Cardiac energy metabolism is the one of the most complex system in the body. To sustain life, but also to respond quickly to any sudden changes (e.g. running, emotional stress), the heart has developed a unique ability and has become a metabolic "omnivore". At physiological conditions, long chain fatty acids (LCFAs) present the major energetic source for the adult myocardium. However, the cardiac energy metabolism may be compromised during pathophysiological states. One of the most dangerous is, undoubtedly, ischaemia-reperfusion injury with its acute form, myocardial infarction. However, the adaptation to chronic hypoxia has been known for decades for its cardioprotective effect against I/R. Changes of cardiac energy metabolism induced by the adaptation have not been fully explored and the system conceals still too many secrets. This thesis has aimed to determine how adaptation to chronic hypoxia affects the cardiac metabolism of the rat LVs in the following set-ups: 1. The effect of chronic normobaric hypoxia (CNH; 3 weeks, 5500m) during a brief I/R protocol in vitro on the protein kinase B/hexokinase (Akt/HK) pathway, including the expression and phosphorylation of Akt, the expression and localization of HK, the expression of mitochondrial creatine kinase (mtCKS), and the level of Bcl-2 family...

Alcohol abuse and dependence are complex disorders that are influenced by many genetic and environmental factors. Acute behavioral responses to ethanol have predictive value for determining an individual’s long-term susceptibility to alcohol abuse and dependence. These behavioral responses are strongly influenced by genetics. Here, we have explored the role of genetic influences on acute behavioral responses to ethanol using the nematode worm, Caenorhabditis elegans. First, we explored the role of ethanol metabolism in acute behavior responses to ethanol. Natural variation in human ethanol metabolism machinery is one of the most reported and reproducible associations found to alter drinking behavior. Ethanol metabolism is conserved across phyla and alteration in this pathway alters acute behavioral responses to ethanol in humans, mice, rats, and flies. We have extended these findings to the worm and have shown that loss of either alcohol dehydrogenase or aldehyde dehydrogenase results in an increase in sensitivity to the acute effects of ethanol. Second, we explored the influence of differences in basal and ethanol-induced gene expression in ethanol responsive behaviors. We identified a set of candidate genes using the basal gene expression differences in npr-1(ky13) mutant animals to enrich for genes involved in AFT. This analysis revealed ethanol changes to the expression of genes involved in a variety of biological processes including lipid metabolism. We focused on a gene involved in the metabolism of fatty acids, acs-2. acs-2 encodes an acyl-CoA synthetase that activates fatty acids for mitochondrial beta-oxidation. Animals carrying mutant acs-2 have significantly reduced AFT and we explored the role of genes in the mitochondria beta-oxidation pathway for alterations in ethanol responsive behaviors. We have shown that knockdown of ech-6, an enoyl-CoA hydratase, enhances the development of AFT. This work has uncovered a role for fatty acid utilization pathways in acute ethanol responses and we suggest that natural variation in these pathways in humans may impact the acute alcohol responses to alcohol that in turn influence susceptibility to alcohol abuse and dependence.

Conselho Nacional de Desenvolvimento Científico e Tecnológico / O acúmulo crônico de gordura no fígado (doença hepática gordurosa não alcoólica ou esteatose hepática não alcoólica - NAFLD) está fortemente associada com a obesidade e a resistência à insulina. O estudo teve como objetivo investigar o efeito do exercício físico (natação) na redução da esteatose hepática e comorbidades associadas, incluindo a expressão hepática de síntese de ácidos graxos e receptor proliferador de peroxissoma atividade alfa. Camundongos machos C57BL/6 foram divididos em dois grandes grupos de acordo com a dieta durante 22 semanas: dieta padrão (10% de gordura, SC) ou dieta rica em gordura (60% de gordura, HF), caracterizando os grupos sedentários SC-Sed e HF-Sed. Nas últimas 10 semanas do experimento, metade dos grupos sedentários foram submetidos ao protocolo de natação com um aumento progressivo no tempo (6/dia até 60/dia, 5x/semana), caracterizando os grupos exercitados: SC-Ex e HF-Ex. No final do experimento, comparado ao grupo SC-Sed, o grupo HF-Sed teve a massa corporal significativamente superior, hiperglicemia, hiperinsulinemia com resistência à insulina, hipertrofia dos adipócitos (com infiltrado inflamatório), hipertrofia das ilhotas pancreáticas, dislipidemia, alteração das enzimas hepáticas e inflamatórias e NAFLD com mudanças na expressão de proteínas hepáticas lipogênicas e oxidativas. O programa de natação, mesmo concomitante com a dieta rica em gordura, reduziu o excesso de peso e todos os outros resultados, especialmente a NAFLD. Os resultados permitem concluir que a natação pode atenuar os efeitos deletérios de uma dieta rica em gorduras combinado com estilo de vida sedentário em camundongos. Estes dados reforçam a idéia que o exercício físico pode ser considerado uma estratégia terapêutica não farmacológica eficaz no tratamento da NAFLD, obesidade e resistência à insulina. / Chronic accumulation of fat in the liver (nonalcoholic fatty liver disease or NAFLD) is a morbid condition strongly associated with obesity and insulin resistance. The study aimed to investigate the effect of swimming training in reducing the NAFLD and associated comorbidities, including the hepatic expression of fatty acid synthesis and peroxisome proliferator receptor activity-alpha . Male C57BL/ 6 mice were separated into two major groups according to their nutrition and studied during 22 weeks: standard chow (10% fat, SC) or high fat chow (60% fat, HF), characterizing the sedentary groups SC-Sed and HF- Sed. In the last 10 weeks of the experiment, half of the sedentary groups were submitted to a swimming training with a progressive increase in duration, characterizing the exercised groups: SC-Ex and HF-Ex. At the end of the experiment, considering the findings in the SC-Sed group, HF-Sed group had significantly higher body mass, hyperglycemia, hyperinsulinemia with insulin resistance, hypertrophy of the adipocytes (with inflammatory infiltrate), hypertrophy of the pancreatic islets, dyslipidemia, altered liver enzymes and inflammatory cytokines, and NAFLD with changes in gene expression of hepatic lipogenic and oxidative proteins. The swimming program, even concomitant with the high-fat diet, reduced overweight and all the other worst findings, especially NAFLD. The results allow the conclusion that swimming training can attenuate the morbid effects of a high-fat diet combined with sedentary lifestyle in mice. These data reinforce the notion that swimming exercise can be considered an efficient nonpharmacologic therapy in the treatment of NAFLD, obesity and insulin resistance.

Conselho Nacional de Desenvolvimento Científico e Tecnológico / O acúmulo crônico de gordura no fígado (doença hepática gordurosa não alcoólica ou esteatose hepática não alcoólica - NAFLD) está fortemente associada com a obesidade e a resistência à insulina. O estudo teve como objetivo investigar o efeito do exercício físico (natação) na redução da esteatose hepática e comorbidades associadas, incluindo a expressão hepática de síntese de ácidos graxos e receptor proliferador de peroxissoma atividade alfa. Camundongos machos C57BL/6 foram divididos em dois grandes grupos de acordo com a dieta durante 22 semanas: dieta padrão (10% de gordura, SC) ou dieta rica em gordura (60% de gordura, HF), caracterizando os grupos sedentários SC-Sed e HF-Sed. Nas últimas 10 semanas do experimento, metade dos grupos sedentários foram submetidos ao protocolo de natação com um aumento progressivo no tempo (6/dia até 60/dia, 5x/semana), caracterizando os grupos exercitados: SC-Ex e HF-Ex. No final do experimento, comparado ao grupo SC-Sed, o grupo HF-Sed teve a massa corporal significativamente superior, hiperglicemia, hiperinsulinemia com resistência à insulina, hipertrofia dos adipócitos (com infiltrado inflamatório), hipertrofia das ilhotas pancreáticas, dislipidemia, alteração das enzimas hepáticas e inflamatórias e NAFLD com mudanças na expressão de proteínas hepáticas lipogênicas e oxidativas. O programa de natação, mesmo concomitante com a dieta rica em gordura, reduziu o excesso de peso e todos os outros resultados, especialmente a NAFLD. Os resultados permitem concluir que a natação pode atenuar os efeitos deletérios de uma dieta rica em gorduras combinado com estilo de vida sedentário em camundongos. Estes dados reforçam a idéia que o exercício físico pode ser considerado uma estratégia terapêutica não farmacológica eficaz no tratamento da NAFLD, obesidade e resistência à insulina. / Chronic accumulation of fat in the liver (nonalcoholic fatty liver disease or NAFLD) is a morbid condition strongly associated with obesity and insulin resistance. The study aimed to investigate the effect of swimming training in reducing the NAFLD and associated comorbidities, including the hepatic expression of fatty acid synthesis and peroxisome proliferator receptor activity-alpha . Male C57BL/ 6 mice were separated into two major groups according to their nutrition and studied during 22 weeks: standard chow (10% fat, SC) or high fat chow (60% fat, HF), characterizing the sedentary groups SC-Sed and HF- Sed. In the last 10 weeks of the experiment, half of the sedentary groups were submitted to a swimming training with a progressive increase in duration, characterizing the exercised groups: SC-Ex and HF-Ex. At the end of the experiment, considering the findings in the SC-Sed group, HF-Sed group had significantly higher body mass, hyperglycemia, hyperinsulinemia with insulin resistance, hypertrophy of the adipocytes (with inflammatory infiltrate), hypertrophy of the pancreatic islets, dyslipidemia, altered liver enzymes and inflammatory cytokines, and NAFLD with changes in gene expression of hepatic lipogenic and oxidative proteins. The swimming program, even concomitant with the high-fat diet, reduced overweight and all the other worst findings, especially NAFLD. The results allow the conclusion that swimming training can attenuate the morbid effects of a high-fat diet combined with sedentary lifestyle in mice. These data reinforce the notion that swimming exercise can be considered an efficient nonpharmacologic therapy in the treatment of NAFLD, obesity and insulin resistance.

La sclérose latérale amyotrophique (SLA) est une maladie neurodégénérative incurable partageant des mécanismes pathogéniques avec la démence frontotemporale (DFT). Elle est caractérisée par la dégénérescence sélective des neurones moteurs de la moelle épinière et du cerveau. Depuis les 25 dernières années, plus de 20 gènes ont été associés avec ces maladies, incluant FUS, C9ORF72 et TARDBP. Cependant, les liens entre la pathologie, le stade de la maladie et les mécanismes cellulaires demeurent incertains, mais semblent être multifactoriels. Bien que la SLA soit principalement considérée comme une maladie affectant le système nerveux, plusieurs d’observations suggèrent que des signaux périphériques, incluant ceux du tractus gastro-intestinal et de son microbiome, pourraient influencer la progression de la maladie. Récemment, de nouvelles études font état de perturbations du microbiome, appelé dysbiose, de la bioénergétique mitochondriale et de la composition lipidiques dans la SLA. Toutefois, il y a un manque considérable de compréhension de l’effet de ces perturbations sur la pathogenèse de la SLA. Une dysbiose a également été identifiée dans d’autres maladies neurodégénératives, telles que la maladie d’Alzheimer (MA) et la maladie d’Huntington (MH). En utilisant l’organisme modèle Caenorhabditis elegans, nous avons identifié une souche probiotique, Lacticaseibacillus rhamnosus HA-114, ayant des propriétés neuroprotectives dans différents modèles de SLA et de MH. Dans la première partie de cette thèse, nous avons démontrés que la neuroprotection conférée par L. rhamnosus HA-114 est unique par rapport aux autres souches de L. rhamnosus et réside dans son contenu en acide gras. Ces effets bénéfiques requièrent acdh-1/ACADSB, kat-1/ACAT1 and elo-6/ELOVL3/6, gènes impliqués dans le métabolisme des lipides et la β-oxydation mitochondriale. De plus, HA-114 retarde l’apparition des symptômes et réduit la neurodégénérescence chez la souris SOD1G93A. Nos résultats suggèrent que des perturbations du métabolisme des lipides contribuent à la neurodégénérescence et que HA-114 restaure l’homéostasie lipidique et énergétique via la β-oxydation mitochondriale. Dans la seconde partie de cette thèse, nous avons utilisé le C. elegans et avons caractérisé l’orthologue de CHCHD10, har-1, dans plusieurs essais afin d’étudier son implication dans la SLA et la DFT. CHCHD10 code pour une protéine impliquée dans la maintenance de la morphologie mitochondriale et la phosphorylation oxydative. Des mutations dans ce gène ont récemment été liées à la SLA. Nous avons caractérisé deux allèles distincts : une délétion de 260 pb (gk3124) et une mutation ponctuelle (ad2155). Les mutants har-1(gk3124) et har-1(ad2155) développent une paralysie, une dégénérescence des neurones GABAergiques et une altération de la santé mitochondriale. Le pioglitazone et le 2,4-thiazolidinedione, deux composés régulant la santé mitochondriale, restaurent plusieurs phénotypes associés à la SLA chez les mutants har-1. De plus, L. rhamnosus HA-114 a également des effets similaires sur ces souches. Ces résultats semblent confirmer un lien entre le microbiome et la SLA et pourraient ouvrir la voie à de futures thérapies via la modulation de l’environnement intestinal. De plus, découvrir les mécanismes impliqués dans cette neuroprotection permettrait sans doute la découverte de nouveaux gènes et de biomolécules actives ayant la capacité de moduler la neurodégénérescence, ouvrant la voie à l’utilisation de nouveaux médicaments. / Amyotrophic lateral sclerosis (ALS) is an incurable neurodegenerative disease sharing pathological pathways with frontotemporal dementia (FTD). It is characterized by the selective degeneration of lower and upper motor neurons in the spinal cord and cerebral cortex. Over the last 25 years, more than 20 genes have been associated with these diseases, including FUS, C9ORF72 and TARDBP. Despite over a century of medical investigation, the links between pathology, disease stage and cellular mechanisms are still unclear, but may be multifactorial involving unresolved gene-environment interactions. While ALS is primarily considered a central nervous system disease, emerging evidence suggests that peripheral signals, including those from the gastrointestinal tract and gut microbiota, may be involved in ALS progression. Over the last year, new evidence showed perturbations in microbiota (called dysbiosis), mitochondrial bioenergetics, and in lipid composition in ALS. However, there is a considerable lack of understanding of the effect of these perturbations in ALS pathogenesis. Interestingly, dysbiosis has also been linked to other neurological conditions like Alzheimer’s disease (AD) and Huntington’s disease (HD). Using the model organism Caenorhabditis elegans, we discovered a probiotic bacterial strain, Lacticaseibacillus rhamnosus HA-114, with neuroprotective properties in models of ALS and HD. In the first part of this thesis, we demonstrated that neuroprotection from L. rhamnosus HA-114 is unique from other L. rhamnosus strains, and resides in its fatty acid content. Neuroprotection by L. rhamnosus HA-114 requires acdh-1/ACADSB, kat-1/ACAT1 and elo-6/ELOVL3/6, which are key fatty acid metabolism and mitochondrial β-oxidation genes. Moreover, L. rhamnosus HA-114 delayed disease onset and suppressed motor neuron degeneration in an aggressive mouse model of ALS. Our data suggest that disrupted lipid metabolism contributes to neurodegeneration and that dietary intervention with L. rhamnosus HA-114 restores lipid homeostasis and energy balance through mitochondrial β-oxidation. In the second part of this thesis, we used C. elegans and characterized the CHCHD10 orthologue har-1, in a number of behavioral assays, to learn more about the biological role of this gene and its implication in ALS-FTD pathogenesis. CHCHD10 is a widely expressed gene coding for a mitochondrial protein with a potential role in cristae morphology maintenance and/or oxidative phosphorylation with mutations recently associated with ALS. We characterized two distinct alleles: a deletion of 260 bp (gk3124) and a point mutation (ad2155). Both har-1 (gk3124) and har-1 (ad2155) worms display age-dependent motility defects leading to paralysis, degeneration of GABAergic neurons and altered mitochondrial health. The small molecules, pioglitazone and 2,4-thiazolidinedione, with known neuroprotective activity, and also shown to regulate mitochondrial health, suppressed several har-1 phenotypes. Moreover, dietary supplementation of L. rhamnosus HA-114 improved several ALS-related phenotypes in these har-1 mutants. These findings may confirm a link between microbiota and ALS and can lead to future therapies, through the modulation of the intestinal environment. L. rhamnosus HA-114 is suitable for human consumption opening the possibility of modifying disease progression by dietary intervention. Furthermore, uncovering the complete neuroprotection pathway may give us insights into new genes and bioactive molecules able to modulate neurodegeneration, thus opening the door to new therapeutic approaches.

Le rôle important joué par la mitochondrie dans la cellule eucaryote est admis depuis longtemps. Cependant, la composition exacte des mitochondries, ainsi que les processus biologiques qui sy déroulent restent encore largement inconnus. Deux facteurs principaux permettent dexpliquer pourquoi létude des mitochondries progresse si lentement : le manque defficacité des méthodes didentification des protéines mitochondriales et le manque de précision dans lannotation de ces protéines. En conséquence, nous avons développé un nouvel outil informatique, YimLoc, qui permet de prédire avec succès les protéines mitochondriales à partir des séquences génomiques. Cet outil intègre plusieurs indicateurs existants, et sa performance est supérieure à celle des indicateurs considérés individuellement. Nous avons analysé environ 60 génomes fongiques avec YimLoc afin de lever la controverse concernant la localisation de la bêta-oxydation dans ces organismes. Contrairement à ce qui était généralement admis, nos résultats montrent que la plupart des groupes de Fungi possèdent une bêta-oxydation mitochondriale. Ce travail met également en évidence la diversité des processus de bêta-oxydation chez les champignons, en corrélation avec leur utilisation des acides gras comme source dénergie et de carbone. De plus, nous avons étudié le composant clef de la voie de bêta-oxydation mitochondriale, lacyl-CoA déshydrogénase (ACAD), dans 250 espèces, couvrant les 3 domaines de la vie, en combinant la prédiction de la localisation subcellulaire avec la classification en sous-familles et linférence phylogénétique. Notre étude suggère que les gènes ACAD font partie dune ancienne famille qui a adopté des stratégies évolutionnaires innovatrices afin de générer un large ensemble denzymes susceptibles dutiliser la plupart des acides gras et des acides aminés. Finalement, afin de permettre la prédiction de protéines mitochondriales à partir de données autres que les séquences génomiques, nous avons développé le logiciel TESTLoc qui utilise comme données des Expressed Sequence Tags (ESTs). La performance de TESTLoc est significativement supérieure à celle de tout autre outil de prédiction connu. En plus de fournir deux nouveaux outils de prédiction de la localisation subcellulaire utilisant différents types de données, nos travaux démontrent comment lassociation de la prédiction de la localisation subcellulaire à dautres méthodes danalyse in silico permet daméliorer la connaissance des protéines mitochondriales. De plus, ces travaux proposent des hypothèses claires et faciles à vérifier par des expériences, ce qui présente un grand potentiel pour faire progresser nos connaissances des métabolismes mitochondriaux. / The important role of mitochondria in the eukaryotic cell has long been appreciated, but their exact composition and the biological processes taking place in mitochondria are not yet fully understood. The two main factors that slow down the progress in this field are inefficient recognition and imprecise annotation of mitochondrial proteins. Therefore, we developed a new computational tool, YimLoc, which effectively predicts mitochondrial proteins from genomic sequences. This tool integrates the strengths of existing predictors and yields higher performance than any individual predictor. We applied YimLoc to ~60 fungal genomes in order to address the controversy about the localization of beta oxidation in these organisms. Our results show that in contrast to previous studies, most fungal groups do possess mitochondrial beta oxidation. This work also revealed the diversity of beta oxidation in fungi, which correlates with their utilization of fatty acids as energy and carbon sources. Further, we conducted an investigation of the key component of the mitochondrial beta oxidation pathway, the acyl-CoA dehydrogenase (ACAD). We combined subcellular localization prediction with subfamily classification and phylogenetic inference of ACAD enzymes from 250 species covering all three domains of life. Our study suggests that ACAD genes are an ancient family with innovative evolutionary strategies to generate a large enzyme toolset for utilizing most diverse fatty acids and amino acids. Finally, to enable the prediction of mitochondrial proteins from data beyond genome sequences, we designed the tool TESTLoc that uses expressed sequence tags (ESTs) as input. TESTLoc performs significantly better than known tools. In addition to providing two new tools for subcellular localization designed for different data, our studies demonstrate the power of combining subcellular localization prediction with other in silico analyses to gain insights into the function of mitochondrial proteins. Most importantly, this work proposes clear hypotheses that are easily testable, with great potential for advancing our knowledge of mitochondrial metabolism.

L’acétyl-coA occupe une place centrale dans le métabolisme intermédiaire. Il constitue le point de jonction de plusieurs voies métaboliques telles que la .-oxydation, la glycolyse, le catabolisme de certains acides aminés, la cétolyse, la cétogenèse et la synthèse d’acides gras. Il est également impliqué dans d’autres processus tels que l’acétylation des protéines. Au cours de mon travail de thèse, je me suis attachée à étudier différents aspects du métabolisme de l’acétyl-coA. La première partie de mon travail a porté sur la modulation pharmacologique de la .- oxydation dans le but de corriger des déficits de cette voie métabolique. L’intérêt de traitements par 400µM de bézafibrate ou 75µM de resvératrol dans les formes modérées de déficit en VLCAD et en CPT2 avait été montré précédemment. Par des méthodes de référence et grâce à la mise au point de nouvelles techniques, j’ai pu montrer sur des fibroblastes de patients déficitaires en LCHAD que des traitements par une combinaison de 35µM de bézafibrate et 30µM de resvératrol permettent d’augmenter les capacités d’oxydation du palmitate en stimulant la synthèse protéique. L’effet de cette combinaison était comparable à celui d’un traitement par 400µM de bézafibrate. Dans un second temps, je me suis intéressée à deux cofacteurs impliqués dans le métabolisme de l’acétyl-coA : l’acide lipoïque, cofacteur de quatre .-cétoacides déshydrogénases (PDHc, BCKDHc, .- KGDHc et GCS) et la riboflavine, cofacteur d’acyl-coA déshydrogénases de la .-oxydation et de déshydrogénases impliquées dans le catabolisme des acides aminés ramifiés. Ainsi, j’ai participé à la description d’anomalies du métabolisme de l’acide lipoïque, un nouveau groupe de maladies héréditaires du métabolisme caractérisé par un déficit combiné en .-cétoacides déshydrogénases. Par ailleurs, j’ai pu montrer qu’une hyperprolinémie constitue un biomarqueur intéressant pour le diagnostic d’acidurie glutarique de type II primaire ou secondaire, ces dernières pouvant se rencontrer en cas d’anomalie du métabolisme de la riboflavine. J’ai également évalué l’utilisation d’un mélange racémique de L,D-3-hydroxybutyrate afin de corriger les déficits énergétiques induits par un déficit en PDHc ou GLUT1. Via la cétolyse, le L,D-3- hydroxybutyrate génère de l’acétyl-coA. De façon surprenante, l’administration de ce composé s’est traduite par une amélioration de l’état clinique des patients atteints de déficits en PDHc, alors qu’une dégradation a été observée chez les patients atteints de déficits en GLUT1. Cette évolution différente pourrait souligner l’importance de l’anaplérose chez les patients déficitaires en GLUT1. Enfin, la dernière partie de mon travail de thèse porte sur la description d’un patient atteint d’une forme modérée de déficit en pyruvate carboxylase, cette enzyme étant régulée par l’acétyl-coA. Les difficultés diagnostiques rencontrées devant ces formes modérées sont rapportées, ainsi que des essais de traitement par des composés anaplérotiques et par le bézafibrate, malheureusement sans bénéfice net que ce soit in vitro ou in vivo. En conclusion, le métabolisme de l’acétyl-coA est altéré dans de nombreuses maladies héréditaires du métabolisme, dont certaines sont de description récente. Il peut être modulé par différentes approches pharmacologiques. Le développement de nouvelles techniques et notamment les analyses de flux métaboliques fournissent des outils utiles à son exploration et à l’étude de nouveaux traitements. / Acetyl-CoA is crucial for intermediary metabolism. It is at the crossroad of several metabolic pathways such as beta-oxidation, glycolysis, aminoacid catabolism, ketolysis, and fatty acid synthesis. It is also involved in other processes such as protein acetylation. In this document I studied different aspects of acetyl-CoA metabolism. First, I tried to correct fatty acid oxidation defects through pharmacological approach. Thanks to well- known methods and new ones, I showed that a combination of 30µM resveratrol and 35µM bezafibrate increased fatty acid oxidation capacities by increasing protein synthesis, as well as 400µM bezafibrate. Acetyl-CoA metabolism is also altered due to cofactors defects such as lipoic acid or riboflavine deficiency. I was involved in new diseases description and research for new biomarkers in this context. PDHc and GLUT1 deficiency are two different diseases with the same consequence : a defect in acetyl- CoA production from glucose. In order to improve patients’ quality of life, I evaluated the substitution of ketogenic diet with a racemic mix of L,D-3-hydroxybutyrate in PDHc and GLUT1 deficiency. The clinical evolution of patients was strikingly different, with an improvement in PDHc patients, whereas a degradation was noticed in GLUT1 patients. This difference might underline the role of anaplerosis in GLUT1 deficiency. Finally, I evaluated anaplerotic treatment and bezafibrate treatment in pyruvate carboxylase deficiency, an enzyme allosterically regulated by acetyl-CoA. To conclude, acetyl-CoA metabolism is altered in numerous inherited errors of metabolism, some of them being recently described. It can be modulated by pharmacological approaches. The development of new techniques such as metabolic flux analysis are useful for its study and for new treatments evaluation.

Recent findings have shown an inverse association between the circulating levels of pentadecanoic acid (C15:0) and heptadecanoic acid (C17:0) with the risk of pathological development in type 2 diabetes, cardio vascular disease and neurological disorders. From previously published research, it has been said that both these odd chain fatty acids are biomarkers of their dietary intake and are significantly correlated to dietary ruminant fat intake. However, there are profound studies that show the contrary where they do not display this biomarker correlation. Additionally, several astute studies have suggested or shown odd chain fatty acid endogenous biosynthesis, most often suggested via alpha oxidation; the cleavage of a single carbon unit from a fatty acid chain within the peroxisomes. To better understand the correlations and interactions between these two fatty acids with pathological development, the origin of these odd chain fatty acids needed to be determined, along with confirming their association with the disease aetiology. To minimise animal & human experimentation we made use of existing sample sets made available through institutional collaborations, which produced both animal and human interventional study samples suitable for odd chain fatty acid investigations. These sample collaborations allowed us to comprehensively investigate all plausible contributory sources of these odd chain fatty acids; including from the intestinal microbiota, from dietary contributions, and derived from novel endogenous biosynthesis. The investigations included two intestinal germ-free studies, two ruminant fat diet studies, two dietary fat studies and an ethanol intake study. Endogenous biosynthesis was assessed through: a stearic acid infusion, phytol supplementation, and an Hacl1 knockout mouse model. A human dietary intervention study was used to translate the results. Finally, a study comparing circulating baseline C15:0 and C17:0 levels with the development of glucose intolerance. We found that the circulating C15:0 and C17:0 levels were not significantly influenced by the presence or absence of intestinal microbiota. The circulating C15:0 levels were significantly and linearly increased when the C15:0 dietary composition increased; however, there was no significant correlation in the circulating C17:0 levels with intake. Circulating levels of C15:0 were affected by the dietary composition and factors affecting the dietary intake, e.g. total fat intake and ethanol, whereas circulating C17:0 levels were found to be independent of these variables. In our studies, the circulating C15:0 levels were not significantly affected by any expected variations in alpha oxidation caused by pathway substrate inhibition or gene knockout. However, C17:0 was significantly related, demonstrating it is substantially endogenously biosynthesised. Furthermore, we found that the circulating C15:0 levels, when independent of any dietary variations, did not correlate with the progression of glucose intolerance when induced, but the circulating C17:0 levels did significantly relate and linearly correlated with the development of glucose intolerance. To summarise, the circulating C15:0 and C17:0 levels were independently derived; the C15:0 levels substantially correlated with its dietary intake, whilst the C17:0 levels proved to be separately derived from its endogenous biosynthesis via alpha oxidation of stearic acid. C15:0 was found to be minimally endogenously biosynthesised via a single cycle of beta oxidation of C17:0 in the peroxisomes, however, this did not significantly contribute to the circulating levels of C15:0. Additionally, only the baseline levels of C17:0 significantly correlated with the development of glucose intolerance. These findings highlight the considerable differences between both of these odd chain fatty acids that were once thought to be homogeneous and similarly derived. On the contrary, they display profound dietary, metabolic, and pathological differences.

Le rôle important joué par la mitochondrie dans la cellule eucaryote est admis depuis longtemps. Cependant, la composition exacte des mitochondries, ainsi que les processus biologiques qui sy déroulent restent encore largement inconnus. Deux facteurs principaux permettent dexpliquer pourquoi létude des mitochondries progresse si lentement : le manque defficacité des méthodes didentification des protéines mitochondriales et le manque de précision dans lannotation de ces protéines. En conséquence, nous avons développé un nouvel outil informatique, YimLoc, qui permet de prédire avec succès les protéines mitochondriales à partir des séquences génomiques. Cet outil intègre plusieurs indicateurs existants, et sa performance est supérieure à celle des indicateurs considérés individuellement. Nous avons analysé environ 60 génomes fongiques avec YimLoc afin de lever la controverse concernant la localisation de la bêta-oxydation dans ces organismes. Contrairement à ce qui était généralement admis, nos résultats montrent que la plupart des groupes de Fungi possèdent une bêta-oxydation mitochondriale. Ce travail met également en évidence la diversité des processus de bêta-oxydation chez les champignons, en corrélation avec leur utilisation des acides gras comme source dénergie et de carbone. De plus, nous avons étudié le composant clef de la voie de bêta-oxydation mitochondriale, lacyl-CoA déshydrogénase (ACAD), dans 250 espèces, couvrant les 3 domaines de la vie, en combinant la prédiction de la localisation subcellulaire avec la classification en sous-familles et linférence phylogénétique. Notre étude suggère que les gènes ACAD font partie dune ancienne famille qui a adopté des stratégies évolutionnaires innovatrices afin de générer un large ensemble denzymes susceptibles dutiliser la plupart des acides gras et des acides aminés. Finalement, afin de permettre la prédiction de protéines mitochondriales à partir de données autres que les séquences génomiques, nous avons développé le logiciel TESTLoc qui utilise comme données des Expressed Sequence Tags (ESTs). La performance de TESTLoc est significativement supérieure à celle de tout autre outil de prédiction connu. En plus de fournir deux nouveaux outils de prédiction de la localisation subcellulaire utilisant différents types de données, nos travaux démontrent comment lassociation de la prédiction de la localisation subcellulaire à dautres méthodes danalyse in silico permet daméliorer la connaissance des protéines mitochondriales. De plus, ces travaux proposent des hypothèses claires et faciles à vérifier par des expériences, ce qui présente un grand potentiel pour faire progresser nos connaissances des métabolismes mitochondriaux. / The important role of mitochondria in the eukaryotic cell has long been appreciated, but their exact composition and the biological processes taking place in mitochondria are not yet fully understood. The two main factors that slow down the progress in this field are inefficient recognition and imprecise annotation of mitochondrial proteins. Therefore, we developed a new computational tool, YimLoc, which effectively predicts mitochondrial proteins from genomic sequences. This tool integrates the strengths of existing predictors and yields higher performance than any individual predictor. We applied YimLoc to ~60 fungal genomes in order to address the controversy about the localization of beta oxidation in these organisms. Our results show that in contrast to previous studies, most fungal groups do possess mitochondrial beta oxidation. This work also revealed the diversity of beta oxidation in fungi, which correlates with their utilization of fatty acids as energy and carbon sources. Further, we conducted an investigation of the key component of the mitochondrial beta oxidation pathway, the acyl-CoA dehydrogenase (ACAD). We combined subcellular localization prediction with subfamily classification and phylogenetic inference of ACAD enzymes from 250 species covering all three domains of life. Our study suggests that ACAD genes are an ancient family with innovative evolutionary strategies to generate a large enzyme toolset for utilizing most diverse fatty acids and amino acids. Finally, to enable the prediction of mitochondrial proteins from data beyond genome sequences, we designed the tool TESTLoc that uses expressed sequence tags (ESTs) as input. TESTLoc performs significantly better than known tools. In addition to providing two new tools for subcellular localization designed for different data, our studies demonstrate the power of combining subcellular localization prediction with other in silico analyses to gain insights into the function of mitochondrial proteins. Most importantly, this work proposes clear hypotheses that are easily testable, with great potential for advancing our knowledge of mitochondrial metabolism.

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