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京都大学 / 0048 / 新制・論文博士 / 博士(農学) / 乙第12822号 / 論農博第2795号 / 新制||農||1025(附属図書館) / 学位論文||H26||N4817(農学部図書室) / 31309 / 京都大学農学研究科食品生物科学専攻 / (主査)教授 喜多 恵子, 教授 三上 文三, 教授 栗原 達夫 / 学位規則第4条第2項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

No description available.

All cells and extracellular matrices of prokaryotes and eukaryotes are made up of glycans, the carbohydrate macromolecules that play a predominant role in cell-to-cell interaction, protection, stabilization, and barrier functions. Glycans are also central to human microbiome-host interactions where bacterial glycans are recognized by innate immune signaling pathways, and host mucins are a major nutrient source for various gut bacteria. Many microorganisms encode glycoside hydrolases (GHs) to utilize the available host cell surface glycans as a nutrient source and to modulate host protein function. The GHs are divided into families having conserved linkage specificity within each family and individual family members can be specific for dramatically divergent macromolecular substrates. In general, within a given GH family very few members have been biochemically characterized and the substrate specificity is poorly understood. GH genes are abundant in the human gut microbiome and culture-enriched metagenomics identified more than 10,000 distinct bacterial GH genes in an individual. The focus of this thesis is endo-β-N-acetylglucosaminidases (ENGases) encoded by GH18 and GH85 families. Bioinformatic analysis shows that the predicted proteins within each of these GH families fell into separate clusters in the Sequence Similarity Networks of each family. The hypothesis of this project is that human microbiome-encoded ENGases from the same GH family differ in their substrate specificities and within the SSN network of the same GH family, enzymes with similar substrate specificity may fall in the same cluster. In this work, I established conditions for overexpression of GH18 and GH85 proteins and investigated the activity of these enzymes on various substrates. / Thesis / Master of Science (MSc) / All the cell surfaces of animals, plants, and microbes are coated with sugars, also known as glycans. These sugars on the cell surface act as a barrier and protect them from the external environment. Glycans on the cells of both microbes and humans are essential for basic interactions between them. Many bacteria produce enzymes such as glycoside hydrolases to obtain nutrients from dietary sugars and alter the sugars on host proteins. There are various families of these enzymes, and they act on specific sugars and cleavage sites. The substrate specificities and characterization of these enzymes from most bacteria found in the human microbiome have not been studied in detail. My work focuses on developing standard enzyme assays for determining specific substrate specificities. This tool can be used to reshape glycans and understand their role in cell processes.

京都大学 / 新制・論文博士 / 博士(農学) / 乙第13567号 / 論農博第2913号 / 新制||農||1101(附属図書館) / (主査)教授 小川, 順, 教授 阪井, 康能, 教授 栗原, 達夫 / 学位規則第4条第2項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

History teaches us that novel materials, such as chlorofluorocarbon and asbestos, can have dire unintended consequences to human and environmental health. The exponential growth of the field of nanotechnology and the products developed along the way provide the opportunity for a new paradigm of design thinking, in which human and environmental impacts are considered early on in product development. In particular, nanocellulose is touted as a promising green nanomaterial, as it is sourced from an effectively inexhaustible feedstock of wood-based cellulose and is assumed to be harmless to the environment since it is derived from a natural material and assumed to be biodegradable. The various forms of nanocellulose possess an impressive diversity of properties, making it suitable for a wide variety of applications such as drug delivery, reinforcement, food additives, and iridescent make-up. However, as nanomaterials can have different properties relative to their bulk form, it is questionable whether they are truly environmentally friendly, particularly in terms of their biodegradability and potential impacts to receiving environments. Given the projected mass-scale application of nanocellulose and the inevitability of its subsequent release into environment, the purpose of this study was to determine the biodegradability of nanocellulose and the response of environmentally-relevant microbial communities. Specifically, it was hypothesized that cellulose in the nano size range would display distinct biodegradation patterns and rates, relative to larger forms of cellulose. Further, it was hypothesized that modification of nanocellulose, in terms of morphology and surface properties (e.g., charge), would further influence its biodegradability. Wetlands and anaerobic digesters were selected as two environmentally-relevant receiving environments that also play critical roles in global carbon turnover. To examine the biodegradability of nanocellulose, two distinct microbial consortia were enriched from wetland (W) and anaerobic digester (AD) inocula and applied in parallel experiments. The consortia were grown under anaerobic conditions with microcrystalline cellulose as the sole carbon substrate over a period of 246 days before being aliquoted to microcosms for subsequent biodegradation assays. Various forms of nanocellulose were spiked into the microcosms and compared with microcrystalline cellulose as a non nano reference. Microcosms were sacrificed in triplicate with time to monitor cellulose degradation as well as various measures of microbial community response. Microbial communities were characterized in terms of gene markers for total bacteria (16S rRNA genes) and anaerobic cellulose degraders (glycoside hydrolase family 48 genes, i.e., cel48) as well as high throughput amplicon sequencing of 16S rRNA genes (V4 region). A series of three studies examined: 1) the effect of nanocrystalline versus microcrystalline cellulose; 2) the effects of nanocellulose morphology (crystalline rod versus filament) and surface functionalization (cationic and anionic); and 3) metagenomic characterization of cellulose degrading communities using next-generation DNA sequencing. It was found that the nano- size range did not hinder cellulose degradation, in fact, nanocrystalline cellulose degraded slightly faster than microcrystalline cellulose according to 1st order kinetics (1st order decay constants: 0.62±0.08 wk-1 for anionic nanocrystalline cellulose versus 0.39±0.05 wk-1 for microcrystalline cellulose exposed to AD culture; 0.69±0.04 wk-1 for anionic nanocrystalline cellulose versus 0.58±0.05 wk-1 for microcrystalline cellulose exposed to W). Experiments comparing the effects of surface functionalization indicated that anionic nanocellulose degraded faster than cationic cellulose (1st order decay constants for cationic nanocrystalline cellulose: 0.48±0.06 wk-1 and 0.58±0.07 wk-1 on exposure to AD and W cultures respectively). Measurements of 16S rRNA and cel48 genes were consistent with this trend of greater biological growth and cellulose-degrading potential in the anionic nanocellulose condition, suggesting that surface properties can influence biodegradation patterns. Taxonomic characterization of 16S rRNA gene amplicons suggested that taxa known to contain anaerobic cellulose degraders were enriched in both W and AD consortia, which shifted in a distinct manner in response to exposure to the different cellulosic materials. This suggests that distinct groups of microbes may drive the biodegradation of different forms of cellulose. Further, metagenomic investigation provided new insight into taxonomic and functional aspects of anaerobic cellulose degradation, including identification of enzymatic families associated with degradation of the various forms of cellulose. Overall, the findings of this study advance understanding of anaerobic cellulose degradation and indicate that nanocellulose is likely to readily degrade in receiving environments and not pose an environmental concern. / Ph. D.

Dans ce projet de thèse, une variété de techniques a été employée pour étudier l’alpha-L-arabinofuranosidase de Thermobacillus xylanilyticus (TxAbf), notamment en ce qui concerne les relations structure/fonctions et son activité de transglycosylation. Nos travaux ont eu pour objectif d’apporter un éclairage quant au rôle de la dynamique dans l’activité catalytique de la TxAbf, en se focalisant sur le mouvement de la boucle bêta2alpha2, et d’explorer la spécificité du sous-site [+1], un élément du site actif qui est particulièrement pertinent pour l’activité de transglycosylation. Enfin, nous avons entrepris des travaux d’ingénierie visant la création de transarabinofuranosylases performantes. Nos résultats confirment le rôle important de la boucle bêta2alpha2 et suggèrent que le mouvement de celle-ci permet de relocaliser les résidus His98 et Trp99 de manière à créer un site actif opérationnel. Le résidu Trp99 apparaît comme un élément clé du sous-site [-1] de la TxAbf, alors que le résidu His98, qui n’est pas conservé dans l’ensemble des enzymes de la famille GH51, participerait à la formation d’un sous-site [+2’]. Concernant le sous-site [+1], nos résultats confirment la large spécificité celui-ci et montrent clairement que l’encombrement stérique à la position C-5 des glycosides accepteurs est défavorable à la réaction de transglycosylation. Par ailleurs, nous avons pu réaliser pour la première fois la synthèse de trisaccharides, utilisant comme accepteur l’alpha-D-xylobioside de benzyle et comme donneur le β-D-galactofuranoside de para-nitrophényle. Enfin, nos travaux de mutagenèse aléatoire et le criblage de banques a permis d’identifier deux mutations Phe26Leu et Trp178Arg, qui se situent au niveau des sous-sites [-1] et [+1], respectivement. Selon nos premières analyses, les mutants correspondants rendraient moins favorable la déglycosylation de l’intermédiaire glycosyl-enzyme par une molécule d’eau, réduisant ainsi l'hydrolyse secondaire et stabilisant par la même occasion le produit de synthèse. En employant une deuxième méthode de criblage plus sophistiquée, impliquant l’utilisation d’accepteurs xylo-oligosaccharidiques, nous avons pu obtenir des enzymes mutées qui (i) catalysent des réactions de transglycosylation en présence de xylobiose (l’enzyme sauvage ne catalysant que très faiblement cette réaction) (ii) se caractérisent par une absence quasi-totale d’hydrolyse secondaire et (iii) comportent des mutations situées à différentes positions (e.g. au niveau des sous-sites [-1], [+1] et [+2’]) et qui semblent moduler le ratio Transglycosylation/Hydrolyse en faveur de la synthèse / In this investigation, a variety of techniques to study the Thermobacillus xylanilyticus alpha-L-arabinofuranosidase (TxAbf) have been employed, especially with regard to structure-functions relations and the enzyme’s ability to catalyze transglycosylation reactions. The aim of our work was to better understand the dynamic role of the bêta2alpha2 loop and to explore the substrate specificity of the subsite [+1], an important active site element with respect to transglycosylation. Finally, this work has focused on the creation of new transarabinofuranosylases using random engineering and screening approaches.Our results confirm the important role of the bêta2alpha2 loop and suggest that its movement during catalysis relocalizes residues His98 and Trp99 and thus permits the formation of a catalytically-viable active site configuration. Trp99 is relocalized from a solvent exposed position into a buried position and forms a critical element of subsite [-1], whereas His98, a residue that is not conserved in all GH51 members, appears to form a part of subsite [+2’]. Regarding subsite [+1], our results confirm its wide specificity and indicate that steric bulkiness at the C-5 position of glycoside acceptors leads to reduced transglycosylation. In this work, we have also demonstrated for the first time the synthesis by TxAbf of trisaccharides, using benzyl alpha-D-xylobioside as the acceptor and para-nitrophenyl β-D-galactofuranoside as the donor. Finally, random mutagenesis and screening has led to the identification of two mutations Phe26Leu and Trp178Arg, which are located in sub-sites [-1] and [+1] respectively, that appear to reduce the water-mediated deglycosylation of the glycosyl-enzyme intermediate. Consequently, the corresponding mutants reduce secondary hydrolysis and favourably affect the operational stability of synthetic products. Using a second more sophisticated screening method that involves the use of xylo-oligosaccharide acceptors, it has been possible to isolate mutant enzymes that (i) catalyze transglycosylation reactions in the presence of xylobioside (a reaction that is poorly catalyzed by wild type TxAbf), (ii) show almost no secondary hydrolysis, (iii) display point mutations at several key locations (e.g. in sub-sites [-1], [+1] and [+2’]) that seem to modulate the Transglycosylation/Hydrolysis ratio in favour of synthesis

Cette thèse a été réalisée dans le cadre du projet Futurol, un projet national français qui vise à produire du bioéthanol à partir de biomasses végétales telles que le bois ou la paille de céréale. Pour cela, la biomasse doit être prétraitée puis digérée enzymatiquement pour libérer des sucres fermentescibles. Ma contribution dans ce projet a été de découvrir des enzymes originales pour l’hydrolyse de l’hémicellulose, un hétéropolysaccharide, constituant majeur de la paroi cellulaire des cellules végétales. Afin de rechercher de nouveaux biocatalyseurs, une approche de métagénomique a été adoptée afin de sonder les intestins de deux espèces de termites : N. corniger, un termite xylophage, et T. hispaniolae un termite humivore / xylophage. 30 000 clones métagénomiques ont été criblés sur 10 substrats cellulosiques et hémicellulosique, et 660 hits ont été obtenus. La comparaison phénotypique a montré une différence claire entre ces deux banques, probablement liée au régime alimentaire des deux espèces de termite. Le séquençage de 45 clones N. corniger a révélé 120 séquences codant pour des enzymes originales, de nombreuses étant multimodulaires et / ou organisées en cluster de gènes. Dans un second temps, une approche à haut-débit a été adoptée pour le clonage, l’expression et la caractérisation légère de 104 enzymes entières ou formes tronquées. 45 protéines recombinantes ont été produites de manière soluble, et les activités de 19 enzymes et de 12 modules enzymatiques ont été montrées, permettant la mise au point d’une boite à outil hemicellulolytique. Dans certains cas, l’activité de modules classés « Inconnus » a pu être déterminée. Cette approche a été particulièrement pertinente dans le cas de Pm69, une enzyme multimodulaire GH3-UNK-CBM48-CE1 montrant les 3 activités glucosidase, xylosidase and estérase. Cette étude a permis de poser les bases d’un brevet sur cette enzyme. D’un autre côté, les enzymes ayant montré une activité xylanase ou féruloyle-estérase se sont révélées complémentaires d’un cocktail cellulolytique durant la dégradation de paille de blé prétraitée. Enfin, dans une troisième partie, nous avons étudié un fragment d’ADN provenant la banque P. militaris, codant pour 19 ORFs et appartenant à une espèce du genre Bacteroides. La caractérisation biochimique d’Abn43A, Abn43B, Abf51A et Abf51B-trunc a montré que ces 4 enzymes portent des actions complémentaires sur l’hydrolyse de l’arabinane, et qu’elles peuvent agir de manière synergique pour la dégradation de ce polymère pectique. Enfin, l’étude détaillée des 19 ORFs codées sur ce fragment d’ADN nous a permis de proposer un schéma global de détection, d’hydrolyse et de métabolisation de l’arabinane par cette espèce du genre Bacteroides. / This thesis was performed in the context of the Futurol project, a French national project that aims at producing bioethanol from plant biomass such as wood and cereal straw. To reach that goal, the biomass must be pretreated, and enzymatically degraded to release fermentable simple sugar. My implication in that project was to discover original enzymes that can hydrolyze the hemicellulose, a major heteropolysaccharide found in plant cell wall.To mine for new biocatalysts, the gut microbial communities of two species of termite were investigated by a metagenomic approach : Nasutitermes corniger, a wood-feeder termite, and Termes hispaniolae supposed to be a soil-wood feeder. 30 000 metagenomic clones were screened on an array of 10 cellulosic and hemicellulosic substrates and 660 hits were obtained. Phenotypic comparison showed clear differences between both environments, probably related to the diet of the termite. The sequence of 45 N. corniger metagenomic inserts revealed 120 original sequences encoding for putative enzymes of interest. Original sequences encoding for multimodular enzymes were revealed and many ORFs were organized in clusters, suggesting that these enzymes are encoded on Polysaccharides Utilization Locus. In a second part, a high-throughput approach was used for the cloning, the expression and the slight characterization of 104 full-size and truncated enzymes. Forty five recombinant proteins were produced soluble, and their investigation revealed the activity of 19 enzymes and of 12 enzymatic modules, representing a hemicellulolytic tool-box for endo- and exo-type activities. In some cases, the implication of “Unkown” domains in the activity of multimodular enzymes was demonstrated. This approach was particularly efficient for the study of the GH3-UNKCBM48-CE1 Pm69, and this study triggered the patent process for this multiactive glucosidase, xylosidase and esterase. The xylanases and the feruloyl esterases were shown to be particularly efficient to supplement cellulolytic cocktails on pretreated wheat straw. In a third part, we investigated a DNA fragment belonging to a species of the genus Bacteroides and that encoded 19 ORFs. The biochemical characterization of Abn43A, Abn43B, Abf51A and Abf51B-trunc showed that these four enzymes harbored complementary actions for the hydrolysis of the arabinan, and that they can act synergistically for the hydrolysis of this pectic polymer. We also revealed that Abn43B had an original mode of action that we classified as exo-arabinanase. Finally, the in-depth study of the 19 ORFs allowed us to propose the entire scheme for arabinan detection, hydrolysis and utilization by the Bacteroides species carrying this DNA sequence

Une approche de métagénomique fonctionnelle a été mise en œuvre afin d’étudier les arsenaux enzymatiques produits par les microbiotes intestinaux de termites phytophages et d’identifier de nouvelles enzymes impliquées dans l’hydrolyse des polysaccharides végétaux, notamment des hétéroxylanes. Le criblage à haut débit des banques métagénomiques constituées à partir de trois espèces de termites sur une gamme de substrats chromogéniques a permis d’identifier plusieurs centaines de clones à activité dépolymérisante (glucanase, xylanase, mannanase, arabinanase), ainsi que des clones exprimant des activités auxiliaires (α-L-arabinofuranosidases, β-D-xylosidases, cellobiose hydrolases). Un total de 42 clones métagénomiques a été séquencé, générant 1,5 Mpb d’ADN assemblé en 58 séquences contigües d’une taille moyenne de 37,8 Kbp. 63 nouvelles Glycoside Hydrolases (GH) ont été identifiées. Ces dernières représentent 19 familles de la classification CAZy, dont les familles GH3, GH8, GH10, GH11, GH43 et GH51. Enfin, huit nouvelles enzymes des familles GH43 et GH51 ont été produites chez E. coli et leurs propriétés biochimiques ont été étudiées. Ces enzymes présentent des activités α-L-arabinofuranosidase, β-D-xylosidase ou L-arabinanase / A functional metagenomics approach was used to reveal the enzymatic diversity present in the guts of biomass-feeding termites and to identify enzymes involved in the degradation of biomass components, notably heteroxylans. High-throughput screening of metagenomic libraries, created using three different termite species, was performed using a variety of chromogenic substrates. This allowed the discovery of hundreds of clones expressing targeted biomass-degrading activities (e.g. depolymerases such as glucanase, xylanase, mannanase arabinanase and auxiliary activities such as α-L-arabinofuranosidases, β-D-xylosidases and cellobiohydrolases). A total of 42 clones were selected for a DNA sequence analysis, thus generating 1.5 Mbp that were assembled into 58 contiguous sequences. 63 new Glycoside Hydrolases (GH) belonging to 19 different families of the CAZy classification were identified, including ones from families GH3, GH8, GH10, GH11, GH43 and GH51. Finally, eight new enzymes, from families GH43 and GH51, were produced in E. coli and their biochemical properties were studied. These enzymes display α-L-arabinofuranosidase, β-D-xylosidase or arabinanase activities

As mudanças climáticas estão causando prejuízos em vários setores da economia mundial. Na reunião da COP21, que teve como foco estas mudanças climáticas, participantes do mundo todo decidiram tomar atitudes urgentes para tentar conter aumento da temperatura média global. Dentro deste cenário, a produção e o consumo de energia têm uma importância central, onde fontes de energia renováveis vêm sendo preferidas às fontes de energias fósseis. O Brasil tem uma participação importante na geração de energia renovável mundial aportando um 40% do total de sua matriz energética. A degradação dos componentes da parede celular vegetal tem um vasto potencial na geração de biocombustíveis e outros compostos verdes a partir da celulose, hemicelulose e lignina. Para isto estudos das enzimas capazes de degradas estes componentes vem sendo realizados, com ênfase nas enzimas hidrolases de glicosídeos. Dentre as hidrolases, encontram-se as arabinanases, enzimas capazes de hidrolisar o arabinano, componente polissacídeo da hemicelulose, em L-arabinose. Neste trabalho, estudos envolvendo duas arabinanases de Bacillus licheniformis foram realizados, iniciando na etapa de clonagem dos genes. Os produtos foram transformados em Escherichia coli e expressos e purificados. A avaliação da estabilidade térmica indicou uma afinidade das enzimas por metais divalentes. Tentativas de cristalização resultaram na formação de um cristal, que possibilitou a determinação da estrutura uma das arabinanases. Através de ensaios bioquímicos, foi determinada a especificidade por substrato, temperatura e pH ótimos e a atividade frente a metais. Foi observado que as enzimas são seletivas para arabinano não ramificado, tem temperatura ótima em 45 e 40 graus, para BlAbn-1 e BlAbn-2, respectivamente, e pH ótimo em 8 e 7. Por último, foram realizados ensaios complementares de sinergismo e atividade oxidativa. Embora os ensaios de atividade oxidativa tenham sido inconclusivos, os ensaios de sinergismo mostraram que a enzima BlAbn-1 é capaz de aumentar em 30% a atividade do coquetel enzimático Accellerase 1500 sobre biomassa pré-tratada e sobre celulose pura. Este efeito é ainda maior na presença de sulfato de níquel. / Climate change is causing losses in different sectors of the world economy. At the meeting of COP21, focused on climate changes, participants from around the world decided to take urgent actions to try to halt the increase in global average temperature. Within this scenario, the production and consumption of energy are of central importance, where renewable energy sources have been preferred to fossil fuels. Brazil has an important role in the global renewable energy generation by contributing 40% of its total energy mix. The degradation of the components of plant cell wall has a vast potential in the generation of biofuels and other green chemical from cellulose, hemicellulose and lignin. Thus, studies of enzymes that degrade these components have been carried out, with emphasis on glycoside hydrolases. Among the hydrolases are the arabinanases, enzymes capable of hydrolyzing arabinan, a polysaccharide component of hemicellulose, in L-arabinose. In this work, studies involving two arabinanases from Bacillus licheniformis were carried out, starting in gene cloning step. The products were transformed into Escherichia coli, expressed and purified. The evaluation of the thermal stability of the enzymes showed an affinity for divalent metals. Crystallization attempts resulted in the formation of a single crystal, which made it possible to determine the crystal structure of one arabinanase. Through biochemical assays, it was determined the substrate specificity, optimum temperature and pH and activity against metals. It was observed that the enzymes are selective for non-branched arabinan, have optimum temperature at 45 and 40 degrees, to BlAbn-1 and BlAbn-2, respectively, and optimum pH of 8 and 7. Finally, additional tests were performed to evaluate the possible synergism and oxidative activity. Although the oxidative activity assays were inconclusive, the synergism tests showed that BlAbn-1 is able to increase by 30% the activity of the enzymatic cocktail Accellerase 1500 on pre-treated biomass and on pure cellulose. This effect is even greater in the presence of nickel sulfate.