Le système ubiquitine-protéasome représente une plateforme de signalisation cellulaire chez les eucaryotes et joue un rôle majeur dans la coordination des processus cellulaires. Des progrès récents suggèrent que l’ubiquitination joue un rôle important dans les phénomènes de séparation de phase liquide-liquide (LLPS), un processus permettant la localisation d’une quantité accrue de protéines dans un compartiment subcellulaire, afin de réaliser une fonction biologique. En effet, il a été démontré que l’ubiquitination joue un rôle central dans les mécanismes qui gouvernent la LLPS durant la formation des granules de stress dans le cytoplasme ou les foci de réparation de l’ADN dans le noyau. D’autre part, chez la levure, des travaux ont montré que le protéasome est capable de s’assembler sous forme de granules dans le cytoplasme suite à un stress métabolique. Toutefois, les mécanismes par lesquels le système ubiquitine-protéasome ainsi que ses régulateurs contrôlent les processus de LLPS restent à déterminer. Dans la première étude de cette thèse, nous avons investigué le mécanisme d’action de la déubiquitinase USP16, qui a été suggérée comme un régulateur négatif de la LLPS, empêchant la formation des foci de réparations de dommages à l’ADN. Cependant, nos résultats démontrent que USP16 est majoritairement cytoplasmique et que seulement une entrée forcée de USP16 dans le noyau empêche la formation des foci de réparation des cassures double brin induites par des radiations ionisagntes et ce en favorisant la déubiquitination de l’histone H2A. De plus, aucune translocation nucléaire de USP16 n’a été observée durant le cycle cellulaire ou suite à des dommages à l’ADN. Nos travaux montrent que USP16 est activement exclue du noyau via son signal d’export nucléaire et régulerait indirectement la LLPS menant à la formation des foci de réparation de l’ADN. Dans la deuxième étude, nous décrivons le comportement dynamique des protéines du protéasome lors d’une LLPS induite par un stress métabolique. Nos résultats indiquent que le protéasome forme des foci distincts dans le noyau des cellules humaines en réponse à une privation de nutriments. Nous avons constaté que ces foci sont enrichis en ubiquitine conjuguée et nous avons démontré que le récepteur d’ubiquitine Rad23B ainsi que l’absence des acides aminés non essentiels sont des éléments clés nécessaires à l’assemblage de ces foci du iv protéasome. De plus, des expériences de survie cellulaire montrent que la présence de ces foci est associée à la mort des cellules par apoptose. En conclusion, nos travaux mettent en lumière l’importance du système ubiquitine-protéasome dans la formation et la régulation des foci cellulaires suite à une LLPS. De même, cette étude aidera également à approfondir notre compréhension sur les mécanismes qui gouvernent l’homéostasie des protéines, la survie cellulaire et le développement du cancer. / The ubiquitin-proteasome system represents a major cell-signaling platform in eukaryotes and plays a pivotal role in the coordination of cellular processes. Recent studies provided evidence that ubiquitination plays a role in liquid-liquid phase separation (LLPS), a process that results in the localization of highly increased levels of a protein in a defined subcellular compartment, in order to achieve a biological function. Indeed, ubiquitination has been shown to play a central role in the mechanisms that govern LLPS and subsequent formation of stress granules in the cytoplasm or the DNA repair foci in the nucleus. On the other hand, several studies have shown that the proteasome itself is able to form granules in the cytoplasm following metabolic stress in yeasts. However, the mechanisms by which the ubiquitin-proteasome system and its regulators control LLPS processes remain to be determined. In the first study of this thesis, we investigated the mechanism of action of USP16 deubiquitinase, which has been suggested as a negative regulator of LLPS preventing the formation of DNA damage repair foci. However, our results demonstrate that USP16 is predominantly cytoplasmic and that only enforced nuclear entry of USP16 prevents the formation of repair foci after double strand breaks induced by ionizing radiation, and this by promoting the deubiquitination of histone H2A. In addition, no nuclear translocation of USP16 was observed during cell cycle or following DNA damage. Our study shows that USP16 is actively excluded from the nucleus via its nuclear export signal and would indirectly regulate LLPS that lead to DNA repair foci. In the second study, we describe the dynamic behavior of proteasome proteins during metabolic stress, a process that involves LLPS. Our results indicate that the proteasome forms distinct foci in the nucleus of human cells in response to nutrients deprivation. We found that these foci are enriched with conjugated ubiquitin and demonstrated that the ubiquitin receptor Rad23B as well as the absence of nonessential amino acids are the key elements necessary for the assembly of these proteasome foci. In addition, cell survival experiments show that the presence of these foci is associated with cell death by apoptosis. In conclusion, our work has shed new light on the importance of the ubiquitin-proteasome system in the formation and regulation of cell foci following LLPS. Likewise, this vi study will also help deepen our understanding of the mechanisms leading to protein homeostasis, cell survival and cancer development.

In thisproject, solubility of butyl paraben in 7 puresolvents and 5 ethanol aqueous solvents has been determined at from 1 ℃to 50 ℃. Thermodynamic properties of butyl paraben have been measured by DifferentialScanning Calorimetey. Relationship between molar solubility of butyl paraben in6 pure solvents and thermodynamic properties has been analyzed. Thisrelationship suggests a method of estimating activity of solute at equilibrium fromcombining solubility data with DSC measurements. Then, activity coefficient accordingto the solubility at different temperatures can be estimated. Duringthe solubility measurements in ethanol aqueous solvents, it is found that whenbutyl paraben is added into aqueous solutions with certain proportion ethanol,solutions separates into two immiscible liquid layers in equilibrium. Water andethanol are primary in top layer, while the butyl paraben is primary in bottomlayer, but the solution turns to cloudy when two layers of solution are mixed. Theaim of this work was to present the phase behaviour of liquid-liquid-phaseseparation for (butyl paraben + water + ethanol) ternary system from 1 ℃ to 50 ℃at atmospheric pressure. Thearea of liquid-liquid-phase separation region in the ternary phase diagram increaseswith the increasing temperature from 10 ℃to 50 ℃. In thisstudy, more than several hundreds of nucleation experiments of butyl paraben havebeen investigated in ethyl acetate, propanol, acetone and 90% ethanol aqueoussolution. Induction time of butyl paraben has been determined at 3 differentsupersaturation levels in these solvents, respectively. Free energy ofnucleation, solid-liquid interfacial energy, and nuclei critical radius havebeen determined according to the classical nucleation theory. Statistical analysis ofinduction time reveals that the nucleation is a stochastic process with widevariation even at the same experiment condition. Butyl paraben nucleates most difficultlyin 90 % ethanol than in other 3 solvents, and most easily in acetone. The interfacialenergy of butyl paraben in these solvents tends to increasing with decreasemole fraction solubility in these solvents. Coolingcrystallizations with different proportions of butyl paraben, water and ethanolhave been observed by Focused Beam Reflectance Method, Parallel VirtualMachine, and On-line Infrared. The FBRM, IR curves and the PVM photos show someof the solutions appeared liquid-liquid phase separation during coolingcrystallization process. The results suggest that if solutions went throughliquid-liquid phase separation region during the cooling crystallizationprocess the distribution of crystals crystal was poor. Droplets from solutions withsame proportion butyl paraben but different proportions of water and ethanolhave been observed under microscope. Induction time of the droplets has been determinedunder the room temperature. Droplets from top layer or bottom layer of solutionwith liquid-liquid phase separation on small glass or plastic plates were alsoobserved under microscope. The microscope photos show that the opposite flows ofcloudy solution on the glass and the plastic plate before nucleation. The resultsof the cooling and evaporation crystallization experiments both revealed thatnucleation would be prevented by the liquid-liquid phase separation. / QC 20110630

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In this work, the solubility of butyl paraben in 7 pure solvents and in 5 different ethanol-water mixtures has been determined from 1 ˚C to 50 ˚C. The solubility of ethyl paraben and propyl paraben in various solvents has been determined at 10 ˚C. The molar solubility of butyl paraben in pure solvents and its thermodynamic properties, measured by Differential Scanning Calorimetry, have been used to estimate the activity of the pure solid phase, and solution activity coefficients. More than 5000 nucleation experiments of ethyl paraben, propyl paraben and butyl paraben in ethyl acetate, acetone, methanol, ethanol, propanol and 70%, 90% ethanol aqueous solution have been performed. The induction time of each paraben has been determined at three different supersaturation levels in various solvents. The wide variation in induction time reveals the stochastic nature of nucleation. The solid-liquid interfacial energy, free energy of nucleation, nuclei critical radius and pre-exponential factor of parabens in these solvents have been determined according to the classical nucleation theory, and different methods of evaluation are compared. The interfacial energy of parabens in these solvents tends to increase with decreasing mole fraction solubility but the correlation is not very strong. The influence of solvent on nucleation of each paraben and nucleation behavior of parabens in each solvent is discussed. There is a trend in the data that the higher the boiling point of the solvent and the higher the melting point of the solute, the more difficult is the nucleation. This observation is paralleled by the fact that a metastable polymorph has a lower interfacial energy than the stable form, and that a solid compound with a higher melting point appears to have a higher solid-melt and solid-aqueous solution interfacial energy. It has been found that when a paraben is added to aqueous solutions with a certain proportion of ethanol, the solution separates into two immiscible liquid phases in equilibrium. The top layer is water-rich and the bottom layer is paraben-rich. The area in the ternary phase diagram of the liquid-liquid-phase separation region increases with increasing temperature. The area of the liquid-liquid-phase separation region decreases from butyl paraben, propyl paraben to ethyl paraben at the constant temperature. Cooling crystallization of solutions of different proportions of butyl paraben, water and ethanol have been carried out and recorded using the Focused Beam Reflectance Method, Particle Vision and Measurement, and in-situ Infrared Spectroscopy. The FBRM and IR curves and the PVM photos track the appearance of liquid-liquid phase separation and crystallization. The results suggest that the liquid-liquid phase separation has a negative influence on the crystal size distribution. The work illustrates how Process Analytical Technology (PAT) can be used to increase the understanding of complex crystallizations. By cooling crystallization of butyl paraben under conditions of liquid-liquid-phase separation, crystals consisting of a porous layer in between two solid layers have been produced. The outer layers are transparent and compact while the middle layer is full of pores. The thickness of the porous layer can reach more than half of the whole crystal. These sandwich crystals contain only one polymorph as determined by Confocal Raman Microscopy and single crystal X-Ray Diffraction. However, the middle layer material melts at lower temperature than outer layer material. / <p>QC 20130515</p> / investigate nucleation and crystallization of drug-like organic molecules