Interferons (IFNs) perform a wide range of biological activities: anti-microbial, anti-proliferative, immunomodulatory etc. The IFN family includes three main classes: Type I, Type II and the recently identified Type III. The two main members of Type I class are IFNα and IFNβ, which are well known for their anti-viral roles. IFNλ, a member of the Type III class of IFNs, also exhibits antiviral activity. IFNγ, also known as immune IFN, is a Type II IFN which is secreted, primarily, by activated T cells, NK cells and macrophages. IFNγ is a potent immunomodulator which plays important roles in host defense. The diverse functions of this cytokine are demonstrated in Ifnγ-/- mice which display increased sensitivity to several pathogens, high incidences of tumors, reduced inflammatory response etc. IFNγ binds to its cognate receptors, which consist of two subunits, IFNγ receptor (IFNGR) 1 and IFNGR2. IFNγ mediates its multifarious biological actions by activating the Janus activated kinase (Jak)-Signal transducer and activator of transcription (Stat) 1 signaling pathway. Jaks belong to a family of non-receptor protein tyrosine kinases and phosphorylate the IFNγ receptor and the transcriptional co-activator, Stat. IFNGR1, the larger subunit, is required for ligand binding and its carboxyl terminus is involved in binding to Jak1, which in turn phosphorylates Stat1. The smaller subunit, IFNGR2, is required for signaling and contains the Jak2 binding site. After binding of IFNγ to its receptor, a series of phosphorylation events occur, resulting in Stat1 phosphorylation and homodimerization of Stat1 to form the gamma activating factor (GAF). These activated molecules translocate to the nucleus and bind to gamma activating sequence (GAS) present in the promoters of several IFNγ-modulated genes. Thus, the cellular responses mediated by IFNγ are, primarily, due to modulation of gene expression. Therefore, the identification and study of IFNγ stimulated genes, signaling mediators and their cross talk with other cellular pathways is an active area of research. The system of our study was a hepatoma cell line, H6, which is derived from a spontaneous tumor from B10.A mice and selected for in vitro cell culture. It is an IFNγ inducible system and has been used to study IFNγ-induced gene expression and functional responses. Treatment of H6 cells with IFNγ greatly enhanced MHC class I levels but also reduced cell growth. High amounts of reactive oxygen species (ROS) and reactive nitrogen intermediates (RNI) play crucial roles in the growth suppressive effect of IFNγ. To better understand the signaling pathways involved in the generation of ROS and RNI, the involvement of Ras was investigated. Ras-GTP levels were determined by pull down assays using GST-Raf1-Ras binding domain fusion protein bound to glutathione agarose. Ras activation (conversion of Ras-GDP to Ras-GTP) was observed in H6 cells upon IFNγ treatment by ~12 hr. To assess the functional role of Ras activation, studies with Manumycin A, a farnesyl transferase inhibitor (FTI), were performed. The formation of functional Ras requires farnesylation, a post-translational modification, which is inhibited by FTIs. Treatment with Manumycin A blocked Ras activation but did not significantly modulate the IFNγ-induced MHC class I. However, the inhibitor reduced ROS amounts leading to increased cell growth in the presence of IFNγ. Together, these results delineated the role of Ras and ROS in modulating some functions of IFNγ. To further understand the mechanisms by which Ras mediates its functions during IFNγ mediated growth suppression, the activation and function of Ras effectors was evaluated. In particular, the role of Ras-like (Ral) guanyl nucleotide-binding proteins, RalA and RalB, was investigated. IFNγ induced transcripts of RalA but not RalB. Also, the induction of RalA and IFNγ induced growth suppression were Stat1-dependent. Studies involving chemical inhibitors and genetic studies revealed that Ras played a role in the induction of RalA during IFNγ treatment. The role of c-Jun N-terminal kinase (JNK), a stress induced kinase, was also elucidated in this system. Together, IFNγ induced activation of Ras and its effectors RalA and JNK, leading to high amounts of ROS that suppressed cell growth. To evaluate the physiological significance of Ras activation during inflammatory responses, the mouse model of acetaminophen (APAP) induced liver injury was established. Hepatotoxicity due to overdose of the analgesic and antipyretic, APAP, is a major cause of liver failure in adults. APAP is metabolized into a reactive metabolite which binds to glutathione. Consequently, the depletion of intracellular glutathione stores leads to oxidative stress and liver injury. Notably, Ifnγ-/- mice are resistant to APAP-induced liver damage demonstrating a crucial role for this cytokine. The role of Ras activation was evaluated after oral dosing of BALB/c mice with APAP. Ras-GTP was induced early and decreased amounts were observed upon treatment with L-methionine, which replenished glutathione amounts. Injection with L-methionine or Manumycin A rescued liver injury as assessed by lowered serum alanine aminotransferase amounts and histological analysis. Kinetic studies were also performed, under different treatment conditions, to estimate different biochemical parameters: glutathione amounts, JNK activation, protein carbonylation, ROS amounts, serum amounts of cytokines, TNFα and IFNγ etc. This study reveals a role of Ras activation in stimulating proinflammatory responses and demonstrates the therapeutic efficacy of FTIs during APAP-induced liver injury. In addition the role of RalA during APAP-induced liver injury was also studied. In summary, this study, involving in vitro cell culture and in vivo liver injury model systems, sheds light on the significant contributions of Ras and its effector, RalA, during IFNγ mediated growth suppression and APAP-induced liver injury.

Spinal muscular atrophy (SMA) is the leading genetic cause of death of young children. It is an autosomal recessive disease caused by the mutation and/or the deletion within the ubiquitously expressed survival motor neuron 1 (SMN1) gene. SMA pathology is characterized by spinal cord motor neuron degeneration, neuromuscular junction (NMJ) defects and muscular atrophy. Upon disease onset, SMA patients progressively become paralyzed and in the most severe cases, they die due to respiratory complications. Over the years, it has become clear that SMN is a multi-functional protein with important roles in small nuclear ribonucleoprotein (snRNP) assembly, RNA metabolism, axonal outgrowth and pathfinding, mRNA transport as well as in the functional development of NMJs, skeletal muscle and cardiac muscle. However, it remains unclear which of these functions, and the respective perturbed molecular pathways, dictate SMA pathogenesis. Here, we have established Smn-depleted PC12 cells and an intermediate SMA mouse model to characterize a role for Smn in the regulation of actin cytoskeleton dynamics. We find that Smn depletion results in the increased expression of profilin IIa and active RhoA (RhoA-GTP) as well as the decreased expression of plastin 3 and Cdc42. Importantly, the inhibition of rho-kinase (ROCK), a direct downstream regulator of RhoA, significantly increased the lifespan of SMA mice and shows beneficial potential as a therapeutic strategy for SMA. In an addition, we have uncovered a muscle- and motor neuron-independent role for SMN in the regulation of pancreatic development and glucose metabolism in SMA mice and type 1 SMA patients. This finding highlights the importance of combining a glucose tolerance assessment of SMA patients with their existing clinical care management. Thus, our work has uncovered two novel and equally important roles for the SMN protein, both of which contribute significantly to SMA pathogenesis.

Lfc is a guanine nucleotide exchange factor (GEF) for RhoA and is negatively regulated by its association with the microtubule array. Tctex-1, a light chain subunit of the dynein motor complex, was identified as an Lfc-interacting protein in a yeast two-hybrid screen. In mouse embryonic fibroblast (MEF) cells, over-expression of Tctex-1 represses Lfc-induced actin stress fiber and focal adhesion complex formation. Here, we present biochemical evidence obtained from a real-time, nuclear magnetic resonance (NMR)-based assay indicating that the microtubule exerts its inhibitory effect on Lfc through a mechanism that is dependent on the presence of Tctex-1. We also present NMR structure data showing that Lfc and the dynein intermediate chain (DIC) bind to different surfaces of Tctex-1. The biochemical and structural data together support a model in which Lfc is recruited to the microtubules through the dynein cargo adaptor function of Tctex-1, resulting in inhibition of Lfc function.

Lfc is a guanine nucleotide exchange factor (GEF) for RhoA and is negatively regulated by its association with the microtubule array. Tctex-1, a light chain subunit of the dynein motor complex, was identified as an Lfc-interacting protein in a yeast two-hybrid screen. In mouse embryonic fibroblast (MEF) cells, over-expression of Tctex-1 represses Lfc-induced actin stress fiber and focal adhesion complex formation. Here, we present biochemical evidence obtained from a real-time, nuclear magnetic resonance (NMR)-based assay indicating that the microtubule exerts its inhibitory effect on Lfc through a mechanism that is dependent on the presence of Tctex-1. We also present NMR structure data showing that Lfc and the dynein intermediate chain (DIC) bind to different surfaces of Tctex-1. The biochemical and structural data together support a model in which Lfc is recruited to the microtubules through the dynein cargo adaptor function of Tctex-1, resulting in inhibition of Lfc function.

Naïvement perçu, le processus d’évolution est une succession d’événements de duplication et de mutations graduelles dans le génome qui mènent à des changements dans les fonctions et les interactions du protéome. La famille des hydrolases de guanosine triphosphate (GTPases) similaire à Ras constitue un bon modèle de travail afin de comprendre ce phénomène fondamental, car cette famille de protéines contient un nombre limité d’éléments qui diffèrent en fonctionnalité et en interactions. Globalement, nous désirons comprendre comment les mutations singulières au niveau des GTPases affectent la morphologie des cellules ainsi que leur degré d’impact sur les populations asynchrones. Mon travail de maîtrise vise à classifier de manière significative différents phénotypes de la levure Saccaromyces cerevisiae via l’analyse de plusieurs critères morphologiques de souches exprimant des GTPases mutées et natives. Notre approche à base de microscopie et d’analyses bioinformatique des images DIC (microscopie d’interférence différentielle de contraste) permet de distinguer les phénotypes propres aux cellules natives et aux mutants. L’emploi de cette méthode a permis une détection automatisée et une caractérisation des phénotypes mutants associés à la sur-expression de GTPases constitutivement actives. Les mutants de GTPases constitutivement actifs Cdc42 Q61L, Rho5 Q91H, Ras1 Q68L et Rsr1 G12V ont été analysés avec succès. En effet, l’implémentation de différents algorithmes de partitionnement, permet d’analyser des données qui combinent les mesures morphologiques de population native et mutantes. Nos résultats démontrent que l’algorithme Fuzzy C-Means performe un partitionnement efficace des cellules natives ou mutantes, où les différents types de cellules sont classifiés en fonction de plusieurs facteurs de formes cellulaires obtenus à partir des images DIC. Cette analyse démontre que les mutations Cdc42 Q61L, Rho5 Q91H, Ras1 Q68L et Rsr1 G12V induisent respectivement des phénotypes amorphe, allongé, rond et large qui sont représentés par des vecteurs de facteurs de forme distincts. Ces distinctions sont observées avec différentes proportions (morphologie mutante / morphologie native) dans les populations de mutants. Le développement de nouvelles méthodes automatisées d’analyse morphologique des cellules natives et mutantes s’avère extrêmement utile pour l’étude de la famille des GTPases ainsi que des résidus spécifiques qui dictent leurs fonctions et réseau d’interaction. Nous pouvons maintenant envisager de produire des mutants de GTPases qui inversent leur fonction en ciblant des résidus divergents. La substitution fonctionnelle est ensuite détectée au niveau morphologique grâce à notre nouvelle stratégie quantitative. Ce type d’analyse peut également être transposé à d’autres familles de protéines et contribuer de manière significative au domaine de la biologie évolutive. / Evolution is a gradual process that gives rise to changes in the form of mutations that are reflected at the protein level. We propose that evolution of new pathways occurs by switching binding partners, hence creating new functions. The different functions encountered in a given family of related proteins have emerged from a common ancestor that has been duplicated and mutated to become implicated in new interactions and to gain new functions. In this study, we will use native and constitutive active mutant variants of the Ras-like family of small GTPases as working model, to explore such gene duplications, followed by neo / sub-functionalization. The reason for choosing this family resides in the fact that it is a defined set of proteins with well known functions that are mediated through multiple protein-protein interactions. The aim of this master is to perform a classification of budding yeast phenotypes using different approaches in order to statistically determine at which level of the population these constitutively active mutations are capable to affect cell morphology. Working with a subset of the Ras-like small GTPases family, we recently developed an approach to catalogue and classify these proteins based on multiple physical and chemical criteria. Using microscopic and bioinformatics methods, we characterized phenotypes associated with over-expression of the native small GTPases of the budding yeast Saccharomyces cerevisiae, showing that an established classification is not very clear. We are interested to investigate how point mutations in small GTPases can affect the cell morphology and their level of impact on asynchronous population. We want to establish a method to determine and quantify mutant and wild type-like phenotypes on these populations using Differential interference contrast microscopy (DIC) images only. As for the first aim of this study, we hypothesize that clustering algorithms can partition mutant cells from wild type cells based on cell shape factor measurements. To prove this hypothesis, we proposed to implement different clustering algorithms to analyze datasets which combines measurements from wild type and respective mutant populations. We created constitutively active forms of these small GTPases and used Cdc42, Rho5, Ras1 and Rsr1 to validate our results. We observed that Cdc42 Q61L, Rho5 Q91H, Ras1 Q68L and Rsr1 G12V mutations induced characteristic amorphous, clumped/elongated, rounded and discrete large phenotypes respectively. This classification allowed us to define a phenotypical classification related to functions. Phenotype classification of the small GTPases has been confirmed using shape factor formulas accompanied with bioinformatics approaches. These approaches which involved different clustering methods allowed an automated quantitative characterization of the phenotypes of up to 7293 mutant cells. Sequence alignment of Cdc42 and Rho5 showed 46.1% identity as well as 62.6% for Ras1 and Rsr1 allowing the identification of diverged residues potentially involved in specific functions and protein-protein interactions. Directed mutagenesis and substitution of these sites from one gene to another have been performed in some positions to test for specificity and involvement in morphology changes. In parallel, interactions observed for native and constitutively active mutants Cdc42 and Rho5 will be assayed with protein-fragment complementation assay (PCA). This will enable us to determine whether a high correlation exists between functions switches and binding partner’s switches. We propose to expand this approach to the whole Ras-like small GTPases family and monitor protein-protein interactions and functions at a network scale. This research will confirm whether enrichment or depletion of residues in specific sites induces a switch of function due to switching binding partners. Understanding the mechanism underlying such correlation is important to gain insight in the biological mechanisms underlying the Ras-like small GTPases and other proteins evolution. Such knowledge is of fundamental importance in biomedical and pharmaceutical fields, since Ras-like small GTPases represent important targets for therapeutic interventions and for the evolutionary biology field.

Chez les vertébrés, le battement coordonné des cils motiles présents par centaines à la surface apicale des cellules multiciliées (MCC) est requis pour propulser directionnellement les fluides biologiques à l'intérieur de certains organes (voies respiratoires, ventricules cérébraux, trompes utérines ou certaines structures embryonnaires). De nombreuses pathologies humaines sont associées à des défauts ciliaires ou à une perte des MCC (dyskinésies ciliaires, mucoviscidose, asthme,...). Dans ce contexte, mon travail de thèse a consisté à élucider les mécanismes complexes contrôlant la différenciation des MCC et donc la formation des cils motiles (multiciliogenèse). Par des approches de génomiques fonctionnelles à partir de deux modèles d'épithéliums multiciliés évolutivement éloignés (épithélium respiratoire humain et épiderme d'embryon de Xénope) nous avons identifié la famille des microARN (petits ARN non-codants régulateurs de l'expression génique) miR-449 comme majoritairement exprimée dans les MCC. Nous avons montré que miR-449 contrôle la multiciliogenèse i) en bloquant le cycle cellulaire, ii) en réprimant directement la voie de signalisation Notch et iii) en inhibant l'expression de la petite GTPase R-Ras. Enfin, nos travaux montrent que l'ensemble de ces mécanismes est conservé chez les vertébrés. En conclusion, miR-449 est un nouveau régulateur clé de la multiciliogenèse conservé au cours de l'évolution. Nos résultats pourraient ouvrir la voie à de nouvelles stratégies thérapeutiques utilisant des petits ARN régulateurs dans le traitement de certaines pathologies associées à des défauts ciliaires.

Les petites GTPases de la famille Arf, régulateurs majeurs du trafic membranaire, sont activé par plusieurs familles de facteurs d'échange nucléotidiques (ArfGEFs). Les ArfGEFs jouent un rôle essentiel dans l'intégration des signaux de régulation qui conduisent à l'activation d'Arf au niveau de compartiments cellulaires spécifiques, cependant les mécanismes par lesquels ils ciblent les Arfs activés aux membranes spécifiques et leur coordination avec l'échange de nucléotide reste peu comprise. Nous utilisons ici la cristallographie et la reconstitution des activités ArfGEF sur des membranes artificielles pour analyser ces mécanismes pour un ArfGEF humain atypique, impliqués dans l'endocytose de récepteurs et associé à l'invasion tumorale dans de nombreuses cellules cancéreuses. Les membres de cette famille ont été décrits comme des GEFs spécifique d'Arf6, et comporte un domaine de type PH après leur domaine Sec7. Dans la deuxième partie de ma thèse, nous voulions savoir comment les isoformes Arf1 et Arf6 achevaient leurs fonctions dans la cellule. Arf1 et Arf6 sont très similaires: elles possèdent plus de 60% d'identité de séquence, et des études structurales ont montré que la surface qu'ils utilisent pour interagir avec leurs régulateurs et effecteurs est essentiellement identique en séquence et en structure. Cependant, elles ont des fonctions différentes dans la cellule et des propriétés différentes in vitro, pour lesquelles aucune donnée structurale n'a donné d'explications. Nous utilisons ici la cristallographie, le SAXS et la RMN pour comprendre la différence entre ces deux isoformes.

Spinal muscular atrophy (SMA) is the leading genetic cause of death of young children. It is an autosomal recessive disease caused by the mutation and/or the deletion within the ubiquitously expressed survival motor neuron 1 (SMN1) gene. SMA pathology is characterized by spinal cord motor neuron degeneration, neuromuscular junction (NMJ) defects and muscular atrophy. Upon disease onset, SMA patients progressively become paralyzed and in the most severe cases, they die due to respiratory complications. Over the years, it has become clear that SMN is a multi-functional protein with important roles in small nuclear ribonucleoprotein (snRNP) assembly, RNA metabolism, axonal outgrowth and pathfinding, mRNA transport as well as in the functional development of NMJs, skeletal muscle and cardiac muscle. However, it remains unclear which of these functions, and the respective perturbed molecular pathways, dictate SMA pathogenesis. Here, we have established Smn-depleted PC12 cells and an intermediate SMA mouse model to characterize a role for Smn in the regulation of actin cytoskeleton dynamics. We find that Smn depletion results in the increased expression of profilin IIa and active RhoA (RhoA-GTP) as well as the decreased expression of plastin 3 and Cdc42. Importantly, the inhibition of rho-kinase (ROCK), a direct downstream regulator of RhoA, significantly increased the lifespan of SMA mice and shows beneficial potential as a therapeutic strategy for SMA. In an addition, we have uncovered a muscle- and motor neuron-independent role for SMN in the regulation of pancreatic development and glucose metabolism in SMA mice and type 1 SMA patients. This finding highlights the importance of combining a glucose tolerance assessment of SMA patients with their existing clinical care management. Thus, our work has uncovered two novel and equally important roles for the SMN protein, both of which contribute significantly to SMA pathogenesis.

No description available.

No description available.