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A minimal structural model encompassing the flow of carbon through the central metabolism of Sacc?ora erythraea was built and used to assess the apphcation of hierarchical clustering techniques for the grouping and, subsequent interpretation of elementary modes. The results indicate that clustering techniques may prove to be a valuable tool for the functional characterisation and grouping of the potentially large datasets yielded by elementary modes analysis, whether clustered by their reaction usage or net stoichiometry.

Zinc is an essential metal that plays a structural or catalytic role in many cellular proteins. In response to zinc limitation, Streptomyces coelicolor produces a high affinity zinc uptake system (ZnuACB). Disruption of this system results in a ΔznuACB-zur mutant growing poorly in the absence of supplemental zinc, implying that the ZnuABC system is a key zinc uptake system for S. coelicolor. The Δzur mutant exhibited a sporulation defect, and appeared to inhibit sporulation of ΔznuA mutants, suggesting there might be cross-talk between the strains. Several important features are presented relating the structure of Zur to its function as a zinc-sensing regulatory protein and help differentiate Zur from the structurally similar iron uptake regulator, Fur. Zur was purified and the interaction between Zur and the promoter region of znuA investigated using electromobility shift assays (EMSA) and DNase I footprinting. SI nuclease digestion assays were used to investigate the role of Zur in controlling expression of znuA.

The Gram negative bacterium Thauera selenatis is able to respire with selenate as the sole terminal electron acceptor, utilising a periplasmic selenate reductase enzyme to reduce selenate to selenite. Previous characterisation of this enzyme has shown that it is a heterotrimeric molybdo-enzyme (SerABC) of the dimethylsulfoxide reductase family, containing a Mo-bis molybdopterin guanine dinucleotide co-factor, Fe-S clusters and a b-type haem (Schroder et al., 1997, J Biol Chem, 272: 23765-68, Dridge et al., 2007, Biochem J, 408: 19-28). In order to elucidate the electron transport pathway to selenate reductase, and how it can generate a proton motive force, detailed study was required. Firstly, the redox potential of the b-haem of SerC was determined by optical redox titration to be +234 mV. The serC gene was cloned and expressed heterologously in E. coli, but the protein was incorrectly folded into inclusion bodies, and attempts to refold and reconstitute SerC with haem were unsuccessful. A profile of c-type cytochromes in T. selenatis was undertaken, and characterisation of a number of cytochromes was carried out. Two cytochromes were purified, cytc7 and cytc4, and cytc4 was shown to be able to donate electrons to SerABC in vitro. Protein sequence was obtained by N-terminal sequencing and LC-MS/MS, and assigned cytc4 to the cytochrome c4 family of dihaem cytochromes. Redox potentiometry combined with UV-visible and electron paramagnetic spectroscopy showed that cytc4 is a dihaem cytochrome with a redox potential of +282 mV and both haems are predicted to have His-Met ligation. To investigate the role of membrane bound cytochromes in selenate respiration, PCR with degenerate primers amplified a partial gene coding for quinol: cytochrome c oxidoreductase (QCR). A microplate growth method was developed to monitor growth of T. selenatis under reproducible conditions, and used to analyse the effect of respiratory chain inhibitors on growth under different conditions. Aerobic metabolism was unaffected by QCR inhibitors, while nitrite reduction was totally inhibited, linking nitrite reduction to the generation of a proton motive force by the QCR. The QCR inhibitor myxothiazol partially inhibited selenate respiration, showing that some electron flux is via the QCR, but total inhibition of selenate respiration was achieved by combining myxothiazol with the more general inhibitor 2-n-heptyl-4-hydroxyquinoline N-oxide (HQNO). These data suggest that electron transfer to selenate reductase occurs via a branched pathway, in which one route is inhibited by myxothiazol and the other by HQNO. Electron transfer via a QCR and a dihaem cytochrome c4 is a novel route for a member of the dimethylsulfoxide reductase family of molybdo-enzymes.

Le laboratoire a établi un modèle de souris α6ΔIEC qui développe une inflammation chronique intestinale associée à la formation d’adénocarcinomes colorectaux. Ce modèle correspond à une délétion ciblée à l’épithélium intestinal de l’intégrine α6β4. Mon projet de thèse a consisté à définir les mécanismes qui influencent la transformation de lésions inflammatoires en adénocarcinomes. La caractérisation du modèle α6ΔIEC a permis de mettre en évidence plusieurs altérations : détachement de l’épithélium, régénération du tissu, prolifération, augmentation de la perméabilité intestinale, hypersécrétion du mucus, ségrégation anormale des bactéries, inflammation chronique et formation de tumeurs.Pour étudier la séquence et la cinétique des mécanismes, j’ai développé un modèle de souris inductible (α6ΔIECTAM). Cette lignée présente, deux semaines après l’invalidation de l’intégrine α6,les mêmes signes d’inflammation que les souris α6ΔIEC. Mon approche a consisté à dissocier les processus impliqués dans chacune des étapes-clés de la pathologie afin de définir la contribution respective de l’infection par les bactéries et du stress mécanique. / We generated a new mouse model, α6ΔIEC, in which the genetic ablation of α6 integrin from intestinal epithelial cells triggered the development of spontaneous colitis and colorectal cancer. My main goal was to define the mechanisms by which inflamed lesions degenerate into infiltrating adenocarcinomas. Loss of α6 integrin in this model resulted in epithelial barrier damage, enhanced permeability, altered mucus layers, abnormal bacterial segregation, chronic inflammation and tumor development.In order to define the sequence of events and the mechanisms involved at each stage of the disease, from inflamed to tumor lesions, I developed an inducible mouse model, α6ΔIECTAM, in which α6 integrin ablation was induced by tamoxifen treatment. This line recapitulates all aspects of inflammation observed in the α6ΔIEC model, as early as two weeks after tamoxifen treatment. In particular, I tried to define the respective contribution of infection by bacteria and mechanical stress during disease progression.

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La voie biosynthétique du mevalonate (MVA) est indispensable à la production de molécules qui sont essentielles dans grand nombre de processus physiologiques mais la plupart des études effectuées sur le rôle physiologique de cet important processus métabolique dans le système nerveux central restent simplement en corrélation. Pour autant, le but des études présentées dans cette thèse a été: évaluer les protéines de la voie du MVA dans différentes régions du cerveaux de rat en prenant en considération l’éventuelle modulation selon le sexe et l’âge; analyser l’impact de la voie sur le développement des neurones set sur le comportement des rats; explorer l’impact de la voie dans une pathologie du neurodéveloppement comme l’autisme. Les résultats démontrent que la voie biosynthétique du MVA est régulée différemment selon la région du cerveau analysée, en fonction de l’âge et du sexe. La voie biosynthétique du MVA revêt un rôle critique dans la modulation physiologique du comportement animal et du développement des neurones Pour finir, mes données démontrent, dans un modèle expérimental d’autisme, que la voie biosynthétique du MVA est modulée dans plusieurs région du SNC selon l’âge. / The mevalonate (MVA) pathway is an essential metabolic pathway that leads to the production of molecules important in several physiological processes and play pivotal roles in the brain. An imbalance of this pathway in CNS is accompanied by the onset of several neuropathological descriptions. Despite these observations, the physiological importance of this metabolic process in the brain has remained unclear. My aim was to study the presence and the regulation of the proteins involved in the MVA pathway in different rat brain areas in a sex- and age-dependent manner, to analyze the impact of the key enzymes on neuronal development and on rat behavior, and to explore whether the MVA pathway is affected in a neurodevelopmental disease such as autism. My results demonstrate that this metabolic process is expressed and modulated in a highly region-dependent manner and that age and sex induce physiological differences. Notably, it impact on behavior and neuronal development suggesting that this pathway may be considered as potential molecular target when designing novel therapeutic approaches for the treatment of these pathologies.

Les myopathies inflammatoires sont des maladies auto-immunes rares dont le dénominateur commun est la faiblesse musculaire et l'inflammation. Leur origine n’est pas connue et les traitements sont conventionnels partiellement efficaces. Par une approche épidémiologique, nous avons montré que l’étude de l’incidence et de la prévalence est un outil utile pour mettre en évidence des déterminants des myopathies inflammatoires. Une meilleure identification et une meilleure classification des patients atteints de ces maladies sont cependant nécessaires pour préciser l’épidémiologie des myopathies inflammatoires.Par une approche translationnelle, nous avons montré que, par rapport aux autres myopathies inflammatoires, des dysfonctions mitochondriales périfasciculaires sont une caractéristique des dermatomyosites, qui jouent un rôle dans l’intolérance à l’effort et le maintien de l’inflammation. Ces résultats ouvrent des nouvelles voies pour mieux comprendre et traités les myopathies inflammatoires. / Inflammatory myopathies are rare autoimmune diseases whose common denominator is muscle weakness and inflammation. Their origin is not known and conventional treatments are partially effective. Using an epidemiological approach, we have shown that the study of incidence and prevalence is an useful tool for identifying determinants of inflammatory myopathies. However, better identification and classification of patients is mandatory to refine the epidemiology of inflammatory myopathies. Using a translational approach, we have shown that, compared with other inflammatory myopathies, perifascicular mitochondrial dysfunctions are a characteristic of dermatomyositis, which play a role in exercise intolerance and in the maintenance of inflammation. These results open up new avenues to better understand and treat inflammatory myopathies.

Le récepteur à neurotrophine TrkC a été identifié comme étant un récepteur à dépendance : en l'absence de son ligand NT-3, il déclenche l'apoptose. En effet, la survie des cellules qui expriment ces récepteurs dépend de la disponibilité en ligand, un mécanisme qui inhibe la prolifération incontrôlée et la migration des cellules tumorales. TrkC, en tant que récepteur à tyrosine kinase, est généralement considéré comme un proto-oncogène. Or nous montrons que l'expression TrkC est diminuée dans une grande fraction des cancers colorectaux humains, principalement par méthylation du promoteur de TrkC. En outre, ce mécanisme confère un avantage sélectif aux lignées cellulaires colorectales pour inhiber la mort des cellules tumorales. De plus, la réexpression de TrkC dans les lignées tumorales colorectales est associée à la mort des cellules tumorales et à l'inhibition in vitro des caractéristiques de transformation cellulaire, et in vivo de la croissance tumorale. Ensemble, ces données permettent de conclure que TrkC est un gène suppresseur de tumeur dans le cancer colorectal. Le mécanisme moléculaire par lequel TrkC déclenche l'apoptose implique le clivage de son domaine intracellulaire, ce qui libère un fragment pro-apoptotique (TrkC KF). Nous montrons que TrkC KF interagit avec Cobra1, un cofacteur de BRCA1, et que Cobra1 est nécessaire à l'apoptose induite par TrkC. Cobra1 conduit TrkC KF à la mitochondrie, où il favorise l'apoptose apoptosome-dépendante. Ainsi, nous proposons qu'en l'absence de NT-3, le clivage protéolytique de TrkC conduit à la libération d'un fragment tueur qui déclenche l'apoptose mitochondriale, via le recrutement de Cobra1 / The neurotrophin receptor TrkC was recently identified as a dependence receptor, and, as such, it triggers apoptosis in the absence of its ligand, NT-3. Indeed cells that express these receptors are thought to be dependent on ligand availability for their survival, a mechanism that inhibits uncontrolled tumor cell proliferation and migration. TrkC, as a classic tyrosine kinase receptor, is generally considered to be a proto-oncogene. We show that TrkC expression is down-regulated in a large fraction of human colorectal cancers, mainly through promoter methylation. Moreover, we show that TrkC silencing by promoter methylation is a selective advantage for colorectal cell lines to limit tumor cell death. Furthermore, reestablished TrkC expression in colorectal cancer cell lines is associated with tumor cell death and inhibition of in vitro characteristics of cell transformation, as well as in vivo tumor growth. Together, these data support the conclusion that TrkC is a colorectal cancer tumor suppressor. TrkC triggers apoptosis in the absence of its ligand NT-3 : the molecular mechanism for apoptotic engagement involves the double cleavage of the receptor's intracellular domain, leading to the formation of a proapoptotic fragment (TrkC KF). We show that TrkC KF interfacts with Cobra1, a putative cofactor of BRCA1, and that Cobra1 is required for TrkC-induced apoptosis. Cobra1 shuttles TrkC KF to the mitochondria, where it promotes apoptosome-dependent apoptosis. Thus, we propose that, in the absence of NT-3, the proteolytic cleavage of TrkC leads to the release of a killer fragment that triggers mitochondria-dependent apoptosis via the recruitment of Cobra1

Nous étudions les interactions hôte/pathogène entre la drosophile et un parasite intracellulaire, la microsporidie Tubulinosema ratisbonensis.Les microsporidies dérivent du groupe des champignons possédant un génome réduit et pas de mitochondrie. Ces parasites dépendent fortement du métabolisme de leur hôte pour proliférer. Les interactions entre les microsporidies et leurs hôtes reste peu étudiées au niveau métabolique.In vivo, les spores ciblent beaucoup de tissues, en particulier le corps gras qui perd ces gouttelettes lipidiques. Les réserves métaboliques sont épuisées au cours de l’infection et les mouches présentent les caractéristiques de famine. La supplémentation en acide gras dans la nourriture des mouches infectées augmente la prolifération du parasite. Cet effet est bloqué lorsque l’on perturbe l’assimilation ainsi que le transport des lipides provenant de l’intestin. En conséquence, les mouches résistent mieux à l’infection lorsque la synthèse des lipides est bloquée. / We study the host/pathogen interactions between Drosophila and a natural intracellular parasite : the microsporidium Tubulinosema ratisbonensis. Microsporidia are highly derived group of fungi with a compact genome and no mitochondria. These obligate parasites thus rely intensively on host metabolism for growth and proliferation. The interactions between microsporidia and their hosts remain poorly understood at the metabolic level.In vivo, spores target many tissues especially the fat body that loses its lipid droplets. Metabolic reserves become depleted during the course of the infection and flies display the hallmarks of severe starvation. Fatty acids supplementation of the infected flies diet increases parasite proliferation and host susceptibility to the parasite. This effect is blocked when perturbing lipid assimilation and transport originating from the gut. Accordingly, flies resist better infection when lipid synthesis is blocked, as the parasite proliferation is hampered.