京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第19194号 / 農博第2133号 / 新制||農||1034(附属図書館) / 学位論文||H27||N4940(農学部図書室) / 32186 / 京都大学大学院農学研究科森林科学専攻 / (主査)教授 髙野 俊幸, 教授 西尾 嘉之, 教授 梅澤 俊明 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

<p>Several plant defense systems consist of enzymes that act on glucosides and produce a toxic compound. In the intact plant tissue the substrate and enzyme are kept apart. The system studied here consists of the substrate 2-O-β-D-glucopyranosyl-4-dihydroxy-1,4-benzoxazin-3-one and the enzyme glucan 1,3-β-glucosidase in rye. The aim was to determine the properties of a cell wall β-glucosidase. Two different systems for expression and purification of β-glucosidase fused to a tag were used: a 6xHistidine tag system and a thioredoxin tag system. The sequence of the β-glucosidase had previously been determined so now the gene was subcloned into E.coli. A direct PCR on colonies, a test expression, a restriction digestion of plasmids and sequencing was made to analyze the transformation, which all turned out successful. Then the β-glucosidase solubility was determined. Finally a purification of the β-glucosidase from E.coli under native conditions and a pNPG assay was carried out. For the (His)6-tagged protein, the recombinant β-glucosidase tended to end up in the insoluble pelleted fraction which indicated formation of inclusion bodies. The cell wall 1,3-β-glucosidase was soluble with the thioredoxin system, but the percentage of soluble protein fraction was around 5% only of the total protein. In eluates from a nickel-nitrilotriacetic acid column the presence of recombinant protein was confirmed with Western blot, but contaminating bands were also present. Purified elauted fractions did not exhibit detectable β-glucosidase activity. It was not possible to purify active enzyme. From a BLAST search it was clear that the most similar enzymes all had putative glycosylation sites and lack of glycosylation could be a reason for the protein not to fold properly.</p>

Several plant defense systems consist of enzymes that act on glucosides and produce a toxic compound. In the intact plant tissue the substrate and enzyme are kept apart. The system studied here consists of the substrate 2-O-β-D-glucopyranosyl-4-dihydroxy-1,4-benzoxazin-3-one and the enzyme glucan 1,3-β-glucosidase in rye. The aim was to determine the properties of a cell wall β-glucosidase. Two different systems for expression and purification of β-glucosidase fused to a tag were used: a 6xHistidine tag system and a thioredoxin tag system. The sequence of the β-glucosidase had previously been determined so now the gene was subcloned into E.coli. A direct PCR on colonies, a test expression, a restriction digestion of plasmids and sequencing was made to analyze the transformation, which all turned out successful. Then the β-glucosidase solubility was determined. Finally a purification of the β-glucosidase from E.coli under native conditions and a pNPG assay was carried out. For the (His)6-tagged protein, the recombinant β-glucosidase tended to end up in the insoluble pelleted fraction which indicated formation of inclusion bodies. The cell wall 1,3-β-glucosidase was soluble with the thioredoxin system, but the percentage of soluble protein fraction was around 5% only of the total protein. In eluates from a nickel-nitrilotriacetic acid column the presence of recombinant protein was confirmed with Western blot, but contaminating bands were also present. Purified elauted fractions did not exhibit detectable β-glucosidase activity. It was not possible to purify active enzyme. From a BLAST search it was clear that the most similar enzymes all had putative glycosylation sites and lack of glycosylation could be a reason for the protein not to fold properly.

Submitted by Luciana Sebin (lusebin@ufscar.br) on 2016-09-27T12:20:20Z No. of bitstreams: 1 TeseRNF.pdf: 5131887 bytes, checksum: 5f32fa62636719671f0675a379d2cd24 (MD5) / Approved for entry into archive by Marina Freitas (marinapf@ufscar.br) on 2016-09-27T19:55:39Z (GMT) No. of bitstreams: 1 TeseRNF.pdf: 5131887 bytes, checksum: 5f32fa62636719671f0675a379d2cd24 (MD5) / Approved for entry into archive by Marina Freitas (marinapf@ufscar.br) on 2016-09-27T19:55:44Z (GMT) No. of bitstreams: 1 TeseRNF.pdf: 5131887 bytes, checksum: 5f32fa62636719671f0675a379d2cd24 (MD5) / Made available in DSpace on 2016-09-27T19:55:52Z (GMT). No. of bitstreams: 1 TeseRNF.pdf: 5131887 bytes, checksum: 5f32fa62636719671f0675a379d2cd24 (MD5) Previous issue date: 2016-01-15 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / The search for new sustainable alternative energy sources has followed the increasing concerns with common welfare and fossil fuel shortage. In this context, Bioethanol is a good option and lignocellulosic biomass is an interesting way of obtaining it. The enzymatic conversion of lignocellulosic biomass in fermentable sugars still is a costly process, which makes characterization mechanisms indispensable to make it economically viable. Being of great importance in the lignocellulosic biomass convertion, β-glucosidases catalyzed reaction is the last step in the saccharification processes. Beta glucosidase hydrolyze non-reduced β-D-glycoside terminals, releasing β-D-glucose. GH 1 and GH 3 are the families of those most studied enzymes. However, structural and functional data from this GH 3 family of enzymes are still scarce. This work aimed at the biochemical and structural characterization of β-glucosidase from Bifidobacterium adolescentis (BaBgl). This enzyme has a catalytic domain (CCD) and a fibronectin III-like domain (FnIII) whose function is still unknown. Biochemical data showed optimal conditions for enzyme activity at pH from 6.0 to 6.5, temperature at 45 ° C and synthetic substrate specificity of 4-nitrophenyl- -Dglucopyranoside (pNPG). The values of kinetic parameters, KM and Vmax, were 0.32±0.03 mM e 0.37±0.01 nmol/min, respectively. The enzyme doesn’t have transglycosylation mechanisms, indicating only hydrolytic activity. Some monosaccharides such as xylose and galactose increased the enzyme activity significantly, while glucose and arabinose inhibited it. The crystal structural model of the BaBgl revealed an N-terminal domain with fold like a TIM barrel, an intermediate sandwich α / β domain and a third C-terminal like FnIII domain. In this work we also studied the transglycosylation mechanisms of two β-glucosidases from Trichoderma harzianum (ThBgl1 and ThBgl2). Both enzymes exhibit transglycosylation reaction but the ThBgl1 showed a hydrolysis/transglycosylation ratio lower than the one for ThBgl2. Crystallographic structures shows a typical folding for GH family 1 β-glucosidases, folding in the form of a TIM barrel (α / β)8. However, ThBgl2 has a more polar active site and therefore, favorites the interaction with water molecules, promoting better the hydrolysis reaction when compared to ThBgl1. / A preocupação ambiental e com a qualidade de vida da população aliados com o esgotamento dos combustíveis fósseis, tem aumentado a busca por energias alternativas e sustentáveis. Neste contexto, a hidrólise da biomassa lignocelulósica é uma opção interessante para obtenção de bioetanol. A utilização de enzimas para conversão da biomassa lignocelulósica a açúcares fermentescíveis ainda é um processo de custo elevado, o que torna imprescindível os estudos de caracterização dos mecanismos dessas enzimas afim de torná-las economicamente mais viáveis. A reação catalisada por β-glicosidases é a última etapa da sacarificação da celulose, sendo de grande relevância na conversão da biomassa ignocelulósica. β- glicosidases hidrolisam terminais não reduzidos β-D-glicosil liberando β-D-glicose e GH 1 e GH 3 são as famílias dessas enzimas mais estudadas. Entretanto dados estruturais e funcionais das enzimas da família GH 3, ainda são escassos. O presente trabalho apresenta a caracterização bioquímica e estrutural de uma β-glicosidase de Bifidobacterium adolescentis (BaBgl). Essa enzima possui um domínio catalítico (CCD) e um domínio do tipo fibronectina III (FnIII) cuja função ainda é desconhecida. Os dados bioquímicos revelaram condições ótimas para atividade da enzima em pH entre 6,0 e 6,5, temperatura de 45 °C e especificidade pelo substrato sintético 4- nitrofenil-β-D-glicopiranosídeo (pNPG). Os parâmetros cinéticos KM e Vmáx apresentaram valores de 0,32±0,03 mM e 0,37±0,01 nmol/min respectivamente. A enzima não apresentou mecanismos de transglicosilação, indicando apenas atividade hidrolítica. Ensaios com monossacarídeos como xilose e galactose aumentaram significativamente a atividade enzimática enquanto que glicose e arabinose inibiram sua atividade. O modelo da estrutura cristalográfica da BaBgl revelou um domínio Nterminal enovelado como um barril TIM, um domínio intermediário na forma de sanduíche α/β e um terceiro domínio C-terminal do tipo FnIII. Neste trabalho também foram estudados os mecanismos de tranglicosilação de duas β-glicosidases de Trichoderma harzianum (ThBgl1 e ThBgl2), sendo que ambas realizam reação de transglicosilação, porém a ThBgl1 possui relação hidrólise/tranglicosilação menor que a ThBgl2. As estruturas cristalográficas demonstram um enovelamento típico para as β-glicosidases da família GH 1, com o enovelamento na forma de um barril TIM (α/β)8. Contudo, a ThBgl2 apresenta sítio ativo mais polar e portanto propício à interação com moléculas de água, favorecendo a reação de hidrólise quando comparada à ThBgl1.

Thesis (Ph. D. (Microbiology)) -- University of Limpopo, 2020 / The use of lignocellulosic biomass for bioethanol production is largely dependent on cost effective production of cellulase enzymes and most importantly, the availability of cellulases with sufficient β-glucosidase activity for complete hydrolysis of cellulose to glucose. Commercial cellulase preparations are often inefficient in the complete hydrolysis of cellulose to glucose. The addition of β-glucosidases to commercial cellulase preparations may enhance cellulolytic activity in the saccharification of cellulose to fermentable sugars. A β-glucosidase producing thermophilic bacterium, Anoxybacillus sp. KTC2 was isolated from a hot geyser in the Zambezi Valley, Zimbabwe. The bacterium identified through biochemical tests and 16S rDNA sequencing, had an optimal growth temperature and pH of 60˚C and pH 8, respectively. The β-glucosidase enzyme had an optimal temperature of 60˚C and a broad pH range for activity, between 4.5 and 7.5 with an optimum at pH 7. The β-glucosidase enzyme retained almost 100% activity after 24 hours’ incubation at 50˚C. The Anoxybacillus sp. KTC2 β-glucosidase was partially purified and a partial amino acid sequence obtained through MALDI-TOF analysis. The whole genome of Anoxybacillus sp KTC2 β-glucosidase was sequenced and a β-glucosidase gene identified. The deduced amino acid sequence corresponded to the peptide sequences obtained through MALDI-TOF, confirming the presence of the a β glucosidase on the genome of Anoxybacillus sp KTC2. Analysis of the deduced amino acid sequence revealed that the β-glucosidase enzyme belongs to the GH family 1. The β-glucosidase gene was isolated by PCR and successfully cloned into an E. coli expression system. The saccharification efficiency of the β-glucosidase enzyme was evaluated through the creation of enzyme cocktails with the commercial cellulase preparation, CelluclastTM. CelluclastTM with the Anoxybacillus sp KTC2 β-glucosidase were used to hydrolyse pure Avicel cellulose, at 50˚C over a 96 hour reaction time. The Anoxybacillus sp KTC2 β-glucosidase enabled a 25% decrease in the total cellulose loading without a decrease in the amount of glucose released. / University of Limpopo staff development programme and VLIR

Silver nanoparticles (AgNPs) are expected to enter aquatic systems, but there are limited data on how they might affect microbial communities in pathogen impaired streams. We examined microbial community responses to citrate-AgNP (10.9 ± 0.7 nm) and polyvinylpyrrolidone (PVP)-AgNP (11.0 ± 0.7 nm) based on microbial concentration and enzyme activity in sediment from a pathogen impaired stream. Addition of each nanoparticle to sediment caused at least a 69% decrease in microbial concentration (1,264 ± 93.6 to 127 ± 29.5 CFU/g) and a 62% decrease in β-glucosidase activity (11.7 ± 2.1 to 1.3 ± 0.3 μg/g/h). Each AgNP reduced alkaline phosphatase activity but their effects were not statistically significant. Sediment exposed to 0.108 mg Ag/kg of AgNO3 resulted in a 92% decrease in microbial concentration and a reduced enzyme activity which was not statistically significant. Measured total silver in sediments treated with AgNPs which exhibited significant inhibition effects on the microbial community ranged from 0.19 ± 0.02 to 0.39 ± 0.13 mg Ag/kg. These concentrations tested in this study are much lower than the expected concentrations (2-14 mg Ag/kg) in freshwater sediments. The results of this study demonstrate that AgNPs can alter microbial community activity and population size, which may lead to false negative fecal indicator bacteria detection and enumeration using methods that rely on β-glucosidase activity. We conclude that the presence of AgNPs in impaired streams and recreational waters can influence pathogen detection methods, potentially affecting public health risk estimates.

Made available in DSpace on 2016-06-02T19:56:45Z (GMT). No. of bitstreams: 1 3875.pdf: 1789055 bytes, checksum: a2495b6571816afdda74f70d8d9b300d (MD5) Previous issue date: 2011-02-25 / Universidade Federal de Sao Carlos / B-glucosidase (BG) is an important enzyme for several biotechnological applications. This enzyme plays an important role in hydrolyses of lignocellulosic biomass in order to produce second generation ethanol (2G ethanol). The enzimatic hydrolysis of cellulose requires the sinergystic action of endoglucanases, exoglucanases and β-glucosidases. Endo e exoglucanases are strongly inhibited by cellobiose and its accumulation into reaction medium decreases the hydrolysis rate. The supplementation of the reaction medium with BG can reduce the inhibition effect, leading to higher conversions of cellulose to glucose. In this work, BG was immobilized on different solid supports in order to obtain an active and stable derivative to be used in hydrolyses of sugarcane bagasse. BG was immobilized on glyoxyl-agarose (GA) and polyacrylic matrix (MP) at 25oC and pH 9.0 and 4.8, respectively. To improve the immobilization yield on glyoxyl-agarose at pH 9.0, a chemical amination of the enzyme surface was required. However, BG was inactivated during the immobilization reaction due to alkaline conditions that are required to immobilize enzymes on glyoxylagarose support. Nevertheless, the presence of a competitive inhibitor (glucose) during immobilization of BG preserved about 70% of the initial activity. However, the reduction step with sodium borohydride (end point of the reaction) drastically reduced the derivative activity even in the presence of glucose. The BG immobilization in presence of competitive inhibitor allowed the preparation of a derivative approximately 4 times more active than one prepared in inhibitor absence. On the other hand, the best derivative was prepared adsorbing the enzyme on polyacrylic resin covered with carboxylic groups. After four hours of reaction, the immobilization yield and the recovered activity were ca. 71% and 97%, respectively. Pretreated sugarcane bagasse (10% w/v, dry basis) was hydrolyzed at 50oC, pH 4.8 (50 mM sodium citrate buffer), for 24 h, using soluble cellulase (Acellerase 1500) in the enzyme/substrate ratio of 20 FPU/gcellulose. Hydrolyses under same conditions were performed by supplementing the reaction medium with BG immobilized on glyoxyl-agarose (BG-GA) or BG immobilized on polyacrylic resin (GA-MP) in the enzyme/substrate ratio of 120 U/gcellulose. Five batches were performed under - xi - conditions described above by reusing the immobilized BG and non-converted cellulose after thoroughly washing with distilled water. The supplementation of the reaction medium with immobilized BG enhanced the cellulose conversions in all batches. This behavior is due to the fact that BG removes cellobiose from the reaction medium, avoiding its accumulation, which could inhibit the endoglucanases and exoglucanases. However, a decrease of the cellulose conversion after the second batch was observed (cellulose conversion decreased from ca. 50% to 15-25%). Anyway, this work shows that supplementation of the commercial enzymatic complexes with immobilized BG is advantagous. However, the stabilization of the immobilized BG is still required. / B-Glicosidase (BG) é uma enzima de grande importância em inúmeras aplicações biotecnológicas. Essa enzima desempenha um papel muito importante na hidrólise enzimática da biomassa lignocelulósica visando a produção de etanol de segunda geração (etanol 2G). A hidrólise enzimática da celulose requer a ação sinergística de endoglicanases, exoglicanases e β-glicosidases. Endo e exoglicanases são fortemente inibidas por celobiose e seu acúmulo no meio reacional reduz a taxa de hidrólise. A suplementação do meio reacional com BG pode reduzir o efeito inibitório, levando a conversões maiores de celulose a glicose. Neste trabalho BG foi imobilizada em diferentes suportes sólidos visando a obtenção de um derivado ativo e estável para uso em reações de hidrólise de bagaço de cana-de-açúcar. BG foi imobilizada em glioxil-agarose (GA) e resina poliacrílica catiônica (MP) a 25ºC e pH 9,0 e 4,8, respectivamente. Para melhorar o rendimento de imobilização de BG em glioxilagarose a pH 9,0 foi necessária uma aminação química da superfície da enzima. Entretanto, BG era inativada durante a imobilização, devido às condições alcalinas requeridas para imobilização de enzimas em glioxilagarose. Contudo, a presença de um inibidor competitivo (glicose) durante a imobilização de BG preservou aproximadamente 70% da atividade inicial. Mesmo na presença de glicose, a etapa de redução com borohidreto de sódio (finalização da reação de imobilização) reduziu drasticamente a atividade da enzima imobilizada. A imobilização de BG na presença de inibidor competitivo permitiu a preparação de um derivado cerca de 4 vezes mais ativo que aquele preparado na ausência do inibidor. Por outro lado, o melhor derivado foi preparado adsorvendo BG em resina poliacrílica funcionalizada com grupos carboxílicos. Após quatro horas de reação, o rendimento de imobilização e a recuperação de atividade foram aproximadamente 71% e 97%, respectivamente. Bagaço de cana pré-tratado (10% m/v, base seca) foi hidrolisado a 50°C, pH 4,8 (tampão citrato de sódio 50 mM), por 24h, utilizando celulase solúvel (Acellerase 1500) na relação enzima/substrato de 20 FPU/gcelulose. Hidrólises nas mesmas condições foram realizadas - ix - suplementando o meio reacional com BG imobilizada em glioxil-agarose (BGGA) ou BG imobilizada em matriz poliacrílica (BG-MP) na relação enzima/substrato de 120 U/gcelulose. Cinco bateladas foram realizadas nas condições descritas acima, reutilizando a BG imobilizada e a celulose não convertida, após lavagem abundante com água destilada. A suplementação do meio reacional com BG imobilizada contribuiu para a obtenção de maiores conversões de celulose em todas as bateladas, devido ao fato da BG remover celobiose do meio reacional, evitando seu acúmulo, o qual poderia inibir a ação das endoglucanases e exoglucanases. Entretanto, observou-se uma redução da conversão de celulose após a segunda batelada (de 50% para 15-25%). De qualquer forma, esse trabalho mostra que a suplementação dos complexos enzimáticos comerciais com BG imobilizada é vantajosa, entretanto, a estabilidade da BG imobilizada ainda precisa ser melhorada.&#61472;

Plants have developed a number of ways how to minimise negative influence of the environment. As a consequence of stress action, plants carbohydrate metabolism is quite often influenced, esp. on the level of expression and activities of different enzymes and also several metabolites concentration. One of key enzymes of carbohydrate metabolism is invertase. The aim of this work was to find out, whether the activity of its isoforms (cytoplasmic, vacuolar and extracellular) in tobacco plants is influenced by Potato virus Y (PVY). It was shown, that activity of cytoplasmic invertase was not affected, but the activity of vacuolar and extracellular isoform was enhanced during potyviral infection. Hence, it is likely, that vacuolar and extracellular invertases are related to plant antiviral defence. The effect of PVY on other enzymes of carbohydrate metabolism and several metabolites content was studied. Activity of α-amylase and phosphorylase, starch-degrading enzymes, was strongly enhanced during potyviral infection. That is probably how plant cells get glucose, which is a key source of energy and metabolites for biosynthesis of different compounds. It may also serve as a signal molecule. Activity of other hydrolytic enzymes, β-glucosidase and β-hexosaminidase, was also slightly increased. There was no...