La CREB Binding Protein (CBP) a une activité lysine acétyltransférase intrinsèque et fonctionne aussi comme un co-activateur transcriptionnel. L'activité acétyltransférase et la fonction de coactivateur transcriptionel sont toutes deux essentielles pour la formation de mémoire à long terme. De plus, la dérégulation de CBP a été observée dans des maladies neurodégénératives comme la maladie d'Alzheimer et la maladie de Huntington. L'objectif de ma thèse était d'étudier le rôle de la CBP et de son activation pharmacologique dans le cadre de la formation de la mémoire spatiale, une forme de mémoire qui est démantelé très tôt dans la MA. Les données obtenues à partir de ma thèse montrent que l'activation de la fonction acétyltransférase CBP par l’activateur CSP-TTK21 améliore les processus mnésiques chez des souris adultes normales et aussi dans un modèle murin de MA (THY-Tau22). Ainsi, la stratégie d’activation pharmacologique de l'activité acétyltransférase de CBP a un énorme potentiel pour une utilisation en tant qu'agent thérapeutique pour le traitement des maladies liées à l'altération de la mémoire tel que la maladie d'Alzheimer. / CREB Binding Protein (CBP) has an intrinsic lysine acetyltransferase activity and alsofunctions as a transcriptional co-activator. Both the acetyltransferase activity and the transcriptional co-activator function are critical for long-term memory formation. Importantly, CBP dysregulation has been observed in neurodegenerative conditions like in Alzheimer’s disease and Huntington’s disease. The focus of my thesis was to study the role of CBP and its activation by a new pharmacological tool, in the context of spatial memory formation, a form of memory that is very early dismantled in AD. Data obtained from my thesis clearly suggests that activation of CBP acetyltransferase function by small molecule activator CSP-TTK21 can improve memory related processes in healthy adult mice and also in a mouse model of AD, (THY-Tau22). Therefore, the strategy of pharmacological activation of CBP acetyltransferase activity has tremendous potential for use as therapeutics for the treatment of diseases related to memory impairment such as Alzheimer’s disease.

Résumé français confidentiel / Résumé anglais confidentiel

CO2 adsorption is considered as a promising strategy to decrease the amount of CO2 in the atmosphere and stop global warming. The goal of this project is to prepare a cellulose-based CO2 adsorbent with a good mass transfer. Monolithic adsorbent based on cellulose nanofibrils (CNF) was fabricated via freeze-casting. 0.1g or 0.5g cellulose acetate (CA) or 0.1g acetylated CNC (aCNC) was dipped into the crosslinked aerogel to increase its CO2 capacity. Acetylation of CNC was confirmed by Fourier transformed infrared spectroscopy (FT-IR) and the degree of substitution was determined to be 1.6 through titration. Scanning electron microscopy (SEM) images showed that monolithic structure was formed through freeze-casting and the structure was maintained after dipping. Compression test suggested that the mechanical properties of the aerogel increased with the increasing amount of dipped CA, while the CO2 capacity of the adsorbent decreased. Furthermore, the outstanding reinforcing effect of aCNC was noticed in the compression test, and the aerogel dipped with aCNC has the highest CO2 capacity with a value of 1.49 mmol/g.

Le peptidoglycane (PG) est le composé majeur de la paroi des bactéries à Gram positif. Il est constitué de chaines de sucres, formées de l’alternance de N-acétyl-glucosamine (GlcNAc) et d’acide N-acétyl-muramique (MurNAc) et reliées entre elles par des chaines peptidiques. Cette structure confère à la bactérie une grande résistance mais aussi une certaine flexibilité qui lui permettent de grandir et de se diviser tout en gardant sa forme. Cette dualité entre rigidité et flexibilité est assurée par un équilibre entre l’activité des enzymes qui polymérisent le PG, les protéines liant la pénicilline (PBP), et de celles qui l’hydrolysent, les hydrolases du PG (PGH). Pendant ou après sa synthèse, la structure du PG peut subir différentes modifications, qui vont moduler l’activité des enzymes de synthèse et dégradation du PG. Au cours de ce travail, nous avons caractérisé les modifications structurales du PG chez deux espèces de lactobacilles et étudié leur rôle fonctionnel. Nous avons identifié la première amidotransférase responsable de l’amidation de l’acide méso-diaminopimélique et montré l’influence de cette modification sur l’activité d’une PGH, la L,D-carboxypeptidase DacB, ainsi que sur la synthèse du PG septal par les PBPs chez Lactobacillus plantarum. Nous avons ensuite mis en évidence pour la première fois une O-acétylation des GlcNAc en plus de l’O-acétylation des MurNAc, ces deux modifications étant réalisées par deux O-acétyl-transférases distinctes, OatA et OatB, qui jouent des rôles antagonistes dans le contrôle de l’activité des PGHs chez L. plantarum. Nous avons aussi révélé l’implication de l’O-acétyl-transférase OatA dans le contrôle de la septation. Enfin, nous avons montré l’influence de l’O-acétylation des MurNAc du PG sur les propriétés anti-inflammatoires d’une souche de Lactobacillus casei. / Peptidoglycan (PG) is the major component of the gram positive cell wall. It is composed of glycan chains formed by the polymerization of the N-acetylglucosamine-N-acetyl muramic acid heterodimer, and cross-linked by peptidic stem. This structure confers high resistance to the bacterial cell wall but also some flexibility allowing growth and shape maintenance. This duality between rigidity and flexibility is the result of a steady-state between the PG polymerizing enzymes, the penicillin binding protein (PBP) and the PG hydrolases (PGH). More or less concomitantly with its synthesis, certain modifications can occur on PG structure that will modulate the activity of PG synthesis and degradation enzymes.During this work, we have characterized the PG structural modifications in two lactobacilli species and studied their functional role. We have identified the first amidotransferase involved in meso-diaminopimelic acid amidation and shown the influence of this modification on the activity of the L,D-carboxypeptidase, DacB, and also on the septal PG synthesis by the PBP in Lactobacillus plantarum. Then, we have highlighted for the first time, the presence of O-acetylation on GlcNAc in addition to O-acetylation on MurNAc. These two modifications are catalyzed by two dedicated O-acetyltransferases, OatB and OatA respectively, that control PGH activity in an antagonistic way. We have also demonstrated the implication of the OatA O-acetyltransferase in septation control. Finally, we have shown the influence of PG MurNAc O-acetylation on the anti-inflammatory properties of a Lactobacillus casei strain.

Les flavonoïdes sont des composés poly-hydroxylés d’origine végétale, connus pour leurs vertus pour la santé. Afin d’obtenir des dérivés plus stables et solubles dans des formulations hydrophobes tout en conservant les activités biologiques des molécules d’origine, une solution consiste à acyler ces composés de manière régiosélective. Ceci peut être accompli en utilisant des lipases comme catalyseurs, en milieu organique. Grand nombre d’études expérimentales sur ces bioprocédés sont disponibles, mais aucune d’entre elles n’apporte d’explication, au niveau moléculaire, de la sélectivité de ces réactions d’acylation. Le but de cette étude est d’appliquer différents outils de simulation moléculaire pour mieux comprendre, au niveau moléculaire, les propriétés de sélectivité de l’acétylation de trois flavonoïdes (quercétine et ses dérivés glycosylés isoquercitrine et rutine), en utilisant les lipases CALB et PCL. D’abord, des simulations de docking ont été appliquées, afin d’obtenir les positions et les orientations les plus probables des flavonoïdes dans la cavité des lipases préalablement acétylées. Ensuite, des simulations de dynamique moléculaire ont été exécutées sur les complexes obtenus par docking, afin d’étudier stabilité structurale des complexes sur une période de temps et notamment la stabilité des interactions enzyme-substrats. Enfin, des simulations basées sur une approche de chimie quantique (DFT) ont été appliquées pour évaluer la réactivité chimique des flavonoïdes dockées dans les complexes. Les premières tendances observées aux cours des simulations ont présenté une bonne corrélation avec les résultats expérimentaux d’acétylation. Globalement, les résultats obtenus ont montré que la sélectivité de ces réactions dépend de l’orientation des substrats (flavonoïde et acétate) dans la cavité catalytique de la lipase, des interactions intermoléculaires stabilisant ces substrats et de la réactivité chimique intrinsèque des groupements OH des flavonoïdes se situant à proximité des résidus catalytiques / Flavonoids are plant-produced polyhydroxylated compounds, well-known for their beneficial health effects. In order to obtain more stable and soluble derivatives for incorporation in hydrophobic formulations without damaging the biological activities of the native molecules, a solution consists to perform a regioselective acylation of these molecules. This can be accomplished by using lipase biocatalysts, in organic media. Several experimental studies dealing with such processes are available, but none of them give any explanation, at the molecular level, for the regioselectivity of such reactions. This study aimed to apply different molecular modelling tools in order to better understand, at the molecular level, the selectivity properties of the acetylation of three flavonoids (quercetin and its glycosylated derivatives isoquercitrin and rutin), by using the lipases CALB and PCL. Firstly, docking simulations were applied, in order to obtain the most probable positions and orientations of the flavonoids in the cavities of acetylated lipases. Then, molecular dynamics simulations were performed, aiming to study the structural stability of the complexes upon a period of time and specially the stability of the enzyme-substrates interactions. Finally, quantum chemical simulations (DFT) were applied to evaluate the chemical reactivity of the flavonoids as docked in the complexes. The trends observed during the simulations were well correlated with previous experimental results on the acetylation reaction of these flavonoids. Overall, the results showed that the selectivity in such reactions depends upon the substrates (flavonoid and acetate) orientations in the enzyme catalytic cavity, the intermolecular interactions that stabilize these substrates and the intrinsic chemical reactivity of the flavonoids OH groups reaching the catalytic residues

Biacetilo (2,3-butanediona) é um contaminante de comida e cigarro, também implicado na hepatoxicidade do álcool e em doenças pulmonares. O metilglioxal (MG), um α-oxoaldeído reativo frequentemente associado ao diabetes e envelhecimento, é produto da fragmentação oxidativa de trioses fosfato, acetona e aminoacetona. Por sua vez, peroxinitrito - um potente oxidante, agente nitrante e nucleófilo formado in vivo pela reação controlada por difusão do ânion radical superóxido com o radical óxido nítrico (k ~1010 M-1s-1) é capaz de se adicionar a CO2 e compostos carbonílicos, gerando produtos potencialmente tóxicos ou sinalizadores celulares. Aminoácidos, peptídeos e nucleobases podem ser acetilados nos grupos amina e na porção desoxiribose. Relativamente ao tratamento com peroxinitrito isolado, níveis superiores de 3-nitrotirosina foram detectados quando tirosina foi tratada com peroxinitrito/biacetilo ou metilglioxal. Ambos os grupos amina de lisina (Lys) ou um deles de derivados de lisina bloqueados e um deles (Ac-Lys-OMe, Z-Lys-OMe) foram acetilados pelo sistema biacetilo ou metilglioxal/peroxinitrito. Em tetrapeptídeos sintéticos contendo lisina como aminoácido amino-terminal (H-KALA-OH, Ac-KALA-OH and H-K(Boc)ALA-OH), a lisina foi acetilada pelo sistemas dicarbonilico/peroxinitrito no grupo α-amina (em maior extensão) e/ou no ε-amina (em menor extensão). No conjunto, estes resultados podem ser interpretados à luz do mecanismo proposto para a reação de compostos α-dicarbonílicos com peroxinitrito, o qual envolve sequencialmente: (i) adição nucleofílica de peroxinitrito à carbonila; (ii) homólise do aduto peroxinitroso formado, liberando •NO2 e um radical oxila do reagente carbonílico; (iii) β-clivagem do radical oxila a um ácido carboxílico (ácido acético no caso de biacetilo e ácido fórmico, a partir de metilglioxal) e radical acetila; (iv) captação do radical acetila pelo oxigênio molecular dissolvido dando acetato, ou por aminoácido ou nucleobase, se presentes, gerando o produto acetilado. Tais resultados são interessantes ao levantar a hipótese de acetilação radicalar como mecanismo de modificação pós-traducional de proteínas, até então considerado um processo realizado apenas por acetilases. / Diacetyl (2,3-butanedione) is a food and cigarette contaminant recently implicated in alcohol hepatotoxicity and lung disease. In turn, methylglyoxal (MG) is an α-oxoaldehyde frequently associated with diabetes and aging that is putatively formed by the oxidative fragmentation of trioses phosphate, acetone and aminoacetone. Peroxynitrite - a potent oxidant, nitrating agent and nucleophile formed in vivo by the diffusion-controlled reaction of superoxide radical with nitric oxide (k ~1010 M-1s-1) - is able to form adducts with carbon dioxide and carbonyl compounds. When initially present in the reaction mixtures before addition of ONOO-, amino acids, peptides and nucleobases undergo acetylation at the amino group and purine moieties in the presence of biacetyl or methylglyoxal. Higher levels of 3-nitrotyrosine nitration were measured when peroxynitrite/biacetyl or metilglioxal was added to tyrosine, in comparison with peroxynitrite alone. Both amino groups of L-lysine or one of the amino groups of L-lysine derivatives (Z-Lys-OH and Ac-Lys-OH) were acetylated by biacetyl and methylglyoxal/peroxynitrite system. Using tetrapeptides containing lysine at the terminal amino acid (H-KALA-OH, Ac-KALA-OH and H-K(Boc)ALA-OH), the lysine residue was acetylated at both or either α-amino (major adduct) and ε-amino group (minor adduct). Altogether these data can be interpreted by the mechanism proposed to describe the reaction of α-dicarbonyls with peroxynitrite as follows: (i) nucleophilic addition of peroxynitrite to the carbonyl group of the reagent; (ii) homolysis of the formed peroxynitroso carbonyl adduct to •NO2 and a carbonyloxyl radical; (iii) β-cleavage of the oxyl radical to acetyl radical plus acetic acid (from diacetyl) or formic acid (from methylglyoxal); (iv) competitive scavenging of the acetyl radical by dissolved molecular oxygen and by added amino acid, peptide or nucleobase, ultimately yielding acetate or acetylated biomolecule. If occurring in vivo, these radical reactions may contribute to the post-translational modification of proteins catalyzed by transacetylases.

Splicing is the process when introns gets removed and exons are spliced together. This is an important step to form a clean mRNA with no unnecessary sequences that could interrupt protein synthesis. There are different types of splicing and some of them need a complex called spliceosome. The spliceosome requires ATP, small nuclear RNAs and splicing factors. The spliceosome and the process splicing can be regulated by epigenetics, and one epigenetic mechanism is histone modification. There are four types of histone modifications; methylation, phosphorylation, ubiquitination and acetylation. They regulate splicing to different extents by altering the chromatin structure, affect the assembly of the spliceosome and regulate the attraction of splicing factors. This review will investigate if histone modifications affect splicing and to what extent. Suggestions for further research regarding the relationship between splicing and histone modifications will also be provided. The review is based on 30 articles and two books and the search was conducted between 30th of March 2020 and 13th of April 2020. Ubiquitination and phosphorylation have a minor effect on splicing meanwhile methylation and acetylation affect splicing in great extent.

This mini-review investigates and compiles the latest knowledge regarding epigenetic changes on the mammalian mitochondrial DNA and its proteins. Methylation of the DNA, acetylation of the proteins and silencing of genes by short non-coding RNAs are the main epigenetic changes known today to affect mitochondrial DNA, mostly leading to repression. Methylation mainly occurs at non-CpG sites in the main non-coding region called the D-loop, with methylation patterns being cell type specific. Acetylation of proteins are mainly controlled by the deacetylase SIRT3, with its function being correlated to longevity. On the other hand, mitochondrial dysfunction is directly associated with a plethora of diseases, such as neurodegenerative disorders and heart disorders. The mitochondrion and nucleus are immensely dependent on each other and exchange vital proteins and RNAs, with epigenetic changes on one potentially affecting the other. Recent research shows that heteroplasmy is a proven cause of mitochondrial malfunction and that paternal inheritance is possible. The mitochondrial haplotype also shows different vulnerability to certain diets and diseases, leading to the conclusion that the mitochondrial haplotype can be used to more than just tracing human origins, such as to predicting and preventing diseases.

京都大学 / 0048 / 新制・論文博士 / 博士(理学) / 乙第13369号 / 論理博第1573号 / 新制||理||1666(附属図書館) / (主査)教授 杉山 弘, 教授 深井 周也, 教授 秋山 芳展 / 学位規則第4条第2項該当 / Doctor of Science / Kyoto University / DGAM

Protein Prp45, the yeast ortholog of the human transcription coregulator SNW1/SKIP, has been previously associated only with the regulation of pre-mRNA splicing. However, our laboratory found that protein Prp45 genetically interacts not only with the proteins involved in pre-mRNA splicing, but also with factors important for transcription elongation and with chromatin modifying enzymes. Our data and the information about the human ortholog SNW1/SKIP suggest that Prp45 could serve as a regulator coupling splicing, transcription and chromatin state in S. cerevisiae. The main aim of this diploma thesis was to find out whether the protein Prp45, which is essential for cotranscriptional assembly of the spliceosome, affects posttranslational modifications of chromatin on transcribed genes. Using chromatin immunoprecipitation, the influence of prp45(1-169) mutation on trimethylation of histone H3 at lysine 4 and acetylation of histone H3 at lysines 9, 14 and 18 on transcriptionally active genes was not confirmed. The other aim was to analyse the behavior of cells synchronized by α-factor by using flow cytometry. According to our results, prp45(1-169) mutation leads to the prolongation of the cell cycle. For the purpose of monitoring the dynamics of nucleosomes in S. cerevisiae strains, the system of...