Microtubules are the most rigid element of the cytoskeleton. They are responsible for the structure of cells and make up the tracks for intracellular cargo transport. Interactions between microtubules, motor proteins, and microtubule-associated proteins drive important mechanisms in the cell, such as cell division, cell motility, cell homeostasis, and cell signaling. I seek to understand how such complex, energy-consuming non-equilibrium biological networks self-organize by studying in vitro microtubules bundled by microtubule-associated protein 65 (MAP65), in kinesin-1 gliding assays. I found that large networks can break into smaller, cell-like networks that can mimic types of cell motility. Dynamics of these networks change with varying concentrations of MAP65 and microtubules.

Cytoskeletal motor proteins are essential to the function of a wide range of intra-cellular mechano-systems. The biophysical characterization of the movement of motor proteins along their filamentous tracks is therefore of large importance. Towards this end, in vitro stepping motility assays are commonly used to determine the motor’s velocities and runlengths. However, comparing results from such experiments has proved difficult due to influences from variations in the experimental setups, the experimental conditions and the data analysis methods. This work describes a novel unified method to evaluate traces of fluorescently-labeled, processive dimeric motor proteins and proposes an algorithm to correct the measurements for finite filament length as well as photobleaching. Statistical errors of the proposed evaluation method are estimated by a bootstrap method. Numerical simulation and experimental data from GFP-labeled kinesin-1 motors stepping along immobilized microtubules was used to verify the proposed approach and it was shown (i) that the velocity distribution should be fitted by a t location-scale probability density function rather than a normal distribution, (ii) that the temperature during the experiments should be controlled with a precision well below 1 K, (iii) that the impossibility to measure events shorter than the image acquisition time needs to be accounted for, (iv) that the motor’s runlength can be estimated independent of the filament length distribution, and (v) that the dimeric nature of the motors needs to be considered when correcting for photobleaching. This allows for a better statistical comparison of motor proteins influenced by other external factors e.g. ionic strength, ATP concentration, or post-translational modifications of the filaments. In this context, the described method was then applied to experimental data to investigate the influence of the nucleotide state of the microtubule on the motility behavior of the kinesin-1 motor proteins. Here, a small but significant difference in the velocity measurements was found, but no significant difference in the runlength and interaction time measurements. Consequently, this work provides a framework for the evaluation of a wide range of experiments with single fluorescently-labeled motor proteins.

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Proteins have been optimized by evolution for billions of years to work on a nanometer scale. Therefore, they are extremely promising for nanotechnological applications. Cytoskeletal filaments propelled by surface-attached motor proteins have been recently established as versatile transport platforms for nano-sized cargo in molecular sorting and nano-assembly devices. However, in this gliding motility setup, cargo and motors share the filament lattice as a common substrate for their activity. Therefore, it is important to understand the influence of cargo-loading on transport properties. By performing single molecule stepping assays on biotinylated microtubules, it was shown that kinesin-1 motors first stop and then detach when they encounter a streptavidin obstacle on their path along the microtubule. Consequently, the deceleration of streptavidin coated microtubules in gliding assays could be attributed to an obstruction of kinesin-1's path on the microtubule rather than to "frictional" streptavidin-surface interactions. The insights gained by studying kinesin-1's behavior at obstacles were then used to demonstrate a novel sensing application: Using a mixture of two distinct microtubule populations that each bind a different kind of protein, the presence of these proteins was detected via speed changes in the respective microtubule populations. In future applications, this detection scheme could be combined with other recent advancements in the field, creating highly integrated lab-on-a-chip devices that use microtubule based transport to detect, sort and concentrate analytes. It has been envisioned that the kinesin-1-microtubule system could be used for even more complex appliances like nano-assembly lines. However, currently available control mechanisms for kinesin-1 based transport are not precise enough. Therefore, improved temporal control mechanisms for kinesin-1 were investigated: Using a polymer that changes its size in solution with temperature, starting and stopping of gliding microtubules was demonstrated. In combination with local heating by light, this effect could be used to control the gliding of single microtubules. Finally, a strategy to create photo-switchable kinesin-1 was developed and tested for feasibility using molecular modeling.

Cytoskeletal motor proteins are essential to the function of a wide range of intra-cellular mechano-systems. The biophysical characterization of the movement of motor proteins along their filamentous tracks is therefore of large importance. Towards this end, in vitro stepping motility assays are commonly used to determine the motor’s velocities and runlengths. However, comparing results from such experiments has proved difficult due to influences from variations in the experimental setups, the experimental conditions and the data analysis methods. This work describes a novel unified method to evaluate traces of fluorescently-labeled, processive dimeric motor proteins and proposes an algorithm to correct the measurements for finite filament length as well as photobleaching. Statistical errors of the proposed evaluation method are estimated by a bootstrap method. Numerical simulation and experimental data from GFP-labeled kinesin-1 motors stepping along immobilized microtubules was used to verify the proposed approach and it was shown (i) that the velocity distribution should be fitted by a t location-scale probability density function rather than a normal distribution, (ii) that the temperature during the experiments should be controlled with a precision well below 1 K, (iii) that the impossibility to measure events shorter than the image acquisition time needs to be accounted for, (iv) that the motor’s runlength can be estimated independent of the filament length distribution, and (v) that the dimeric nature of the motors needs to be considered when correcting for photobleaching. This allows for a better statistical comparison of motor proteins influenced by other external factors e.g. ionic strength, ATP concentration, or post-translational modifications of the filaments. In this context, the described method was then applied to experimental data to investigate the influence of the nucleotide state of the microtubule on the motility behavior of the kinesin-1 motor proteins. Here, a small but significant difference in the velocity measurements was found, but no significant difference in the runlength and interaction time measurements. Consequently, this work provides a framework for the evaluation of a wide range of experiments with single fluorescently-labeled motor proteins.

Proteins have been optimized by evolution for billions of years to work on a nanometer scale. Therefore, they are extremely promising for nanotechnological applications. Cytoskeletal filaments propelled by surface-attached motor proteins have been recently established as versatile transport platforms for nano-sized cargo in molecular sorting and nano-assembly devices. However, in this gliding motility setup, cargo and motors share the filament lattice as a common substrate for their activity. Therefore, it is important to understand the influence of cargo-loading on transport properties. By performing single molecule stepping assays on biotinylated microtubules, it was shown that kinesin-1 motors first stop and then detach when they encounter a streptavidin obstacle on their path along the microtubule. Consequently, the deceleration of streptavidin coated microtubules in gliding assays could be attributed to an obstruction of kinesin-1's path on the microtubule rather than to "frictional" streptavidin-surface interactions. The insights gained by studying kinesin-1's behavior at obstacles were then used to demonstrate a novel sensing application: Using a mixture of two distinct microtubule populations that each bind a different kind of protein, the presence of these proteins was detected via speed changes in the respective microtubule populations. In future applications, this detection scheme could be combined with other recent advancements in the field, creating highly integrated lab-on-a-chip devices that use microtubule based transport to detect, sort and concentrate analytes. It has been envisioned that the kinesin-1-microtubule system could be used for even more complex appliances like nano-assembly lines. However, currently available control mechanisms for kinesin-1 based transport are not precise enough. Therefore, improved temporal control mechanisms for kinesin-1 were investigated: Using a polymer that changes its size in solution with temperature, starting and stopping of gliding microtubules was demonstrated. In combination with local heating by light, this effect could be used to control the gliding of single microtubules. Finally, a strategy to create photo-switchable kinesin-1 was developed and tested for feasibility using molecular modeling.

Salmonella est un pathogène intracellulaire qui établit une niche de réplication (SCV) grâce à l’activité des toxines que la bactérie injecte dans le cytosol des cellules infectées. La Kinésine-1, une protéine moteur des microtubules, est la cible de certaines de ces toxines. Ce travail démontre le rôle critique de la kinésine-1 pour la formation de tubules membranaires induits par Salmonella et qui émanent des SCVs. Des travaux antérieurs avaient montré que la toxine PipB2 lie la kinésine-1 à la SCV. Nos résultats écartent une interaction potentielle de PipB2 avec d’autres protéines moteur et renforcent l’idée d’une activité spécifique du couple PipB2/kinésine-1. Grâce à l’utilisation de systèmes in vitro, nous avons montré que: 1) l’activité du complexe PipB2/Kinésine-1 est suffisante pour permettre la formation de tubules membranaires à partir de vésicules artificielles; 2) PipB2 lie et active le moteur moléculaire qui s’engage alors sur les microtubules. Il a été suggéré que la protéine de l’hôte SKIP activait la kinésine-1 en se liant à la toxine SifA. Ce travail met en lumière un mécanisme plus précis grâce à un partenariat entre PipB2 et SifA. / Salmonella is an intracellular pathogen that establishes a replication niche (SCV) through the activity of toxins that the bacterium injects into the cytosol of infected cells. Kinesin-1, a microtubule motor protein, is the target of some of these toxins. This work demonstrates the critical role of kinesin-1 in the formation of Salmonella-induced membrane tubules emanating from the SCVs. Previous work has shown that PipB2 toxin binds kinesin-1 to the SCVs. Our results rule out a potential interaction of PipB2 with other motor proteins and reinforce the idea of a specific activity of the PipB2/kinesin-1 pair. Through the use of in vitro systems, we have shown that: 1) the activity of the PipB2/Kinesin-1 complex is sufficient to pull membrane tubules from artificial vesicles; 2) PipB2 binds and activates the molecular motor which then engages on the microtubules. It has been suggested that the host protein SKIP activates kinesin-1 by binding to the SifA toxin. This work highlights a more precise mechanism thanks to a partnership between PipB2 and SifA.

Le transport intracellulaire de cargos est un processus critique au sein des cellules eucaryotes, et notamment au niveau des neurones, pour contrôler différentes fonctions dont la maturation et la transmission synaptique. La kinésine-1 est un moteur moléculaire capable de transporter différents types de cargos, comme des organelles, des vésicules ou des assemblages macromoléculaires le long des microtubules. La kinésine-1 est un hétérotétramère constitué d’un homodimère de chaînes lourdes (KHC) associé à deux chaînes légères (KLC) ; les deux chaînes, KHC et KLC étant capables de recruter des cargos. L’un des premiers cargos de la kinésine-1 à avoir été identifiés sont les protéines JIP3/4 (JNK-Interacting Protein 3/4) ; elles jouent aussi un rôle de protéines adaptatrices pour le transport d’autres cargos de la kinésine-1. La kinésine-1 recrute les protéines JIP3/4 de deux façons distinctes et indépendantes (i) via KHC et (ii) via KLC. Le recrutement de JIP3/4 par KHC et KLC est capable, via des mécanismes moléculaires distincts, d’activer la motilité de la kinésine-1 et donc de contrôler le transport intracellulaire dans lequel elle est impliquée et les fonctions associées au sein des neurones.Au cours de mon travail de thèse, j’ai contribué à caractérisé par des approches bio-informatiques, biochimiques/biophysiques et structurales, les deux modes de recrutement des protéines JIP3/4 par la kinésine-1 : (i) via KHC et (ii) via KLC. Ce travail a permis d’apporter des nouveaux éléments pour comprendre le mode de recrutement de ces protéines cargos/adaptatrices par la kinésine-1, mais aussi de mieux comprendre les mécanismes moléculaires de son activation par les protéines JIP3/4. / The intracellular transport of cargos is a crucial process on eukaryotic cells, and notably in neurons, in order to regulate different functions as cell’s maturation and synaptic transmission. The Kinesin-1 is a molecular motor capable of transporting different types of cargos as organelles, vesicles and macromolecular assemblies along the microtubules. It is a heterotetramer composed by a homodimer of heavy chains (KHC) bound to two light chains (KLC), where both KHC and KLC are capable of cargos recruitment. One of the first identified cargos of Kinesin-1 is JIP3/4 (JNK-Interacting Protein 3/4), which are also adaptor proteins, intermediating the transport of other cargos. Kinesin-1 recruits JIP3/4 by two different and independent modes, (i) via KHC and (ii) via KLC. Therefore, JIP3/4 recruitment by KHC and KLC activates the motility of Kinesin-1, by distinct mechanisms, allowing the intracellular transport of cargos and the associated functions in neurons. During my PhD, I contributed to the characterization of the dual binding mode of Kinesin-1 and JIP3/4 by bioinformatical, biochemical/biophysical and structural approaches. This work allowed a better understanding of the cargos’ recruitment by Kinesin-1, as well as the molecular mechanisms of Kinesin-1 activation by JIP3/4.

Intracellular transport is provided by two major types of molecular motors kinesins and cytoplasmic dynein. Kinesin-1 is a molecular motor that transports molecules and organelles along microtubule tracks anterogradely. Specific protein-protein interactions are required to activate kinesin-1 as the free kinesin exist in an autoinhibited state. The activation of kinesin-1 induces its conformational change, enables microtubule binding and ATP hydrolysis necessary for the directional cargo transport. HDAC6 is a multifunctional protein composed of several domains. It plays an important role in many microtubule dependent processes as HDAC6 is a major tubulin deacetylase. It has been shown that HDAC6 manipulation (inhibition/genetic ablation) affects transport along microtubules but the exact mechanisms are unknown. The effect can be caused either by deacetylation microtubules or direct interaction with molecular motors. This thesis is focused on characterization of interactions between kinesin-1 and HDAC6 that have not been described so far. To this end, we expressed and purified various constructs of kinesin-1 and HDAC6 and tested their interactions by microscale thermophoresis (MST) and hydrogen deuterium exchange (HDX) to determine affinity and interaction sites, respectively. MST data revealed that...

La plupart des cellules du système immunitaire sont des cellules sécrétrices capables de libérer des molécules immuno-modulatrices en réponse à des stimuli variés. Cette sécrétion régulée qui permet l’orchestration de la réponse immunitaire et inflammatoire est assurée grâce aux organites apparentés aux lysosomes (LRO) qui vont contenir les molécules nécessaires à la fonctionnalité des cellules immunes. On retrouve par exemple les granules lytiques des lymphocytes T cytotoxiques qui permettent à ces cellules d’effectuer leurs fonctions lytiques ou encore les granules de sécrétion des mastocytes qui contiennent les médiateurs de l’inflammation. Le transport et l’exocytose des LRO impliquent une machinerie commune et conservée. C’est notamment le cas de la petite GTPase Rab27 qui joue un rôle central dans le transport et la sécrétion de ces LRO. De précédentes études réalisées au sein de notre laboratoire ont pu mettre en évidence l’implication du complexe moléculaire Rab27a/Slp3/kinésine-1 dans le transport terminal des granules lytiques des lymphocytes T cytotoxiques chez l’homme. De plus, un modèle murin dont la chaîne lourde de la kinésine-1 est spécifiquement invalidée dans les cellules immunitaires a pu être généré. L’objectif de ma thèse a été dans un premier temps de caractériser le phénotype de ce modèle murin déficient pour la kinésine-1 puis d’analyser plus précisément l’impact de l’absence de la kinésine-1 sur la fonctionnalité des lymphocytes T cytotoxiques et mastocytes murins. Dans un premier temps nous avons pu montrer que les souris déficientes pour la kinésine-1 ont un phénotype comparable à celui des souris contrôles à l’état basal. Nous avons ensuite montré que l’absence de la kinésine-1 au sein des lymphocytes T cytotoxiques murins n’induit pas de défauts d’activation et de sécrétion des granules lytiques in vitro. Cependant les comportements des granules lytiques à la synapse immunologique semblent anormaux. Néanmoins après un test d’infection au LCMV, qui ne révèle aucunes différences entre les souris contrôles et déficientes en kinésine-1, nous en venons à la conclusion que des mécanismes compensateurs pourraient compenser l’absence de la kinésine-1 dans les lymphocytes T cytotoxiques chez la souris. Pour finir des études fonctionnelles réalisées au niveau des mastocytes murins nous ont permis de mettre en évidence l’implication de la kinésine-1 dans le mécanisme de transport des granules de sécrétion. En effet, l’absence de kinésine-1 conduit à des défauts de dégranulation des mastocytes in vitro mais aussi in vivo (souris moins sensibles aux chocs anaphylactiques). En revanche l’absence de kinésine-1 n’affecte pas les capacités d’activation et de sécrétion des cytokines des mastocytes. Enfin, nous avons pu caractériser le complexe moléculaire Rab27b/Slp3/kinésine-1 impliqué dans le transport des granules mastocytaires et avons pu constater que la formation de ce complexe était dépendante de la voie d’activation liée à la PI3K (Phospatidylinositol 3-kinase). Ce travail permet d’apporter de nouveaux éléments quant aux mécanismes gouvernant la sécrétion des granules mastocytaires et ouvre ainsi de nouvelles perspectives thérapeutiques pour le traitement des hypersensibilités de type 1 (dépendantes des IgE). / Most of immune cells are secretory cells capable of releasing immunomodulatory molecules in response to various stimuli. This regulated secretion, which allows the orchestration of the immune and inflammatory responses, is ensured by the lysosome-related organelles (LRO) which will contain the molecules necessary for the functionality of the immune cells. For example we found the lytic granules of cytotoxic T lymphocytes, which allow their lytic functions or the secretory granules of mast cells which contain the inflammatory mediators. The transport and exocytosis of LRO involves a common and conserved machinery. This is particularly the case of the small GTPase Rab27 which plays a central role in the transport and secretion of these LRO. Previous studies carried out in our laboratory have highlighted the involvement of the molecular complex Rab27a / Slp3 / kinesin-1 in the terminal transport of lytic granules of cytotoxic T lymphocytes in humans. In addition, a murine model in which the heavy chain of kinesin-1 is specifically invalidated in immune cells has been generated. The objective of my thesis was first to characterize the phenotype of this murine model deficient for kinesin-1, then to analyze more precisely the impact of kinesin-1 absence on the cytotoxic T lymphocyte and mast cell functionality. In a first step, we have been able to demonstrate that mice deficient for kinesin-1 have a phenotype comparable to the control mice in a basal state. We have then shown that the absence of kinesin-1 in murine cytotoxic T lymphocytes does not induce defects in activation and in lytic granules’ secretion in vitro. However, the behavior of the lytic granules at the immunological synapse seems abnormal. Nevertheless, after an infection essay with LCMV, which revealed no differences between control and kinesine-1-deficient mice, we conclude that compensatory mechanisms may complement the absence of kinesin-1 in mice. Finally, functional studies carried out on murine mast cells have enabled us to demonstrate the involvement of kinesin-1 in the mechanism of granules’ transport. Indeed, the absence of kinesin-1 leads to degranulation defects in vitro and also in vivo (mice were less sensitive to anaphylactic shocks). On the other hand, the absence of kinesin-1 does not affect the activation and cytokines secretion capacities of mast cells. Finally, we were able to characterize the molecular complex Rab27b / Slp3 / kinesin-1 involved in mastocytic granules’ transport and found that this complex formation was dependent on the PI3K-related activation pathway (Phospatidylinositol 3-kinase). This work allows us to introduce new elements for the mechanisms governing the secretion of mast cell granules and thus opens new therapeutic perspectives for the treatment of type I hypersensitivity (IgE dependent).