<p> The biosynthesis of lycopodine was studied by feeding radioactive acetate, acetoacetato, lysine and pelletierine to Lycopodium tristachyum. Partial degration of the radioactive lycopodine recovered from these experiments revealed specific incorporation of these precursors. The labeling pattern obtained is discussed in the light of the two major blogenetic hypothesis advanced for the Lycopodium alkaloids. </p> <p> The results obtained disproved Conroy's polyacetate hypothesis. They are consistent with the hypothesis that regards these alkaloids derived from lysine and acetate. </p> / Thesis / Doctor of Philosophy (PhD)

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The work focused on addressing four main objectives. The first objective was to quantify protein and amino acid substitution reactions. Michael addition reactions were used to modify the amino acids and protein. Amino acids alanine, cysteine, and lysine, and protein ovalbumin (OA) were substituted with different concentrations of ethyl vinyl sulfone (EVS). The substituted products were analyzed using Raman spectroscopy and UV-spectroscopy based ninhydrin assay. In case of alanine, Raman and UV results correlated with each other. With cysteine at lower EVS substitutions amine on the main chain was the preferred site while the substitution shifted to thiols at higher substitutions. This could only be discerned using Raman spectroscopy. Lysine has amines on the main chain and side chain while main chain amine was the most reactive site at lower concentrations of EVS while at higher concentrations side chain amines were also substituted. This information could be discerned using Raman spectroscopy only and not UV spectroscopy. In case of protein as observed by Raman and UV spectroscopy the reaction continued at higher concentrations of EVS indicating the participation of glutamine and asparagines at higher substitutions. However, the reaction considerably slowed down at higher EVS substitutions. The second objective of the study was to decrease the glass transition temperature (Tg) of OA through internal plasticization and also study the effects of the substituents on the thermal stability of OA. The hypothesis was by covalently attaching substituents to OA, number of hydrogen bonds can be reduced while increasing the free volume and this would reduce Tg. EVS, acrylic acid (AA), butadiene sulfone (BS) and maleimide (MA) were the four groups used. EVS was the most efficient plasticizer of all the four substituents. The Tg decreased with the increasing concentration of EVS until all of the reactive of groups on OA were used up. Tg decreased slightly with AA and BS while no change was observed with MA. However, the substituents showed exact opposite trend in thermal stability as measured using thermogravimetric analysis (TGA). The thermal stability of MA substituted OA was the highest and that of EVS substituted OA was least. FT-IR spectroscopy results indicated that all four substituents caused structural changes in OA. This implied that there were intermolecular interactions between substituted protein chains in case of AA, BS, and MA. This caused an increase in the thermal stability. EVS on the other hand is a linear chain monomer with a hydrophobic end group and hence could not participate in the intermolecular interactions and hence caused a decrease in Tg. As mentioned above the limitation to this technique is the number of available reactive groups on the protein. However, we successfully demonstrated the feasibility of this method in decreasing Tg of protein. The third objective was to create hydrogels by crosslinking OA with divinyl sulfone (DVS). Protein hydrogels due to their biocompatible nature find applications in drug delivery and tissue engineering. For tissue engineering applications the hydrogels need to be mechanically stable. In this study the protein was substituted with EVS or AA and then crosslinked with DVS. The swelling ratio was measured as a function of pH. All the hydrogels showed the same trend and swelled the least at pH 4.5 which is the isoelectric point of the protein. At basic pH conditions EVS substituted hydrogels swelled the most while AA substituted hydrogels showed least swelling. The static and dynamic moduli of the hydrogels were determined using tensile tester and rheometer respectively. The static modulus values were three times the dynamic modulus. The modulus of the control which is crosslinked OA was least and that of AA substituted OA was highest. The stress relaxation test also showed similar results in which AA substituted OA relaxed the most and the control relaxed the least. FT-IR of the dry hydrogels showed that the amount of hydrogen bonding increased with AA substitution. The hydrophilic AA end groups interacted with each other forming hydrogen bonds. These hydrogen bonds served as additional crosslinks there by increasing the modulus of the hydrogels. EVS on the other hand was incapable of interactions due to the lack of hydrophilic end groups. We were successfully able to create protein hydrogels and control the swelling and mechanical properties by varying the amount of substituted group. The final objective of the study was to create and characterize microstructures from substituted alanine and lysine. Alanine and lysine were substituted with different concentrations of EVS. Bars and fibers were observed for alanine at moderate substitutions while at higher concentrations random structures were observed using scanning electron microscopy (SEM). Lysine formed tubes at moderate EVS substitutions and rosettes at high concentrations of EVS as evidenced by SEM. FT-IR results suggested that instead of carbonyl one of sulfonyl bonded to the available amine in modified amino acids. And only in this case fibers, tubes and rosettes were observed. X-ray diffraction (XRD) results supported this observation. Using these results we hypothesized that the self assembled structures very much depended on the amount of EVS present in the substituted product and sulfonyl forming β-sheet analogs with amine. / Ph. D.

L'acétylation des histones module la structure de la chromatine et joue un rôle critique dans les processus liés à l'ADN, notamment l'expression génique. Dans la levure bourgeonnante *Saccharomyces cerevisiae*, le complexe NuA4 acétyle les histones H4 et H2A, ainsi que la variante d'histone Htz1, pour réguler la transcription. La formation de ribosomes fonctionnels nécessite la transcription coordonnée de 138 gènes de protéines ribosomiques (RP) et de plus de 200 gènes de biogenèse des ribosomes (RiBi). NuA4 est recruté aux promoteurs de ces gènes et acétyle les nucléosomes proches du promoteur. Cette thèse de doctorat examine les fonctions biologiques de NuA4 en tant que coactivateur dans la régulation de l'expression des gènes RP et RiBi en réponse à divers signaux environnementaux. Nous explorons l'interaction fonctionnelle entre NuA4 et Sfp1, un facteur de transcription sensible aux nutriments et au stress, et détaillons les implications de l'acétylation des lysines dépendante de NuA4 sur Sfp1. Le **Chapitre I** présente la méthode Anchor Away (AA), un outil de déplétion conditionnelle des protéines. Nous décrivons des procédures expérimentales détaillées pour réaliser la déplétion des protéines nucléaires, accompagnées de conseils pratiques. En utilisant AA, nous démontrons la déplétion rapide de Sfp1 et d'Esa1 (la sous-unité catalytique de NuA4) du noyau, comme en témoigne la diminution de la liaison de Sfp1 aux promoteurs des gènes RP et la perte de l'acétylation des histones dépendante de NuA4. Le **Chapitre II** présente nos principales conclusions concernant les rôles de Sfp1 et NuA4 dans l'expression des gènes RP et RiBi. À l'aide d'approches biochimiques et génomiques, nous révélons que NuA4 interagit avec Sfp1 pour faciliter la transcription des gènes RiBi et RP par des mécanismes distincts. De plus, nous examinons les conséquences fonctionnelles de l'acétylation de Sfp1 dépendante de NuA4 dans diverses conditions de croissance. Cette thèse enrichit notre compréhension des mécanismes moléculaires par lesquels l'acétylation dépendante de NuA4 influence la transcription génique. / Histone acetylation modulates chromatin structure and plays a critical role in DNA-templated processes, including gene expression. In the budding yeast *Saccharomyces cerevisiae*, the NuA4 complex acetylates histones H4 and H2A, as well as the histone variant Htz1, to regulate transcription. The formation of functional ribosomes requires the coordinated transcription of 138 ribosomal protein (RP) genes and over 200 ribosome biogenesis (RiBi) genes. NuA4 is recruited to the promoter of these genes and acetylates the promoter-proximal nucleosomes. This doctoral thesis investigates the biological functions of NuA4 as a coactivator in regulating RP and RiBi gene expression in response to various environmental cues. We explore the functional interaction between NuA4 and Sfp1, a transcription factor sensitive to nutrients and stress, and detail NuA4-dependent lysine acetylation of Sfp1 and its implications. **Chapter I** introduces the Anchor Away (AA) method, a conditional protein depletion tool. We describe detailed experimental procedures to complete nuclear protein depletion in a step-by-step fashion, accompanied by troubleshooting tips. Using AA, we demonstrate rapid depletion of Sfp1 and Esa1 (the NuA4 catalytic subunit) from the nucleus, evidenced by reduced Sfp1 binding at RP gene promoters and loss of NuA4-dependent histone acetylation. **Chapter II** presents the main findings regarding the roles of Sfp1 and NuA4 in RP and RiBI gene expression. Using biochemical and genomic approaches, we reveal that NuA4 interacts with Sfp1 to facilitate transcription of RiBi and RP genes via distinct mechanisms. Additionally, we explore the functional consequences of NuA4-dependent acetylation of Sfp1 under various growth conditions. This thesis extends our understanding of the molecular mechanisms of NuA4-dependent acetylation on gene transcription.

Les objectifs étaient de valider une méthode d’estimation des besoins individuels en lysine et d’étudier l’effet d’une déplétion-réplétion en lysine chez le porc en croissance. Les performances de 148 porcs répartis en 4 traitements alimentaires, soit 70, 85, 100 et 115 % des besoins en lysine, montrent que la méthode développée sous-estime les besoins en début croissance, mais estime adéquatement ceux en finition. Quarante-sept porcs ont reçu 70 ou 100 % de leurs besoins en lysine pendant 3 phases consécutives de 28 jours selon les séquences: 70-70-70, 70-70-100, 70-100-70, 70-100-100 et 100-100-100. La restriction cause une diminution de la consommation, du gain de poids (GMQ) et du dépôt protéique (PD). Le groupe 70-100-100 a rattrapé son retard en termes de poids vif et de masse protéique comparativement au groupe 100-100-100 montrant ainsi une croissance compensatrice de faible amplitude.

De part son profil équilibré en acides aminés essentiels (AAE), la farine de poisson (FP) est la source protéique principale utilisée dans l’alimentation des crevettes d’élevage. Cependant, compte tenu des enjeux du développement durable de la production aquacole, son utilisation doit être réduite, et remplacée par d’autres sources protéiques comme les protéines végétales (PV), qui sont souvent carencées en lysine et méthionine mais riches en cystine. Les conséquences d’un tel changement alimentaire sont peu connues chez la crevette tigrée Penaeus monodon. Pour les évaluer, nous avons utilisédes aliments semi-purifiés reflétant les carences/excès en AA des PV pour estimer les besoins en protéine, lysine et méthionine pour l’entretien et la croissance. Tout en confirmant les données antérieures sur les besoins pour la croissance des stades postlarves, nous avons pu préciser la contribution de l’apport en ces deux acides aminés pour l’entretien. Au niveau métabolique, la variation de l’apport protéique (10, 30, 50% protéine brute) et la carence en méthionine (-30% par rapport au besoin) entraînent une modification de l’activité des enzymes du catabolisme des AA, mais pas celle des voies de reméthylation et transsulfuration. En revanche, et pour la première fois chez la crevette, nos résultats démontrent une épargne de la méthionine par la cystine (et la choline), soulignant l’importance de l’apport en AA soufrés totaux (methionine + cystine). Nos résultats illustrent aussi l’importance qu’il convient d’accorder à la disponibilité des AAE dans les études de remplacement de la FP par un mélange de PV pour améliorer l’utilisation azotée chez la crevette P. monodon. / Due to its well balanced essential amino acid (EAA) profile, fishmeal (FM) is the major protein source used in the formulation of aquafeed for cultured shrimp. To sustain farming systems, its incorporation, however, must be reduced and substituted by other protein sources less well nutritionally balanced, such as plant protein ( PP) which are often low in lysine and methionine but rich in cystine. The metabolic consequences of such a shift in dietary profile are not well known for the black tiger shrimp, Penaeus monodon. To describe these consequences, we used semi-purified diets limiting in lysine and methionine (to reflect PP profile) to determine juvenile requirements of protein, lysine and methionine for both maintenance and growth, applying a factorial approach. Our results confirm the previous data on growth requirement for post-larvalstages of P. monodon while also providing new data on maintenance requirements. At the metabolic level, a variation in the dietary protein level (10, 30, 50 % crude protein) and methionine (adequate or 30% lower) resulted in a significant change in the activity of transdeaminating enzyme, but not those of remethylation and transsulfuration. Nevertheless, we found for the first time that methionine utilisation for body protein accretion can be spared by cystine and choline (up to 50%) in this species, illustrating the importance to consider total sulphur AA supply. Our data also show that full consideration should be given to AA availability in order to develop practical diets with low FM levels for P. monodon.

Ce travail a eu pour objectif de déterminer les conditions optimales de production d’un caroténoïde original, la torularhodine, par Sporobolomyces ruberrimus, cultivée en réacteur discontinu. Cette souche est capable d’utiliser le glycérol technique comme source de carbone et d’énergie pour sa croissance et pour la production de caroténoïdes. D’abord, il s’est agi d’identifier les facteurs opératoires majeurs qui sont susceptibles d’avoir une influence sur la production de la torularhodine, au travers d’une étude préliminaire. L’identification expérimentale de ces facteurs d’action - la température, le taux d’oxygène dissous et la supplémentation en acide oléique - a été validée statistiquement, à des degrés divers, avant d’engager une étape d’optimisation par la construction d’un plan d’expériences multicritère. Celui-ci a conduit à l’établissement de modèles polynômiaux du second degré pour représenter l’effet conjugué des facteurs retenus et permettre la prédiction des valeurs de µmax et de concentration de torularhodine rapportée à la biomasse. Cette étude a alors été consacrée à un essai de fonctionnalisation de la torularhodine, à partir de sa fonction carboxylique, en vue de la stabilisation de la molécule dont l’activité antioxydante est élevée. L’acylation enzymatique de la lysine par la torularhodine a été envisagée. Les conditions d’acylation par la lipase B de C. antarctica ont été déterminées avec un caroténoïde modèle, la bixine. Le produit dérivé obtenu après transacylation a été purifié et a montré une activité antiradicalaire supérieure à celle de la bixine. Ces résultats permettent d’envisager la synthèse de peptides acylés avec ce type de caroténoïdes / The aim of this work was to determine the optimum of an original carotenoid, the torularhodin, produced by Sporobolomyces ruberrimus, in batch culture. A very interesting characteristic of this strain is its ability to consume raw glycerol as a carbon and energy source for microbial growth and carotenoid production. In the fist part of this study, the identification of operating parameters that have an influence on the optimum torularhodin production, was achieved. Experimental assays reinforced by a statistical study allowed to identify temperature, dissolved oxygen pressure and oleic acid supplementation, as the major parameters of influence, and then the integration of these data was performed for the construction of a multiobjective optimization based on a multicriteria experimental design. The establishment of a mathematical model of a second degree polynomial type was developed for the prediction of the values of µmax and of the torularhodin concentration reported to biomass. In the last part, considering that torularhodin has an important antioxidant property and it exhibits a free carboxyl acid function which can be used as acyl agent, a study of its structure modifying by an enzymatic way as a stabilization pattern was started. The experimental conditions of lysine acylation by the lipase B of Candida antarctica were determined using a model carotenoid, the bixin. The resulting product of the synthesis of bixin derivative was purified and showed an antiradical activity of 2.5 times higher than that of bixin. This result showed the ability of the acylation reaction of peptides with this kind of carotenoids