Les matières premières biosourcées s'avèrent être une possibilité de substitution du pétrole de plus en plus prisée dans le domaine des matériaux. De plus, l'utilisation de procédé propre limitant l'impact environnemental du développement de matériau est aujourd'hui incontournable. Dans ce contexte, l'acide aminé L-lysine, un nouveau synthon issu des biotechnologies blanches peu étudié dans le domaine de la chimie des matériaux, a été retenu. Ce synthon sera modifié pour la conception de macromonomères polymérisables sous irradiation UV. En effet, la technique de photopolymérisation est un procédé propre en plein essor, et qui permet le développement de revêtement.La L-lysine étant peu soluble dans les milieux organiques classiques, une étape de transformation est nécessaire pour améliorer sa processabilité. Ainsi, la polycondensation en masse de la L-lysine a conduit à des oligomères de poly-L-lysine de faibles masses molaires. La détermination de la structure obtenue a été réalisée par différentes techniques d'analyses. Ces oligomères sont alors greffés par des fonctions photopolymérisables dans des conditions douces. Le choix s'est porté sur des fonctions accepteur et donneur d'électron. Enfin, l'étude de la photopolymérisation des oligomères de L-lysine greffés accepteurs donneurs a été effectuée par la technique UV aqueuse, une technique innovante et respectueuse de l'environnement, dans différentes conditions pour en optimiser le système. / Biobased raw materials are an interesting and promising option for the substitution of fossil resources in material design. Moreover, using green processes which limit environmental impact of the material conception can't be avoided nowadays. In this context, the L-lysine amino acid, a building block made by white biotechnologies and poorly described in material field has been evaluated. As photopolymerization is a green process in great expansion and allowing coating design, this building block has been modified into a photocurable macromonomer.L-lysine is hardly soluble in usual organic solvents, a transformation step is necessary in order to improve its processability. Thus, L-lysine polycondensation has been tackled and led to oligomers of poly-L-lysine with low molar mass and improved solubility. In addition, the structure determination has been undertaken by different analytic technics. These oligomers can thus be grafted with photocurable functional groups in mild conditions. The chosen photocurable functional groups are donor acceptor of electron. At last, the photopolymerization of L-lysine based oligomers grafted with donor acceptor functional groups has been done by UV waterborne technic which is innovative and environmentally friendly. The photopolymerization has been carried out in different conditions in order to optimize the process.

Plasma membrane transport proteins play a crucial role in all cells by conferring to the cell surface a selective permeability to a wide range of ions and small molecules. The activity of these transporters is often regulated by controlling their amount at the plasma membrane, via intracellular trafficking. The recent boom in the numbers of crystallized transporters shows that many of them that belong to different functional families with little sequence similarity adopt the same structural fold implying a conserved transport mechanism. These proteins belong to the APC (Amino acid-Polyamine-organoCation) superfamily and their fold is typified by the bacterial leucine transporter LeuT. This LeuT fold is characterized by inverted structural repeats of 5 transmembrane domains that harbor the central substrate-binding site and a pseudo-symmetry axis parallel to the membrane. The yeast Saccharomyces cerevisiae possesses about 16 amino acid permeases (yAAPs) that belong to the APC superfamily and that display various substrate specificity ranges and affinities. Topological, mutational analysis and in silico data indicate that yAAPS adopt the LeuT fold.<p><p>In this work we combined computational modeling and yeast genetics to study substrate binding by yAAPs and the endocytosis of these transporters in response to substrate transport. In the first part of this work, we analyzed the selective recognition of arginine by the yeast specific arginine permease, Can1. We constructed three-dimensional models of Can1 using as a template the recently resolved structure of AdiC, the bacterial arginine:agmatine antiporter, which is also a member of the APC superfamily. By comparison of the binding pockets of Can1 and Lyp1, the yeast specific lysine permease, we identified key residues that are involved in the recognition of the main and side chains of arginine. We first showed that the network of interactions of arginine in Can1 is similar to that of AdiC, and that the selective recognition of arginine is mediated by two residues: Asn 176 and Thr 456. Substituting these residues by their corresponding residues in Lyp1 converted Can1 into a specific lysine permease. In the second part of this work, we studied the regulation of two permeases, Can1 and the yeast general amino acid permease, Gap1. In the presence of their substrates, Gap1 and Can1 undergo ubiquitin-dependent endocytosis and targeting to the vacuolar lumen for degradation. We showed that this downregulation is not due to intracellular accumulation of the transported amino acids but to transport catalysis itself. By permease structural modeling, mutagenesis, and kinetic parameter analysis, we showed that Gap1 and Can1 need to switch to an intermediary conformational state and persist a minimal time in this state after binding the substrate to trigger their endocytosis. This down-regulation depends on the Rsp5 ubiquitin ligase and involves the recruitment of arrestin-like adaptors, resulting in the ubiquitylation and endocytosis of the permease.<p><p>Our work shows the importance of the structural analysis of yAAPs to get further insight into the different aspects of their function and regulation. We validate the use of a bacterial APC transporter, AdiC, to construct three-dimensional models of yAAPs that can be used to guide experimental analyses and to provide a molecular framework for data interpretation. Our results contribute to a better understating of the recognition mode of amino acids by their permeases, and the regulation of this transport in response to substrate binding. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

The whole genome duplication (WGD) event is an intriguing mechanism from an evolutionary perspective. Such an event may be the source of new genes, functions or species. Traces of WGD event have been detected in the genome of all four eukaryotic kingdoms: plants, animals, fungi and protists. In fungi, an ancestor of Saccharomyces cerevisiae underwent an event of WGD, about 100 million years ago, after diverging from the Kluyveromyces lineage. In S. cerevisiae, only ten percent of the resulting duplicated genes survived as duplicates. In particular, some of these duplicates encodes for transcription factors in several nutrient sensing pathways. <p>The main subject of this thesis’s work is the external amino acid sensing system in S. cerevisiae. The detection of extracellular amino acids in yeast begins with a transporter homologue devoid of any uptake activity, the Ssy1 sensor. The binding of extracellular amino acids to Ssy1 leads to the successive activation of Ptr3 and the Ssy5 endoprotease. This endoporotease catalyses the processing of two transcriptions factors: Stp1 and Stp2. The Stp factors, released from their N-terminal cytoplasmic-anchored domains, are then translocated into the nucleus, where they activate the transcription of several amino acid permease genes (e.g. AGP1 and DIP5). Starting this work, the Stp factors were considered as functionally redundant. <p> We first determined that the STP1 and STP2 genes derivate from the event of WGD. The conservation of these two genes in S. cerevisiae was accompanied by a functional divergence of their products at several levels: processing sensibility, transcriptional activation capacity, target genes, cellular abundance level and stability. The Stp2 factor with its high abundance in the cells and its higher Ssy5-processing sensibility is specialized towards induction of the AGP1 gene when the external amino acid signaling is weakly stimulated. Under strong stimulation conditions, the amino acids induce cleavage-triggered destabilization of Stp2 through the proteasomal pathway and the induction of AGP1 is mediated mainly by the Stp1 transcription factor. Unlike Stp2, the Stp1 factor is characterized by its high transcriptional activation capacity and weaker sensitivity towards Ssy5-processing. The Stp factors differ also by their genetic targets. Indeed, only Stp2 regulates the expression of DIP5. Finally, we determined that the processing sensibility and the transcriptional activation capacity of each Stp factors is directly linked to their N- and C-terminal domains, respectively. <p> The phosphorylation states and the degradation of the Stp2 factor were also examined. The event of degradation concerns only the processed forms of this factor and takes places principally in the nucleus. Some data indicate that such an event might be important to limit the activation capacity of this factor. The role of the Stp2 phosphorylation in the external amino acid signaling pathway is still unknown but this event might be important for the Stp2 degradation or its transcriptional activity. <p> The unique Stp factor from Kluyveromyces lactis (Kl-Stp), a pre-WGD species, was also studied. The Kl-Stp factor shares at least two characteristic with the S. cerevisiae Stp2 factor: high sensibility towards processing and high levels of degradation. This observation leads us to conclude to that the STP genes may have been conserved after WGD though a mechanism called neofunctionalization (one of the duplicate obtained after duplication retains the ancestral function while the other evolves to perform a novel function). <p> Finally, a new model for the external amino acid signaling pathway that brings together all the data obtained during this thesis’s work is proposed. <p> / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Le domaine des polymères biosourcés connait une croissance rapide mais se pose toujours le problème d’une synthèse plus respectueuse de l’environnement. En cela, la catalyse enzymatique est une voie prometteuse. Ce travail vise donc à étudier et comprendre la polymérisation enzymatique par ouverture de cycle (eROP) afin d’en dépasser les limitations qui sont principalement : une cinétique lente, une faible masse molaire des polymères obtenus ou une variété limitée des fonctions chimiques polymérisables. La première partie de notre étude, portant sur les lactones, a mis en évidence la possibilité d’activer la réaction via une amine tertiaire. La seconde, qui traite des thiolactones, a mis en exergue des mécanismes spécifiques de copolymérisation avec plusieurs étapes de croissance de chaînes. Enfin, nous avons synthétisé des polyesters porteurs d’acides aminés, ouvrant ainsi la voie à des polymères « fonctionnalisables » et à de nouvelles architectures macromoléculaires. / The field of biobased polymers is experiencing a rapid growth but the development of more environmentally friendly synthesis methods remains a problem. With this in mind, enzymatic catalysis is a promising tool but it has some limitations such as slow polymerization kinetics, the low molecular weight of the produced polymers and a limited range of polymerizable monomers. This work aims at a better understanding of the enzymatic ring opening polymerization reactions (eROP) with a view to overcoming these limitations. To achieve this, three main topics have been investigated. The first, focusing on lactones, has demonstrated the possibility of activating the polymerization reaction with a tertiary amine. The second part, dealing with thiolactones as sulfur-based monomers, highlighted specific copolymerization mechanisms comprising of several distinct steps of polymer chain growth. Finally, polyesters bearing amino acids were synthesized, thus paving the way for functionalizable polymers and new macromolecular architectures.

Solute carriers (SLCs) are membrane-bound transporter proteins, important for nutrient, ion, drug and metabolite transport across membranes. A quarter of the human genome codes for membrane-bound proteins, and SLCs make up the largest group of transporter proteins. Due to their ability to transport a large repertoire of substances across, not just the plasma membrane, but also the membrane of internal organelles, they hold a key position in maintaining homeostasis affecting metabolic pathways. Unfortunately, some of the more than 400 identified SLCs are still not fully characterized, even though a quarter of these are associated with human disease. In addition, there are about 30 membrane-bound proteins with strong resemblance to SLCs, of which very little is known. The aim of this thesis is to characterize some of these putative SLCs, focusing on their localization and function in the central nervous system. Since many of the known SLCs play a vital part in metabolism and related pathways, the response to different nutritional conditions has been used as a key method. MFSD14A and MFSD14B, characterized in Paper I, are putative SLCs belonging to the Major Facilitator Superfamily (MFS) and found to be neuronal, differentially expressed in the mouse central nervous system and transiently upregulated in mouse embryonic cortex cultures due to amino acid deprivation. They were also altered in areas of the mouse brain after starvation as well as after high fat diet. In Paper II, the effect on gene regulation due to complete amino acid starvation was monitored in a mouse hypothalamic cell line and 47 different genes belonging to SLCs, or putative SLCs, were found to be affected. Of these, 15 genes belonged to already known amino acid transporters, whereas 32 were putative SLCs with no known function or SLCs not known to react to amino acids. The three SV2 proteins, SV2A, SV2B and SV2C, were studied in Paper III using human neuroblastoma cell lines. The high metabolic state of cancers often result in an upregulation and alteration of transporter proteins, and alterations of the SV2 proteins were found following different treatments performed in this study. Paper IV focused on putative SLCs of MFS type and their role in glucose metabolism. Mouse embryonic cortex cultures were subjected to glucose starvation and the gene expression of 19 putative transporters were analyzed. All but four of the putative transporters were affected either at 3h or 12h of glucose deprivation. In conclusion, several SLCs and putative SLCs studied in this thesis are strongly affected by alteration in metabolism, either due to amino acids or glucose or both. This makes the putative SLCs dynamic membrane-bound proteins, possibly transporters, highly affected by nutritional status and most likely regulated to maintain homeostasis.

Title: Effect of protein (amino acid) ingestion on muscle protein synthesis following resistance exercise. Purpose: The main objective of this thesis is to verify the three basic factors of the amount, type and timing of protein intake based on scientific studies and literature, to provide the most objective and accurate information and procedure on the methodology of nutrition and supplementation associated with the intake of protein / amino acids after strength training and how it all affects muscle synthesis. Summery: The theoretical part of the thesis, discusses the factors affecting muscle protein synthesis, which stimulate growth and tissue regeneration, based on optimal stress response. Logically, it starts from general, i.e. the explanation of terms such as muscle tissue, the stimulation of muscle tissue and its manifestations and changes, nutrition factors and muscle stimulation, the mechanism of dietary factors (proteins/amino acids), specificity of protein/ amino acids in their application to answer the three key issues, which are summarized in the section named scientific studies, which focuses on the effect of intake of protein/ amino acids, in relationship to the efficiency of protein synthesis after strength training. The section summarizes, in detail, the questions of timing,...

Ce travail de thèse avait pour objectif d’étudier la régulation de l’expression des gènes du métabolisme intermédiaire par les acides aminés alimentaires dans le foie de truite arc-en-ciel. Ces études ont permis de caractériser, pour la première fois dans le foie de truite, les principaux acteurs de la voie de signalisation Akt/TOR et leurs régulations. Nos résultats in vitro montrent qu’un mélange d’acides aminés, seul ou avec l’insuline, est capable de réguler l’expression de nombreux gènes impliqués dans la lipogenèse, la néoglucogenèse et la glycolyse. Les régulations observées en présence conjointe d’un mélange d’acides aminés et d’insuline semblent être, pour la plupart, dépendantes de la voie TOR. Par la suite, nous avons étudié l’effet de certains acides aminés comme la leucine (connue pour son effet « signal ») ainsi que la lysine et la méthionine (souvent ajoutées dans les aliments piscicoles riches en matières premières végétales afin d’atteindre l’équilibre en acides aminés). En présence d’insuline, la leucine, contrairement à la lysine et la méthionine, active la voie de signalisation TOR et régule l’expression de certains gènes (néoglucogenèse et lipogenèse) de façon similaire à un mélange d’acides aminés. Parallèlement, in vivo, nous avons étudié la régulation de l’expression des gènes du métabolisme intermédiaire lors d’un remplacement partiel ou total des huiles et farines de poisson par des produits végétaux dans l’aliment piscicole. Cette expérimentation a montré que, ni les voies de signalisation Akt/TOR, ni l’expression des gènes cibles ne sont affectés par ces nouveaux aliments. En conclusion, ces travaux ont montré que les acides aminés semblent jouer un rôle important dans la régulation de l’expression des gènes hépatiques du métabolisme intermédiaire chez la truite arc-en-ciel. / The objective of my PhD was to characterize the regulation of the intermediary metabolism related gene expression by dietary amino acids in the liver of rainbow trout. This work allowed us to characterize, for the first time in the liver of trout, the main proteins of the Akt/TOR signalling pathway and their regulations. In vitro results showed that a mixture of amino acids, in the presence or absence of insulin, is able to regulate the expression of numerous genes involved in lipolysis, gluconeogenesis and glycolysis. Such regulations induced by an amino acid mix together with insulin appear to be, at least partly, TOR-dependent. Afterwards, I studied the effect of specific amino acids known to be a signalling molecule (leucine) or having potential application as supplements to reach essential amino acid balance in plant ingredients-rich diet (lysine and methionine). In the presence of insulin, leucine, in contrast to lysine and methionine, is able to activate the TOR signalling pathway and regulate the expression of several genes involved in gluconeogenesis and lipogenesis in the same way as a mixture of amino acids. Furthermore, we studied in vivo, the effect of partial or total replacement of fish oil and fish meal by plant products in fish feed on .the regulation of intermediary metabolism related gene expression. This study showed that neither Akt/TOR signalling pathway nor the expression of the target genes were affected by such diets. In conclusion, these studies showed that amino acids seem to play an important role in the hepatic regulation of intermediary metabolism gene expression in the rainbow trout.

Demosponges of the order Verongida such as Ianthella basta exhibit skeletons containing spongin, a collagenous protein, and chitin. Moreover, Verongida sponges are well known to produce bioactive brominated tyrosine derivatives. We recently demonstrated that brominated compounds do not only occur in the cellular matrix but also in the skeletons of the marine sponges Aplysina cavernicola and I. basta. Further investigations revealed the amino acid composition of the skeletons of A. cavernicola including the presence of several halogenated amino acids. In the present work, we investigated the skeletal amino acid composition of the demosponge I. basta, which belongs to the Ianthellidae family, and compared it with that of A. cavernicola from the Aplysinidae family. Seventeen proteinogenic and five non-proteinogenic amino acids were detected in I. basta. Abundantly occurring amino acids like glycine and hydroxyproline show the similarity of I. basta and A. cavernicola and confirm the collagenous nature of their sponging fibers. We also detected nine halogenated tyrosines as an integral part of I. basta skeletons. Since both sponges contain a broad variety of halogenated amino acids, this seems to be characteristic for Verongida sponges. The observed differences of the amino acid composition confirm that spongin exhibits a certain degree of variability even among the members of the order Verongida.

Autism is a lifelong neurodevelopmental disorder. The etiology of autism still remains unclear due to the heterogeneous and complex nature of the disorder, however synergistic actions between genetic components and environmental factors have been suggested. Acetaminophen (APAP) is one of the most popular over-the-counter drugs that possess antipyretic and analgesic effects. It is considered a relatively safe and effective within therapeutic doses. Recently, early exposure to APAP has been suggested to be one of the underlying cause of autism. Children are often prescribed APAP to lessen fever or irritability after vaccination during the first year, and APAP may adversely affect the normal brain development. In order to better understand the association with APAP and autism, we used an inbred mouse strain BTBR T+tf/J (BTBR). BTBR exhibits behavioral deficits that mimic the core behavioral deficits of human autism. In the study, investigated 1) if BTBR mice showed differences in thiol biochemistry and EAAT3 levels in brain compared with C57BL/6J (C57) mice, 2) if early exposure to APAP induced behavioral changes worsening the autistic phenotypes of BTBR in adolescence, and 3) if APAP exposure in neonatal mice induced possible toxicity at various doses. As a result, we observed that BTBR mice have significantly lower plasma sulfate levels and EAAT expression levels in the frontal cortex compared to C57 mice. Surprisingly, neonatal therapeutic dose of APAP administration did not induce behavioral changes in both C57 and BTBR in adolescence. However, we showed that a supratheraputic dose of APAP significantly elevated levels of oxidative stress marker in the brain. Overall, the results suggested that BTBR mice would be a useful mouse model to investigate effects of various environmental factors that have been associated with autism. In addition, early exposure to APAP at supratherapeutic doses may negatively affect normal brain development.

Les acides aminés ont de nombreuses fonctions dans l’organisme en plus de leur rôle comme constituants élémentaires des protéines. Ils peuvent par exemple servir de neurotransmetteur ou de signal pour l’activation de voies de signalisation intracellulaires. Leur passage à travers la membrane plasmique est facilité par des transporteurs de la famille des protéines SLC. Les transporteurs hétérodimériques d’acides aminés HAT appartiennent aux SLC. Les HAT sont constitués d’une chaîne légère SLC7 assurant la spécificité de transport et d’une chaîne lourde SLC3 impliquée dans l’adressage du complexe protéique à la membrane. Ma thèse a porté sur l’étude du rôle d’un homologue de SLC7 chez la drosophile, Minidiscs (Mnd), dans le fonctionnement du système nerveux. Mnd appartiendrait aux transporteurs du système L, principalement connus pour leur rôle dans la prolifération cellulaire. Mes travaux de thèse ont permis de mettre en évidence la localisation de Mnd dans le cerveau de drosophile dans certains neurones (corps pédonculés, neurones dopaminergiques) et dans certaines cellules gliales (glie corticale). La présence de Mnd dans le cerveau semble intervenir dans la modulation de certains comportements, tels que le réflexe de géotaxie négative. Ces travaux ont aussi montré que, comme les HAT de mammifères, Mnd s’associe de façon covalente à un partenaire protéique. Les expériences de transport semblent par ailleurs confirmer l’appartenance de Mnd au système L.Ces résultats suggèrent que Mnd est probablement impliqué dans la régulation de l’activité neuronale et donc dans le fonctionnement du système nerveux, ce qui n’avait encore jamais été décrit pour un transporteur du système L. / Amino acids have many functions in the body in addition to their role as basic constituents of proteins. They can for example serve as a neurotransmitter or signal for the activation of intracellular pathways. Carriers of the SLC protein family facilitate their path through the plasma membrane. The heterodimeric amino acid transporters HAT belong to SLC proteins. HAT are composed of a light chain SLC7 ensuring the specificity of transport and a heavy chain SLC3 involved in the addressing of the protein complex to the plasma membrane. My thesis focused on studying the role of a SLC7 homologue in drosophila, Minidiscs (Mnd), in the functioning of the nervous system. Mnd might belong to system L carriers, mainly known for their role in cell proliferation. My thesis work led to highlight the location of Mnd in the drosophila brain in some neurons (mushroom bodies, dopaminergic neurons) and some glial cells (cortical glia). The presence of Mnd in the brain seems to be involved in the modulation of some behaviors such as negative geotaxis reflex. This work also showed that, as for mammal HAT, Mnd is associated covalently to a protein partner. Transport experiments seem also to confirm the belonging of Mnd to the system L. These results suggest that Mnd is probably involved in the regulation of neuronal activity and thus in the functioning of the nervous system, which had never been described for a system L carrier.