers with the highest transfection efficiency were also the most toxic, and were also able to induce the most nuclear envelope permeability. It is possible that these polymers' ability to permeabilize the nuclear envelope is what causes their high transfection efficiency and high toxicity. In addition, flow cytometry and confocal microscopy studies revealed that polymer structure plays a role in nuclear trafficking; poly(glycoamidoamine)s G4 and T4 more dependent on intracellular machinery than PEI. This research demonstrates the impact that changes in polymer structure have on intracellular mechanisms. / Ph. D.

The Escherichia coli twin-arginine translocation (Tat) system transports fully folded and assembled proteins across the inner membrane into the periplasmic space. The E. coli Tat machinery minimally consists of three integral membrane proteins: TatA, TatB and TatC. A popular model of Tat translocation is that cargo first interacts with a substrate binding complex composed of TatB and TatC and then is transported across the inner membrane through a channel comprised primarily of TatA. The most common method for observing the kinetics of Tat transport, a protease protection assay, lacks the ability to distinguish between individual transport sub-steps and is limited by the inability to observe translocation in real-time. Therefore, a real-time FRET based assay was developed to observe interactions between the cargo protein pre-SufI, and its initial binding site, the TatBC complex. The cargo was found to first associate with the TatBC complex, and then, in the presence of a membrane potential (∆psi), migrate away from the initial binding site after a 20-45 second delay. Since cargo migration away from the TatBC complex was not directly promoted by the presence of a ∆psi, the delay likely represents some preparatory step that results in a transport competent translocon. In addition, the Tat system has long been identified as a potential biotechnological tool for protein production. However, much is still unknown about which cargos are suitable for transport by the Tat system. To probe the Tat system’s ability to transport substrates of different sizes and shapes, 18 different cargos were generated using the natural Tat substrate pre-SufI as a base. Transport efficiencies for these cargos indicate that not only is the Tat machinery’s ability to transport substrates determined by the protein’s molecular weight, as well as by its dimensions. In total, these results suggest a dynamic translocon that undergoes functionally significant, ∆psi-dependent changes during translocation. Moreover, not every protein cargo can be directed through the Tat translocon by a Tat signal peptide, and this selectivity is not only related to the overall size of the protein, but also dependent on shape.

Une réponse immunitaire efficace contre un large spectre de pathogènes ou contre des cellules tumorales nécessite l’activation des lymphocytes T CD4+. L’engagement du récepteur T par un peptide antigénique apprêté sur les produits de classe-II du complexe majeur d’histocompatibilité (peptide-CMH, pCMH) portés par une cellules présentatrices d’antigène (CPAg), conduit à de nombreux remaniements du lymphocyte T. Il s’établit notamment à l’interface entre le lymphocyte T et la CPAg, une structure spécialisée qui est la synapse immunologique (ou synapse immune). La synapse est le siège d’événements de signalisation intenses où diverses molécules de signalisation nécessaires l’amplification et la diversification du signal provenant du TCR sont recrutées. Ces évènements de signalisation sont régulés par l’adaptateur transmembranaire LAT (« Linker for Activation of T cells ») qui est présent à la membrane plasmique ainsi que dans des compartiments intracellulaires. La fraction intracellulaire de LAT est recrutée à la synapse immune et il est proposé que ces compartiments vésiculaires participent à la signalisation lymphocytaire T. L’objectif de ce travail de thèse a été de déterminer les voies de trafic intracellulaire nécessaires au recrutement de la fraction intracellulaire de LAT à la synapse immunologique et de comprendre le rôle de ce transport dans l’activation et la réponse lymphocytaire T. Par des approches d’extinction de l’expression de différentes molécules de transport intracellulaires dans les cellules T Jurkat ou des lymphocytes T CD4+ primaires humains ou par l’utilisation de souris Knock-Out (KO), nous avons mis en évidence plusieurs voies de transport impliquées dans le transport de LAT. Nous avons ainsi mis en évidence que le recrutement de LAT à la synapse immunologique nécessite une voie de sécrétion dépendante de la protéine SNARE vésiculaire VAMP7. L’analyse plus avant du transport de LAT a par ailleurs permis de montrer que LAT est présente dans des compartiments de recyclage alors que VAMP7 est principalement localisée dans l’appareil de Golgi. L’étude de la petite GTPase Rab6 et de la protéine t-SNARE syntaxine-16 qui sont impliquées dans des voies de transport rétrograde entre les endosomes de recyclage et l’appareil de Golgi, a permis de dévoiler que cette voie de transport est requise dans le recrutement de LAT à la synapse immunologique, ainsi qu’à la réponse lymphocytaire T in vitro, ex vivo et in vivo. Enfin, le rôle de la protéine de transport intraflagellaire IFT20, qui a déjà été mis en cause dans le transport du TCR, a été analysé chez la souris et a également montré des défauts de recrutement de LAT à la synapse et dans l’activation lymphocytaire T ex vivo et in vivo. Nos résultats mettent ainsi en évidence que la régulation du transport intracellulaire dans les lymphocytes T joue un rôle crucial dans l’activation lymphocytaire T. Nous proposons ainsi un modèle dans lequel LAT est constitutivement internalisé depuis la membrane plasmique et poursuit une voie de recyclage dépendante de l’appareil de Golgi qui contient la machinerie de sécrétion associé à VAMP7. Cette voie de transport intracellulaire, conditionnerait la resécrétion polarisée de LAT à la synapse immunologique dans les conditions d’activation et une réponse lymphocytaire T robuste. / The immune response against a broad spectrum of pathogens or against tumor cells requires the CD4 + T lymphocytes activation. The triggering of T Cell Receptor (TCR) by peptide-MHC through antigen-presenting cells (APC) leads to numerous T-cell remodeling and the establishment of a specialized structure at the interface between the T lymphocyte and the APC: the immunological synapse. The synapse is the site of intense signaling events where various signaling molecules are recruited in order to amplify and diversify the signal initiated by the TCR. These signaling events are regulated by the transmembrane adapter LAT ("Linker for activation of T cells") which is present at the plasma membrane as well as in intracellular compartments. The intracellular fraction of LAT is recruited at the immune synapse and it is proposed that these vesicular compartments participate in T lymphocyte signaling. The objective of this thesis work was to determine the intracellular trafficking pathways required for the recruitment of the intracellular pool of LAT to the immunological synapse and understand the role of this transport in T cell activation and response. By silencing the expression of different intracellular transport molecules in Jurkat T cells or primary human CD4 + T lymphocytes, or by using Knock-Out (KO) mice, we have highlighted several trafficking pathways involved in the transport of LAT to the immune synapse. We have demonstrated that the recruitment of LAT to TCR activation sites requires a secretion pathway dependent on the vesicular SNARE protein VAMP7. Further analysis of the transport of LAT showed that LAT is present in recycling compartments whereas VAMP7 is mainly located in the Golgi apparatus. The study of the small GTPase Rab6 and the t-SNARE syntaxin-16 protein that are involved in the retrograde transport pathways between the recycling endosomes and the Golgi apparatus, demonstrated that this route of transport is required for the recruitment of LAT to the immunological synapse and for T lymphocyte response in vitro, ex vivo and in vivo as well. Finally, the role of intraflagellar transport protein IFT20, which has already been implicated in the transport of TCR, was analyzed in mice and also showed defects in LAT recruitment to synapse and T lymphocyte activation ex vivo and in vivo. Our results thus show that the regulation of intracellular transport plays a crucial role in T lymphocyte activation. We thus propose a model in which LAT is constitutively internalized from the plasma membrane and pursues a Golgi-dependent recycling pathway that contains the secretion machinery associated with VAMP7. This intracellular transport pathway would thus allow the polarized LAT re-secretion to the immunological synapse under activation conditions and a robust T lymphocyte response.

Linfócitos T CD8 e células NK atuam no combate à infecções por bactérias intracelulares, vírus e células tumorais, provocando a morte dessas células por meio da secreção de grânulos citotóxicos. Proteínas RAB GTPase têm se destacado em estudos de tráfego intracelular, porém, são escassos dados sobre o papel destas proteínas em células citóxicas. Um estudo prospectivo de proteômica realizado por nosso grupo identificou a RAB2A, RAB5A, RAB17 e RAB18 em grânulos citotóxicos. Análises mais aprofundadas revelaram que a RAB2A está associada a proteínas como LAMP-1 e LAMP-2, enquanto que RAB5A, RAB17 e RAB18 estavam presentes na mesma linhagem em um contexto não contemplado neste estudo. Desenvolvemos ainda uma abordagem de silenciamento gênico da RAB2A, e por fim, adaptamos uma série de protocolos de simples execução e baixo custo para avaliar funções efetoras de células NK. O conhecimento da maquinaria secretória é fundamental, uma vez que defeitos nas vias de tráfego intracelular constituem a base de um grande número de doenças que desencadeiam quadros fatais. / CD8 T lymphocytes and NK cells fight against infections by intracellular bacteria, viruses and tumor cells by killing those cells through the secretion of cytotoxic granules. RAB GTPase has been highlighted in studies of intracellular trafficking, however there are scarce reports regarding the role of these proteins in cytotoxic cells. A proteomic study performed by our group identified RAB2A, RAB5A, RAB17 and RAB18 in cytotoxic granules. Further analysis revealed that RAB2A is associated with LAMP-1 and LAMP-2, while RAB5A, RAB17 and RAB18 were present in the same cell line, but in a context not included in this study. We also have developed a gene silencing approach for RAB2A and adapted a number of protocols, simple and low-cost, that can be used to evaluate effector functions of natural killer cells The knowledge of secretory machinery involved in the movement cytotoxic granules of cytotoxic cells is critical, since defects in intracellular trafficking pathways constitute the basis for a large number of diseases which trigger death.

Linfócitos T CD8 e células NK atuam no combate à infecções por bactérias intracelulares, vírus e células tumorais, provocando a morte dessas células por meio da secreção de grânulos citotóxicos. Proteínas RAB GTPase têm se destacado em estudos de tráfego intracelular, porém, são escassos dados sobre o papel destas proteínas em células citóxicas. Um estudo prospectivo de proteômica realizado por nosso grupo identificou a RAB2A, RAB5A, RAB17 e RAB18 em grânulos citotóxicos. Análises mais aprofundadas revelaram que a RAB2A está associada a proteínas como LAMP-1 e LAMP-2, enquanto que RAB5A, RAB17 e RAB18 estavam presentes na mesma linhagem em um contexto não contemplado neste estudo. Desenvolvemos ainda uma abordagem de silenciamento gênico da RAB2A, e por fim, adaptamos uma série de protocolos de simples execução e baixo custo para avaliar funções efetoras de células NK. O conhecimento da maquinaria secretória é fundamental, uma vez que defeitos nas vias de tráfego intracelular constituem a base de um grande número de doenças que desencadeiam quadros fatais. / CD8 T lymphocytes and NK cells fight against infections by intracellular bacteria, viruses and tumor cells by killing those cells through the secretion of cytotoxic granules. RAB GTPase has been highlighted in studies of intracellular trafficking, however there are scarce reports regarding the role of these proteins in cytotoxic cells. A proteomic study performed by our group identified RAB2A, RAB5A, RAB17 and RAB18 in cytotoxic granules. Further analysis revealed that RAB2A is associated with LAMP-1 and LAMP-2, while RAB5A, RAB17 and RAB18 were present in the same cell line, but in a context not included in this study. We also have developed a gene silencing approach for RAB2A and adapted a number of protocols, simple and low-cost, that can be used to evaluate effector functions of natural killer cells The knowledge of secretory machinery involved in the movement cytotoxic granules of cytotoxic cells is critical, since defects in intracellular trafficking pathways constitute the basis for a large number of diseases which trigger death.

Les microtubules (MTs) sont importants pour des processus cellulaires majeurs comme la polarisation, le trafic membranaire, la division cellulaire ainsi que pour l'architecture intracellulaire. En retour, les organites influencent l'organisation et la dynamique des MTs. Mon projet de thèse vise à élucider les interactions fonctionnelles existantes entre les MTs et la sécrétion en adoptant une approche quantitative et systématique. En synchronisant le trafic de différents cargos grâce au système RUSH (Retention Using Selective Hooks) et à une dépolymérisation complète des MTs, nous avons montré que les MTs ne sont pas strictement nécessaires à la sécrétion des cargos. D'une manière générale nous avons observé que le trafic intracellulaire est ralenti mais toujours possible en présence d'un appareil de Golgi dispersé. Nous avons caractérisé deux populations d'éléments golgiens. Elles sont présentes peu après la dépolymérisation des MTs et sont différentes en terme de composition et de capacité de sécrétion. Nos résultats montrent qu'une maturation fonctionnelle des éléments golgiens est nécessaire pour le trafic post-golgien, basée sur l'acquisition de certains facteurs golgiens non identifiés à ce jour. Dans une deuxième partie, nous nous sommes intéressés à l'exocytose au niveau de la membrane plasmique. Nous avons observé une sécrétion préférentielle des protéines à proximité des adhésions focales. Différentes techniques de biologie cellulaire nous ont permis de caractériser cet adressage préférentiel vers les sites d'adhésion de la cellule. Nous avons également corrélé les forces exercées par la cellule sur le substrat avec la direction du transport antérograde. / Microtubules (MTs) are important for major cellular processes like cell polarization, intracellular trafficking, cell division, intracellular architecture. Organelles influence back the MTs organization and dynamics. The goal of my project was to study the involvement of MTs in the intracellular trafficking. Thanks to the Retention Using Selective Hooks (RUSH) system to synchronize the trafficking of cargos and with an efficient way to depolymerize MTs, we showed that MTs were not strictly essential to secretion of cargos. More generally, we showed that intracellular trafficking is slowed down but still possible in the presence of a dispersed Golgi apparatus. Moreover, we characterized two populations of Golgi elements in cells without MTs that are different in terms of secretion ability and composition. Our results demonstrated that functional maturation of Golgi elements is needed to ensure post-Golgi trafficking and that MTs driven post-Golgi transport is not strictly required. Besides working on intracellular trafficking without MTs, we conducted a study on the exocytosis at the plasma membrane. By using an antibody coating on coverslips to immobilize secreted cargos, we visualized the first step of arrival at the plasma membrane. We observed a directed and polarized secretion close to focal adhesions that we characterized by different cell biology technics and microscopy (spinning disk, TIRF…). We highlighted a close relationship between forces exerted by the cell on its substrate and the directionality of the anterograde transport by using patterning and Traction Force Microscopy (TFM).

Glucans are fungal cell wall PAMPs that promote survival in polymicrobial and candidal sepsis. Dectin-1 is the primary PRR for glucans. The goals of the present study were to characterize 1) the effects of fungal infection on Dectin-1; 2) the effects of polymicrobial sepsis in the presence and absence of glucan on Dectin-1; 3) the effects of systemic administration of glucans on Dectin-1; and 4) the intracellular trafficking of glucans. Mice were either systemically infected with Candida albicans, or made septic by CLP with and without glucan phosphate (GP) injection, or injected with GP. Flow cytometry was performed to assess cell surface Dectin-1 expression. C. albicans sepsis resulted in an increase in the percentage of Dectin-1 positive (Dectin+) blood and splenic leukocytes by increasing the percentage of neutrophils. C. albicans infection increased the percentage of Dectin+ splenic T cells. CLP decreased the percentage of highly Dectin-1 positive leukocytes in the blood by decreasing the percentage of Dectin+ neutrophils. GP treatment in sepsis further decreased the percentages of Dectinhigh blood leukocytes and Dectin+ neutrophils. CLP decreased the percentage of Dectin+ splenic leukocytes by decreasing the percentage of splenic macrophages. GP administration to CLP mice further decreased the percentage of Dectin+ splenocytes by decreasing the percentage of Dectin+ macrophages. Administration of GP resulted in a prolonged decrease in the percentage of Dectinhigh blood leukocytes. The changes in Dectin-1 expression with GP were because of decreases in the percentage of Dectin+ neutrophils and monocytes. In the trafficking studies, macrophages were incubated with fluorescent labeled glucans and then stained for intracellular organelles and signal transduction molecules. Cells were imaged using confocal microscopy. GP is internalized by clathrin and trafficked to the Golgi apparatus. GP internalization is regulated but not dependent on caveolin-1. GP co-localized with SRA, TLR2, and PI3K/p85. The trafficking of laminarin and particulate glucan is similar. We speculate that loss of cell surface Dectin-1 may be important in the protection conferred by glucans in sepsis. Additionally, intracellular trafficking and interaction with signaling components may be important steps in modulation of cellular function by glucan-pattern recognition receptor complexes.