Ce travail de thèse repose sur le développement de méthodes en spectrométrie de masse native et mobilité ionique pour la caractérisation structurale de protéines d’intérêt thérapeutique et de complexes multiprotéiques. L’optimisation fine et conséquente de la préparation d’échantillon et des conditions analytiques ont permis la caractérisation de protéines membranaires solubilisées en milieu détergent, protéines hydrophobes habituellement réfractaires à l’analyse par MS. D’autre part, une nouvelle approche de mobilité ionique appelée Collision Induced Unfolding a été évaluée et mise en place au laboratoire. Elle a permis une caractérisation conformationnelle approfondie et originale de plusieurs formats d’anticorps monoclonaux thérapeutiques. Enfin, les techniques de MS native et de mobilité ionique ont été utilisées pour caractériser des complexes multiprotéiques d’hétérogénéité variable mettant ainsi en lumière leurs avantages et les progrès réalisés dans le domaine de la MS structurale. / This PhD work focuses on developments in native mass spectrometry and ion mobility methods for the structural characterization of therapeutic proteins and multiprotein complexes. First, careful optimizations of sample preparation and analytical conditions allowed the characterization of membrane proteins, which are hydrophobic proteins difficult to analyze by MS approaches in detergent environment. Then, a new ion mobility-based activation approach called Collision Induced Unfolding has been set up and evaluated. CIU allowed extensive and original conformational characterization of several therapeutic monoclonal antibody formats. Finally, native MS and ion mobility techniques were used for the characterization of heterogeneous multiprotein complexes depicting their benefit when combined to other biophysical techniques for the structural characterization of multiprotein complexes.

Environ 30% des CDS prédits d'un génome code pour des protéines de fonction inconnue ou hypothétiques. La compréhension du rôle de ces protéines est donc l'un des grands challenges de la communauté scientifique.L'objectif principal de cette thèse est de comprendre la fonction de six protéines de fonction inconnue spécifiques de l'anaérobiose formant un complexe, appelé complexe ORP chez Desulfovibrio vulgaris Hildenborough (DvH). Ce système est répandu dans de nombreuses espèces anaérobies, et certaines de ses protéines possèdent des homologies significatives avec des protéines impliquées dans la division cellulaire.Des outils de microscopie dédiés à l'anaérobiose ont été développés au cours de cette thèse et ont permis, pour la première fois, l'observation du cycle cellulaire de DvH. L'étude de l'effet de l'oxygène à l'échelle de la cellule unique a montré une inhibition réversible de la division cellulaire en présence d'oxygène révélant une nouvelle stratégie impliquée dans l'aérotolérance de DvH.Chez DvH, le complexe ORP est codé par des gènes organisés en deux opérons divergents, orp1 et orp2, dont la transcription est gouvernée par l'ARN polymérase sigma54, le facteur de transcription IHF et l'activateur de transcription DVU2106.La diminution de la quantité de complexe ORP conduit à une hétérogénéité de la taille des cellules en accord avec un rôle potentiel du complexe dans le contrôle de la division cellulaire. Alors que l'absence de certaines protéines ORP n'affecte pas de manière significative la division de la bactérie en anaérobiose, la protéine DVU2109 présente une localisation dynamique au cours du cycle cellulaire et semble être essentielle chez DvH. / Up to now, approximately 30% of the predicted CDS in genomes encode for hypothetical or unknown function proteins. Understanding the role and the function of these proteins is now a major challenge for the scientific community.The main objective of this thesis is to determine the function of six proteins of unknown function specific of anaerobiosis and able to forming a multiprotein complex in Desulfovibrio vulgaris Hildenborough (DvH), named the ORP complex. This system is widely found in many anaerobic microorganisms, and some proteins of this system have significant homologies with proteins involved in cell division.Tools for microscopy in anaerobiosis have been developed during this thesis and have allowed observation, for the first time, of a complete DvH cell cycle. The study of oxygen effect on DvH at a single cell level has showed a reversible inhibition of cell division during oxygen exposure revealing a new strategy involved in DvH aerotolerance.In DvH, the ORP complex is encoding by genes organized in two divergent operons, orp1 and orp2, whose transcription is governed by sigma 54 RNA polymerase, the transcription factor IHF and the transcriptional regulator DVU2106. The decreased in the amount of ORP complex leads to heterogeneity of the cell size in accordance with a potential role of this complex in the spatio-temporal control of DvH cell division. While the absence of the majority of ORP proteins doesn't significantly affect DvH division in anaerobic conditions, the protein DVU2109 has a dynamic location during cell cycle and appears to be essential in the cell.

Le complexe Arp2/3 génère des réseaux d’actine branchés, qui produisent une forcée de poussée permettant à la cellule de remodeler ses membranes. Le complexe WASH active le complexe Arp2/3 à la surface des endosomes et facilite ainsi la scission membranaire des intermédiaires de transports contenants des récepteurs internalisés tels que les intégrines α5β1. De ce fait, le complexe WASH en favorisant le recyclage des intégrines, joue un rôle crucial dans l’invasion des cellules tumorales durant la progression tumorale. Cependant, le mécanisme d’assemblage du complexe WASH est inconnu. Dans cette étude, nous rapportons l’identification du premier facteur d’assemblage du complexe WASH. Nous avons identifié la protéine HSBP1 grâce à un crible des protéines qui se lient aux formes précurseurs des sous-unités mais plus au complexe une fois assemblé. La reconstitution biochimique et la modélisation moléculaire nous a permis de montrer que HSBP1 est associé avec le précurseur trimérique CCDC53, le dissocie et forme un hétérotrimère qui va éventuellement libérer une forme monomérique de CCDC53 pour l’assemblage du complexe WASH. Le rôle de HSBP1 dans l’assemblage du complexe WASH est conservé. En effet, WASH est déstabilisé dans des cellules mammaires par le knock-down de HSBP1 et dans l’amibe Dictyostelium par le knock-out de HSBP1. La déstabilisation du complexe WASH par le knock-out de HSBP1 phénocopie la déplétion de WASH dans l’amibe Dictyostelium. Dans des cellules humaines de carcinomes mammaires l’inhibition de l’expression de HSBP1 altère le recyclage des intégrines à la membrane plasmidique. Il en résulte des adhésions focales défectueuses et des capacités invasives réduites. De plus, HSBP1 est localisé aux centrosomes et est requis pour la polarité des cellules lors de la migration. Enfin, nous avons trouvé que la surexpression de HSBP1 dans des tumeurs mammaires est associée à une augmentation des niveaux du complexe WASH et à un mauvais pronostic pour les patientes atteintes de cancer du sein. En conclusion, HSBP1 est un facteur d’assemblage conservé qui contrôle les niveaux du complexe WASH. / The Arp2/3 complex generates branched actin networks, which produces a pushing force that helps the cell to remodel its membranes. The WASH complex activates the Arp2/3 complex at the surface of endosomes and thereby, facilitates the membrane scission of the transport intermediates containing internalized receptors such as α5β1 integrins. Hence, by promoting integrin recycling, the WASH complex plays a crucial role in tumor cell invasion during cancer progression. However, how cells assemble the WASH complex at first is unknown. Here we report the identification of the first assembly factor of the WASH complex. We identified HSBP1 in a proteomics screen for proteins binding to precursor forms of subunits, but not to the fully assembled WASH complex. Through biochemical reconstitution and molecular modeling, we found that HSBP1 associates with the precursor CCDC53 trimer, dissociates it and forms a heterotrimer that will eventually contribute a single CCDC53 molecule to the assembling WASH complex. The role of HSBP1 in WASH complex assembly is well conserved since WASH is similarly destabilized upon HSBP1 knock-down in mammalian cells or upon HSBP1 knock-out in Dictyostelium amoeba. In line with the defective assembly of the WASH complex, the HSBP1 knock-out closely phenocopies WASH knock-out in amoeba. In human mammary carcinoma cells, HSBP1 depletion results in impaired integrin recycling to the plasma membrane leading to the defective development of focal adhesions and reduced invasion abilities. Moreover, HSBP1 was found to localize at the centrosome and was required for the polarization associated with the migration. On the other end, in mammary breast tumors, we found that HSBP1 was often overexpressed and that its overexpression was associated with increased levels of the WASH complex and with poor prognosis for breast cancer patients. Hence, HSBP1 is a conserved assembly factor that controls the levels of the WASH complex.

Recent studies suggest adipose tissue plays a critical role in regulating whole body energy homeostasis in both animals and humans. In particular, activating brown adipose tissue (BAT) activity is now appreciated as a potential therapeutic strategy against obesity and metabolic disease. However, the signaling circuits that coordinate nutrient uptake and BAT function are poorly understood. Here, I investigated the role of the nutrient-sensing mTOR signaling pathway in BAT by conditionally deleting Rictor, which encodes an essential component of mTOR Complex 2 (mTORC2) either in brown adipocyte precursors or mature brown adipocytes. In general, inhibiting BAT mTORC2 reduces glucose uptake and de novo lipogenesis pathways while increases lipid uptake and oxidation pathways indicating a switch in fuel utilization. Moreover, several key thermogenic factors (Ucp1, Pgc1α, and Irf4) are elevated in Rictor-deficient BAT, resulting in enhanced thermogenesis. Accordingly, mice with mTORC2 loss in BAT are protected from HFD-induced obesity and metabolic disease at thermoneutrality. In vitro culture experiments further suggest that mTORC2 cell-autonomously regulates the BAT thermogenic program, especially Ucp1 expression, which depends on FoxO1 activity. Mechanistically, mTORC2 appears to inhibit FoxO1 by facilitating its lysine-acetylation but not through the canonical AKT-mediated phosphorylation pathway. Finally, I also provide evidence that β-adrenergic signaling which normally triggers thermogenesis also induces FoxO1 deacetylation in BAT. Based on these data, I propose a model in which mTORC2 functions in BAT as a critical signaling hub for coordinating nutrient uptake, fuel utilization, and thermogenic gene expression. These data provide a foundation for future studies into the mTORC2-FoxO1 signaling axis in different metabolic tissues and physiological conditions.

A cellular pre-mRNA undergoes various post-transcriptional processing events, including capping, splicing and polyadenylation prior to nuclear export. Splicing is particularly important for mRNA nuclear export as two distinct multi-protein complexes, known as human TREX (hTREX) and the exon-junction complex (EJC), are recruited to the mRNA in a splicing-dependent manner. In contrast, a number of Kaposi's sarcoma-associated herpesvirus (KSHV) lytic mRNAs lack introns and are exported by the virus-encoded ORF57 protein. Herein we show that ORF57 binds to intronless viral mRNAs and functions to recruit the complete hTREX complex, but not the EJC, in order assemble an export component viral ribonucleoprotein particle (vRNP). The formation of this vRNP is mediated by a direct interaction between ORF57 and the hTREX export adapter protein, Aly. Aly in turn interacts directly with the DEAD-box protein UAP56, which functions as a bridge to recruit the remaining hTREX proteins to the complex. Moreover, we show that a point mutation in ORF57 which disrupts the ORF57-Aly interaction leads to a failure in the ORF57-mediated recruitment of the entire hTREX complex to the intronless viral mRNA and inhibits the mRNAs subsequent nuclear export and virus replication. Furthermore, we have utilised a trans-dominant Aly mutant to prevent the assembly of the complete ORF57-hTREX complex; this results in a vRNP consisting of viral mRNA bound to ORF57, Aly and the nuclear export factor, TAP. Strikingly, although both the export adapter Aly and the export factor TAP were present on the viral mRNP, a dramatic decrease in intronless viral mRNA export and virus replication was observed in the absence of the remaining hTREX components (UAP56 and hTHO-complex). Together, these data provide the first direct evidence that the complete hTREX complex is essential for the export of KSHV intronless mRNAs and infectious virus production.

No / Hyperphosphorylated tau plays an important role in the formation of neurofibrillary tangles in brains of patients with Alzheimer's disease (AD) and related tauopathies and is a crucial factor in the pathogenesis of these disorders. Though diverse kinases have been implicated in tau phosphorylation, protein phosphatase 2A (PP2A) seems to be the major tau phosphatase. Using murine primary neurons from wild-type and human tau transgenic mice, we show that the antidiabetic drug metformin induces PP2A activity and reduces tau phosphorylation at PP2A-dependent epitopes in vitro and in vivo. This tau dephosphorylating potency can be blocked entirely by the PP2A inhibitors okadaic acid and fostriecin, confirming that PP2A is an important mediator of the observed effects. Surprisingly, metformin effects on PP2A activity and tau phosphorylation seem to be independent of AMPK activation, because in our experiments (i) metformin induces PP2A activity before and at lower levels than AMPK activity and (ii) the AMPK activator AICAR does not influence the phosphorylation of tau at the sites analyzed. Affinity chromatography and immunoprecipitation experiments together with PP2A activity assays indicate that metformin interferes with the association of the catalytic subunit of PP2A (PP2Ac) to the so-called MID1-alpha4 protein complex, which regulates the degradation of PP2Ac and thereby influences PP2A activity. In summary, our data suggest a potential beneficial role of biguanides such as metformin in the prophylaxis and/or therapy of AD.

No / Resveratrol is a polyphenolic phytoestrogen that has been shown to exhibit potent anti-oxidant, anti-inflammatory, and anti-catabolic properties. Increased osteoclastic and decreased osteoblastic activities result in bone resorption and loss of bone mass. These changes have been implicated in pathological processes in rheumatoid arthritis and osteoporosis. Receptor activator of NF-kappaB ligand (RANKL), a member of the TNF superfamily, is a major mediator of bone loss. In this study, we investigated the effects of resveratrol on RANKL during bone morphogenesis in high density bone cultures in vitro. Untreated bone-derived cell cultures produced well organized bone-like structures with a bone-specific matrix. Treatment with RANKL induced formation of tartrate-resistant acid phosphatase-positive multinucleated cells that exhibited morphological features of osteoclasts. RANKL induced NF-kappaB activation, whereas pretreatment with resveratrol completely inhibited this activation and suppressed the activation of IkappaBalpha kinase and IkappaBalpha phosphorylation and degradation. RANKL up-regulated p300 (a histone acetyltransferase) expression, which, in turn, promoted acetylation of NF-kappaB. Resveratrol inhibited RANKL-induced acetylation and nuclear translocation of NF-kappaB in a time- and concentration-dependent manner. In addition, activation of Sirt-1 (a histone deacetylase) by resveratrol induced Sirt-1-p300 association in bone-derived and preosteoblastic cells, leading to deacetylation of RANKL-induced NF-kappaB, inhibition of NF-kappaB transcriptional activation, and osteoclastogenesis. Co-treatment with resveratrol activated the bone transcription factors Cbfa-1 and Sirt-1 and induced the formation of Sirt-1-Cbfa-1 complexes. Overall, these results demonstrate that resveratrol-activated Sirt-1 plays pivotal roles in regulating the balance between the osteoclastic versus osteoblastic activity result in bone formation in vitro thereby highlighting its therapeutic potential for treating osteoporosis and rheumatoid arthritis-related bone loss.