京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第19883号 / 理博第4210号 / 新制||理||1605(附属図書館) / 32960 / 京都大学大学院理学研究科化学専攻 / (主査)教授 三木 邦夫, 教授 杉山 弘, 教授 藤井 紀子 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

No description available.

Enzymatic pathways have evolved over billions of years to carry out essential cellular processes and ensure the survival of their host species. These reaction pathways rely on the interconnectedness of multiple enzymes and substrate, encouraging cross-talk and, at times, competition. In many cases, enzymes require the assistance of a diffusible secondary biomolecule, known as a cofactor, to participate in catalytic reactions. This network of reactions is unfavorable when trying to optimize the production of a specific product. In order to circumvent surrounding reactions, researchers have been engineering orthogonal enzymatic pathways that operate independently from endogenous reactions within a cell. Orthogonal pathways can be created by utilizing biomimetics molecules; most enzymes have not naturally evolved affinity and activity with these are non-canonical cofactors. Nicotinamide adenine dinucleotide (NAD(H) and nicotinamide adenine dinucleotide 2’-phosphate (NADP(H)) are vital cofactors that participate in redox reactions within cells. NAD(P)(H) have been the target of enzymatic research for several decades due to their extensive involvement in reactions across species and their utility in the biotechnology industry. Creation of orthogonal pathways dependent on NAD(P)(H) analogs has massive potential in various industries, such as biofuels and biopharmaceuticals. Nicotinamide mononucleotide (NMN(H)) is a precursor molecule in the biosynthesis of NAD(H); it currently exists within cells but, in general, does not participate as a cofactor. Nicotinamide adenine dinucleotide 3’-phosphate (3’-NADP(H)) is another analog that closely resembles NAD(P)(H) for which most enzymes have not evolved natural affinity and activity. Computation and structural inspection techniques were used in an attempt to engineer formate dehydrogenase from Candida boidinii (CbFDH) for activity with the non-canonical cofactors NMN(H) and 3’-NADP(H). Amino acid positions proximal to the NAD(H) binding site were input into a PyRosetta algorithm, which then outputted a list of recommended mutations ranked by their Rosetta energy scores. Structural alignment and visual inspection were also used to design mutations. The mutations were recombinantly expressed, and the purified enzymes were assays with NAD+, NADP+, NMN+ and 3’-NADP+. None of the designed single mutations led to CbFDH activity gain with NMN+ to any meaningful degree; however, various mutations led to the removal of NAD+ activity. A strength of PyRosetta was identifying key mutations that would lead to activity removal. The single mutants D195A and D195G attained the largest specific initial rates with 3’-NADP+ under the screening assay conditions. Kinetics parameters of a simplified ordered bi bi model were calculated for these mutants. Double mutants were created in an attempt to further enhance activity. The double mutations resulted in decreased activity but enhanced the specificity for 3’-NADP+ over NAD+. To complete the 3’-NADP(H) enzymatic cycle, a non-specific cofactor oxidizer, xenobiotic reductase A (XenA), was expressed and assayed with 3’-NADPH. It was found that XenA is able to oxidize 3’-NADPH back to 3’-NADP+. The avirulence factor AvrRxo1 from a rice plant pathogen was explored since it specifically catalyzes NAD+ phosphorylation at the 3’ position. The AvrRxo1 gene was expressed in LysY/IQ competent E. coli cells and it was found that the presence of AvrRxo1 caused a longer lag phase, but the bacteria were later able to recover. Co-expressing AvrRxo1, XenA, and D195A CbFDH has the potential to create an orthogonal pathway depending on biosynthesized 3’-NADP(H) in vivo. Another in vivo non-canonical cofactor source is NAD(H)-capped RNA, which have recently captured researchers’ attention. NAD+-RNA was synthesized using the polymerase chain reaction, and it was shown that D195A and D195G CbFDH were able to reduce the NAD+ cap.

No description available.

The NAD glycohydrolase (NADase) from Bungarus fasciatus venom was purified over 1000-fold to electrophoretic homogeneity through a 3-step procedure which included affinity chromatography on Cibacron Blue agarose. The enzyme exhibited a broad pH profile with the optimum range between 7-8. Studies on the substrate specificity of B. fasciatus venom NADase demonstrated that alterations in the purine ring were less pronounced then alterations in the pyridinium moiety of NAD. Product inhibition studies indicated nicotinamide to be a noncompetitive inhibitor with a K_i = 1.4 mM and ADP-ribose to be a competitive inhibitor with a K_i =0.4 mM. The purified enzyme was inactivated by both 2,4-pentane-dione and Woodward's Reagent K suggesting the involvement of a lysine and carboxyl group in the catalytic process. In contrast to other known NADases, the snake venom enzyme did not self-inactivate. The purified B. fasciatus venom NADase catalyzed a transglycosidation reaction (ADP-ribose transfer) with a number of acceptor molecules. The functioning of a variety of substituted pyridine bases as acceptor molecules was demonstrated through the formation of the corresponding NAD analogs. The enzyme also catalyzed the transfer of ADP-ribose to aliphatic alcohols (methanol to hexanol, inclusive) and a positive chainlength effect was observed in the functioning of these acceptors. Kinetic studies of transglycosidation reactions were consistent with the partitioning of an enzyme-ADP-ribose intermediate between water and nucleophilic acceptors as has been proposed in earlier studies of mammalian NADases. The partitioning of this intermediate between water and pyridine bases can be correlated with the basicity of the ring nitrogen of the pyridine derivative. The K_i of pyridine bases in the hydrolytic reaction did not equate to the K_m of these bases in the pyridine base exchange reaction suggesting two forms of the NADase with varying affinity for the pyridine bases. This implys the pyridine base exchange reaction to be more complicated than originally proposed. / Ph. D.

Dans le cadre des recherches menées au sein du laboratoire de Physiologie Animale le gène codant pour la nicotinamide phosphorybosyltransférase (NAmPT) à été identifié et cloné. Au cours de ce travail, nous avons étudié le rôle de cette enzyme du métabolisme du Nicotinamide Adénine Dinucléotide ainsi que celui des enzymes dépendantes du NAD (PARP et sirtuines) dans le contrôle de la réponse inflammatoire. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Les bienfaits des acides gras oméga-3, essentiellement l’EPA (C20:5n-3) et le DHA (C22:6n-3) sont bien élucidés dans la littérature. Ils jouent en effet, un rôle essentiel dans la prévention de nombreuses maladies neurodégénératives et cardiovasculaires. Ces acides gras polyinsaturés à longue chaîne sont majoritairement retrouvés dans des sources d’origines marines. Dans ce contexte, nous nous sommes intéressés d’une part à l’effet du complexe phospholipopeptidique provenant de l’hydrolyse enzymatique des têtes de saumon, sur l’anxiété et le stress oxydant dans le cadre d’une étude comportementale effectuée sur un modèle murin. D’autre part, nous avons mis en place une approche de double vectorisation, sous formes de nanoémulsions, visant à augmenter la biodisponibilité de deux molécules hydrophobes et bioactives (coenzyme Q10 et curcumine) en utilisant les lipides totaux (phospholipides et triacylglycérols) du complexe phospholipopeptidique riche en EPA et en DHA. Les résultats de ce travail ont montré que le CPLP, sa fraction lipidique et peptidique ont un effet anxiolytique à une dose de 600 mg de CPLP/jour pendant 14 jours de traitement. Il a également été démontré dans cette étude que l’hydrolysat peptidique du CPLP diminue significativement, à double dose, le stress oxydant en baissant le niveau endogène des espèces réactives de l’oxygène (ROS) dans les neurones. D’autre part, pour une utilisation thérapeutique, la biodisponibilité du CoQ10 vectorisé à forte dose est améliorée jusqu’à 38 fois par la formulation huileuse composée de lipides polaires du CPLP. Concernant la supplémentation classique en CoQ10 en tant que complément alimentaire, la formulation émulsionnée présente une meilleure disponibilité à dose aigüe, avec une concentration plasmatique deux fois plus élevée que la formulation de référence. Malgré une activité anticancéreuse reconnue pour la curcumine, sa faible solubilité diminue sa biodisponibilité et limite de ce fait son utilisation. La formulation nanoémulsionnée de curcumine contribue à inhiber la prolifération de cellules cancéreuses (MCF7) / The benefits of omega 3 fatty acids, mainly EPA (C20:5n-3) and DHA (C22:6n-3) are well understood in the literature. They indeed play an essential role in the prevention of many neurodegenerative and cardiovascular diseases. These polyunsaturated fatty acids are mostly found in marine sources. In this context, we were interested on the effects of phospholipopeptidic complex from the enzymatic hydrolysis of salmon heads on anxiety and oxidative stress using a behavioural study (mouse model). On the other hand, we have developed a double vectorization operating nanoemulsions, to increase the bioavailability of two hydrophobic and bioactive molecules (conenzyme Q10 and curcumine) by total lipids (phospholipids and triacylglycerols) from the phospholipopeptidic complex rich in EPA and DHA. The results of this study showed that the CPLP, its lipid and peptide fractions have an anxiolytic effect at a dose of 600 mg of CPLP / day for 14 days of treatment. It was also demonstrated that the peptide’s hydrolyzate ingested at double dose decreases significantly the oxidative stress by lowering the endogenous level of reactive oxygen species (ROS) in neurons. For therapeutic uses, the bioavailability of CoQ10 increased up to 38 times compared to referential formulation when verctorized at high dose in the oily formulation composed of CPLP’s total lipids. Regarding conventional CoQ10 supplementation as a dietary supplement, the emulsified formulation has a better availability at single dose, with plasma concentrations two times higher than the reference formulation. Although the anti-cancer activity of curcumine is highlighted, its low solubility and hence its low bioavailability, are factors limiting its use. The formulation of nanoemulsified curcumine allows a significant reduction in the proliferation of cancer cells (MCF7)

ARCA2 est une ataxie autosomique récessive rare, caractérisée par une atrophie du cervelet et un léger déficit en Coenzyme Q10 (CoQ). La majorité des patients présentent des signes neurologiques supplémentaires comme l’épilepsie ou l’intolérance à l’exercice. La maladie est due à des mutations dans le gène COQ8A qui semble encoder une protéine kinase-like atypique, impliquée dans la biosynthèse du CoQ. Pour comprendre les mécanismes physiopathologiques, une souris Coq8a knock-out (KO) constitutif a été générée et récapitule les symptômes observés chez les patients. Le but de ce travail de thèse était de mieux comprendre certains aspects, notamment l’intolérance à l’exercice et l’ataxie. Malgré un déficit en CoQ dans les muscles, aucun défaut de respiration mitochondriale n’a été détecté dans un modèle cellulaire de muscle. Néanmoins, dans le cervelet, les niveaux de transcrits de 27 gènes sont dérégulés, précocement dans l’apparition de la pathologie chez les souris KO. Les voies métaboliques vont être explorées, ce qui devrait permettre de relier la fonction de COQ8A au taux de CoQ et aux symptômes observés chez les patients. / ARCA2, a rare form of recessive ataxia, is characterized by early onset progressive ataxia, cerebellar atrophy and a mild Coenzyme Q10 deficiency. Most of the patients show additional neurological signs such as epilepsy and exercise intolerance. Mutations in the COQ8A gene lead to ARCA2. COQ8A is suggested as being an unorthodox protein kinase like, with a regulatory role in CoQ biosynthesis, in mammals. To better understand ARCA2, a constitutive Coq8a knock-out (KO) mouse model was generated, which recapitulates most of the patient’s symptoms. Here we report the use of cellular models and the affected tissues to uncover the molecular signature of COQ8A loss and CoQ deficit. Despite CoQ deficit in the muscle, no mitochondrial bioenergetics defect was uncovered. In parallel, we have identified, by RT-qPCR, a key set of genes that are dysregulated in cerebellum, very early on in the pathology. We are currently investigating these pathways to uncover the link with COQ8A function. Altogether, our experiments will shed light on the early molecular events that lead to ARCA2 and may help draw a link between COQ8A function, CoQ pools and the symptoms observed in patients.

Nicotinamide adenine dinucleotide (NAD+) represents a long-known key molecule in cellular metabolism. It was initially identified for its ability to convey electrons and protons between redox partners in multiple bioenergetic and biosynthetic reactions. In addition, NAD+ also serves as a substrate for NAD+-consuming enzymes such as sirtuins and poly ADP-ribose polymerases (PARPs). These latter enzymes catalyze dynamic post-translational modifications that control virtually every signaling pathway orchestrating cell fate. The aim of this work was to analyze the role of NAD+ in the context of programmed cell death mechanisms.<p>Our findings indicate that NAD+ is protective against DNA damage-induced cell death and FAS-induced apoptosis, while, unexpectedly, it promotes TNF-induced necroptosis, a regulated form of necrosis. Indeed raising NAD+ cellular levels sensitized culture cells to necroptosis, while NAD+ depletion protected cells from this form of cell death. Furthermore, specific silencing of NAD+-dependent sirtuins was also found to be protective against TNF-induced necroptosis. Consistently, a pharmacological pan-sirtuin inhibitor called cambinol protected cells from necroptosis. Then, as necroptosis represents a back-up mechanism that may have evolved in response to viral pathogens expressing anti-apoptotic proteins, we demonstrated in an in vitro model mimicking viral infection that pharmacological sirtuin inhibition protected cells from poly I:C-induced necroptotic cell death. In vivo, we demonstrated that cambinol partially protected kidney from necrosis after ischemia/reperfusion. We have also shown that enhancing liver NAD+ concentration via isonicotinamide increases the susceptibility of mice to systemic inflammatory response syndrome (SIRS). Moreover, our preliminary data show that isonicotinamide substantially improves the ability of cyclophosphamide to trigger the rejection of the murine mastocytoma P815 tumor cell line.<p>Collectively, our observations point to a role for NAD+ in the control of necroptosis in a sirtuin-dependent manner. These observations may bear relevance to the better understanding of the pathophysiological consequences of excessive production of the pro-inflammatory cytokine TNF and the control of viral infections and tumor progression/immunotherapy. & / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Le nicotinamide est un des deux constituants de la vitamine B3. C’est aussi un agent pharmacologique qui a été testé dans le traitement du HIV chez l’homme, et comme traitement contre diverses pathologies. Il présente également des capacités cytoprotectrices dans plusieurs modèles de stress cellulaire et est considéré comme un agent pharmacologique prometteur dans le traitement des maladies de dégénérescence cérébrale d’origine vasculaire. Il module la réponse innée en inhibant notamment la synthèse de molécules pro-inflammatoires. Toutefois, son influence sur la réponse adaptative n’a pas encore été analysée. <p>Le nicotinamide intervient dans la biosynthèse du NAD comme précurseur dans la voie de « sauvetage ». Le rôle du NAD comme coenzyme dans de nombreuses réactions enzymatiques du métabolisme de la cellule est bien connu. De plus, le NAD peut être dégradé par différentes enzymes impliquées dans différentes modifications post-traductionnelles de protéines (PARPs, Sirtuines et MARTs). Le nicotinamide est un produit de la dégradation du NAD mais également un inhibiteur de ces enzymes et constitue donc un outil permettant d’étudier le rôle de ces enzymes dans la transduction de signaux intracellulaires. <p>Nous avons utilisé le nicotinamide comme un inhibiteur non toxique des différentes enzymes impliquées dans les réactions d’ADP-ribosylation et étudié son effet sur l’activation des lymphocytes B. Le nicotinamide inhibe la prolifération et la différentiation de ces cellules. Il ne module pas les étapes précoces du BCR mais inhibe l’activation des MAPKs et de la kinase Akt. L’inhibition des MAPKs Erk est corrélée avec une réduction de l’expression de la cycline D2 et du marqueur d’activation CD69. L’utilisation d’un inhibiteur des PARPs ne nous a pas permis de reproduire les effets du NAm sur la voie MAPK Erk et CD69. Par contre, le MIBG, un inhibiteur des MARTs inhibe bien la surexpression du CD69 ainsi que la phosphorylation des kinases Erk. Bien que le nicotinamide soit capable d’inhiber l’expression du CD69 in vivo, nos expériences ne nous ont pas permis de moduler la réponse immune adaptative in vivo. <p>Ceci suggère dès lors que l’utilisation de fortes doses de nicotinamide comme traitement pharmacologique de certaines affections chez l’homme ne devrait pas poser de problème au niveau de la réponse adaptative. De plus, notre mise en évidence des MARTs dans le contrôle de l’activation des lymphocytes B ouvre des perspectives encourageantes pour de nouveaux traitements modulant la réponse adaptative. Cette réponse étant particulièrement impliquée dans certaines maladies auto-immunes, il est potentiellement intéressant de trouver des inhibiteurs de ces enzymes plus puissants que le nicotinamide afin de moduler la réponse immune adaptative in vivo<p> / Doctorat en sciences, Spécialisation biologie moléculaire / info:eu-repo/semantics/nonPublished