The human gut is host to a vast consortium of microorganisms, collectively referred to as the microbiota or microflora, which play important roles in health and disease. Current applications focus only on a single type of bacteria, which are not the most dominant numerically, and without detailed knowledge of the specific functions of these bacteria. A good indicator of the function of a bacterial species involves detailed analysis of its enzymes. Bacteroides thetaiotaomicron is one of the predominant bacterial species with a great representation of the carbohydrate processing enzymes, glycoside hydrolases in its proteome. This thesis reports the production and purification of one such enzyme, BT3299, suitable for kinetic and structural studies. The enzyme displayed a broad substrate specificity with a slight preference for 1-->3 and 1-->6 glycosidic linkages and longer chain saccharides. Future work will focus on structural analysis as an aid to the understanding of the enzyme function.

Hemicellulases are key components in the degradation of plant biomass and carbon flow in nature. Thermotoga hypogea is a bacterium that can grow anaerobically at 90°C. It utilizes carbohydrates and peptides as energy and carbon sources. Three hemicellulytic enzymes: β-xylosidase, α-L-arabinofuranosidase and acetylesterase were investigated. Xylan and xylose were the best substrates for the growth as well as for yielding high activity for all three enzymes in the cells. Glucose grown cells possessed the least amount of enzyme activity for all three enzymes. More than 87% ± 3.0 of β-xylosidase and α-L-arabinofuranosidase activities and 34% ± 11 of acetylesterase activity were associated with the cells. Arabinofuranosidase and acetylesterase were partially purified but β-xylosidase was purified to homogeneity using the Fast Performance Liquid Chromatography system. The latter enzyme has an apparent molecular mass of 75 kDa demonstrated through sodium dodecyl sulfate-polyacrylamide gel electrophoresis and a nondenatured weight of 130 kDa estimated by Gel-filtration. Its optimal temperature and pH-value for activity were 70°C and 6.0, respectively. The purified enzyme had a half life of 22 min at 70°C and pH 6.0. Among all tested substrates, the purified enzyme had specific activities of 44, 32, 4.5, 1.71 U/mg on p-nitrophenyl-β-xylopyranoside (pNβxp), 4-nitrophenyl-β-D-glucopyranoside (pNβgp), 4-nitrophenyl-α-L-arabinofuranoside (pNαLaf) and 4-nitrophenyl-α-D-xylopyranoside (pNαxp) respectively. The apparent Km of the xylosidase with pNβxp, was 2.6 mM and Vmax was 196 U/mg and for pNβgp the Km and Vmax values were 0.31 mM and 24 U/mg respectively. Based on N-terminal analysis, xylosidase showed high homology with Family 3 β-glucosidases.

Hemicellulases are key components in the degradation of plant biomass and carbon flow in nature. Thermotoga hypogea is a bacterium that can grow anaerobically at 90°C. It utilizes carbohydrates and peptides as energy and carbon sources. Three hemicellulytic enzymes: β-xylosidase, α-L-arabinofuranosidase and acetylesterase were investigated. Xylan and xylose were the best substrates for the growth as well as for yielding high activity for all three enzymes in the cells. Glucose grown cells possessed the least amount of enzyme activity for all three enzymes. More than 87% ± 3.0 of β-xylosidase and α-L-arabinofuranosidase activities and 34% ± 11 of acetylesterase activity were associated with the cells. Arabinofuranosidase and acetylesterase were partially purified but β-xylosidase was purified to homogeneity using the Fast Performance Liquid Chromatography system. The latter enzyme has an apparent molecular mass of 75 kDa demonstrated through sodium dodecyl sulfate-polyacrylamide gel electrophoresis and a nondenatured weight of 130 kDa estimated by Gel-filtration. Its optimal temperature and pH-value for activity were 70°C and 6.0, respectively. The purified enzyme had a half life of 22 min at 70°C and pH 6.0. Among all tested substrates, the purified enzyme had specific activities of 44, 32, 4.5, 1.71 U/mg on p-nitrophenyl-β-xylopyranoside (pNβxp), 4-nitrophenyl-β-D-glucopyranoside (pNβgp), 4-nitrophenyl-α-L-arabinofuranoside (pNαLaf) and 4-nitrophenyl-α-D-xylopyranoside (pNαxp) respectively. The apparent Km of the xylosidase with pNβxp, was 2.6 mM and Vmax was 196 U/mg and for pNβgp the Km and Vmax values were 0.31 mM and 24 U/mg respectively. Based on N-terminal analysis, xylosidase showed high homology with Family 3 β-glucosidases.

Cancer incidence is increasing and novel anticancer drugs with new mechanisms of action are essential for future chemotherapeutic treatment. Natural products have historically played an important role in the development of anti-cancer drugs and have potential to do so also in the future. In this thesis two classes of natural products are identified as possible drug lead candidates, and the mechanisms of their action are elucidated. Initially, in a screening of a compound library for cytotoxic effects in colon cancer cells, natural products with potent activity were identified. Based on their potency, and on previously reported activities in cancer cells, two main groups of compounds, cardiac glycosides (CGs) and gambogic acid (GA) analogues, were selected for further in-depth studies. The concentration-dependent cytotoxicity was confirmed in cell lines of different origin. Cardiac glycosides were mainly evaluated for their activity in colon cancer cells and in leukemic cells, whereas the GA analogues were studied using a resistance-based panel of ten human cancer cell lines. Using activity profiles and the ChemGPS-NP model, the compounds were compared, structurally and mechanistically, to standard chemotherapeutic drugs. The results from these analyses suggested that the CGs and the GA analogues act by mechanisms different from those of antimetabolites, alkylating agents, topoisomerase I and II inhibitors, or tubulin-active agents. By analysis of drug-induced gene expression, one GA analogue, dihydro GA, was identified as a possible inhibitor of the ubiquitin-proteasome system (UPS), and the CGs showed similarities to protein synthesis inhibitors. Starting from these hypotheses, we further investigated the mechanisms of actions on a molecular level. The results showed that GA and dihydro GA act as inhibitors of the 20S proteasome chymotrypsin activity, leading to accumulation of ubiquitinated proteins. The CGs were confirmed to inhibit protein synthesis in colon cancer cell lines. However, interestingly, in leukemia cell lines, it seemed that the CGs act through a different, yet unexplored, mechanism of action. The leukemic cells (pre-B and T-ALL) were particularly susceptible to the cytotoxic effects of CGs, including at concentrations that may be achievable in the clinic.

Le but de mon projet de doctorat est la recherche de chitosanases thermostables qui peuvent mener la réaction d'hydrolyse du chitosane à de hautes températures. La procédure mise au point pour isoler ces chitosanases était planifiée pour moduler l'effet antimicrobien du chitosane qui augmente avec son poids moléculaire. Les objectifs spécifiques de ce projet sont, mettre au point un nouveau dosage de Csn, purifier, caractériser et cloner le gène des chitosanases les plus thermostables sélectionnées et mettre au point un milieu de production de chitosanase. La première étape du projet est la recherche de nouvelles chitosanases thermostables, via un criblage ciblé de bactéries productrices de chitosanases. En effet, une nouvelle méthode d'enrichissement était utilisée par l'ajout de chitosane de différents poids moléculaires à notre source bactérienne, soit les composts. La deuxième étape, est la réalisation d'un dosage de l'activité chitosanase en utilisant le soluble-dyed Remazol Brillant Bleu-Chitosane (sRBB-C) qui a été mise au point pour détecter à grande échelle une activité chitosanase de manière facile et rapide. Enfin, la troisième étape est un test de thermostabilité en présence de substrat, appliqué à des chitosanases choisies, pour sélectionner les plus performantes à l'étape de la purification. Parmi le lot de chitosanases testées, la chitosanase notée Csn1794 s'est distinguée par sa thermostabilité à 70 degrés C, ainsi elle a été retenue pour des études plus approfondies. Les études biochimiques réalisées sur la Csn1794 après purification ont révélé qu'elle a un poids moléculaire de 40 kDa, un pH optimal de 4.8 et des K[indice inférieur m] et k[indices inférieurs cat] de 0.042 mg/ml et 7588 min[indices supérieurs -1] respectivement. Le temps de demi-vie de la Csn1794 en présence de chitosane est plus de 20 heures à 70 degrés C. L'activité de la Csn1794 varie légèrement avec le degré d'acétylation du chitosane, elle hydrolyse la carboxyméthyl-cellulose, mais pas la chitine. Le clonage du gène de la Csn1794 par génétique inverse a permis de déterminer sa séquence. Ce gène codé pour une protéine de 441 acides aminés. La Csn1794 appartient à la famille 8 des glycosides hydrolases (GH8). Le rang taxonomique de l'isolat produisant la Csn1794 a été déterminé par des méthodes classiques ainsi que par des tests de biologie moléculaire. Les résultats obtenus indiquent qu'il s'agit d'un isolat appartenant à une espèce non caractérisée appartenant au genre Paenibacillus qu'on a appelé Paenibacillus sp. 1794. Enfin, la méthode de plan d'expériences était utilisée pour mettre au point le milieu de production de la Csn1794. Les essais réalisés par les plans d'expériences Plackett-Burman ont permis non seulement de définir un milieu de base pour la production de la Csn1794, mais aussi les oligosaccharides et le sucrose se sont distingués comme facteurs à effet nettement positif sur la production de la Csn1794. Les essais par plans d'expérience Box-Hunter ont permis l'étude d'interactions entre les différents facteurs dont le niveau était déterminé par les plans Taguchi. Les résultats obtenus indiquent qu'en plus de milieu de base, l'ajout de 10g/l de glucosamine, 7g/l d'oligosaccharide et 4g/l de sucrose constitue la meilleure combinaison pour un milieu qui permet de produire une moyenne de 7U/ml de Csn1794 d'une manière constante. En conclusion, nous disposons d'une nouvelle chitosanase thermostable, facile à produire et à purifier, qui sera un outil adéquat pour l'application au niveau industriel. Ceci va non seulement permettre de mener le processus d'hydrolyse de chitosane à haute température, mais aussi d'utiliser de grandes concentrations de substrat sans que la viscosité ne devienne excessive. Au niveau de la recherche fondamentale, la Csn1794 peut nous apporter plus d'informations d'une part, sur la thermostabilité des enzymes et d'autre part, sur les enzymes de la famille GH8, notamment les chitosanases.

Ready-to-eat meat products such as dry-fermented sausages have been associated with foodborne outbreaks despite the multiple hurdles used in the manufacturing process to prevent growth of pathogens. As a result, new strategies such as natural products with antimicrobial activity are being used to control pathogens of importance like Escherichia coli O157:H7. This study investigated how different concentrations and sources of mustard can influence its antimicrobial activity against E. coli O157:H7 in dry-fermented sausage, as well as the contribution of residual myrosinase enzyme in mustard to this process. The genetic basis for the degradation of mustard glucosinolate by E. coli O157:H7, which is associated with the antimicrobial action of mustard, was also characterized. The ability of E. coli O157:H7 to withstand inhibitory allyl isothiocyanate (AITC) concentrations and the role of the two-component BaeSR system as a defense mechanism against AITC was also investigated. Results showed that 4% (w/w) deodorized yellow mustard powder was effective to control E. coli O157:H7 in dry-fermented sausage at 28 d. The presence of endogenous plant myrosinase in the mustard powder or meal enhanced E. coli O157:H7 reduction rates. Fully-deodorized, deoiled, yellow mustard meal as low as 2% (w/w) containing either 0.1% or 0.2% of residual plant myrosinase achieved the same results as 4% (w/w) mustard powder also containing similar residual myrosinase. Regardless of the type of mustard, the antimicrobial activity of yellow mustard derivatives were more pronounced than those of Oriental mustard. The initial genetic assessment through in silico analysis found similarity between plant myrosinase and enzymes encoded by genes (bglA, ascB, and chbF) from β-glucosidase families in E. coli O157:H7 strains. After disruption of these genes using lambda-red replacement, single (∆bglA, ∆ascB, ∆chbF) and double (∆bglAascB, ∆chbFascB, ∆chbFbglA) mutant strains were created and assessed for glucosinolate degradation. The comparison of the gene expression profiles and changes in the extent of sinigrin degradation by different mutants suggested that ascB have a prominent role in the degradation of this β-glucoside by E. coli O157:H7. E. coli O157:H7 did not develop resistance to AITC, the essential oil formed from sinigrin degradation that is responsible for the antimicrobial activity of Oriental mustard.

Although carbohydrates are a principal component of the human diet, the mechanism of the final stages of starch digestion is not fully understood. One approach to treating metabolic diseases such as type II diabetes, obesity, and congenital sucrase isomaltase deficiency is inhibition of intestinal α-glucosidases and pancreatic α-amylases. Intestinal α-glucosidases, sucrase isomaltase (SI) and maltase glucoamylase (MGAM), are responsible for the final step of starch hydrolysis in mammals: the release of free glucose. MGAM and SI consist of two catalytic subunits: N-terminal and C-terminal, with overlapping, but variant substrate specificities. The objective of this thesis is to increase the understanding of the differential substrate specificity seen in the catalytic subunits of SI and MGAM. Through inhibitor studies, the structural and biochemical differences between the enzymatic subunits are explored, illustrating that each individual catalytic subunit can be selectively inhibited. In Chapter 3, homology models of ctSI and ctMGAM-N20 are presented, giving insight into the residues hypothesized to impact substrate specificity, enhancing our understanding of the functionality of these enzymatic subunits and overlapping substrate specificity. The structural implications of mutations seen in ntSI in CSID patients and the potential functional and structural implications are discussed in Chapter 4 in addition to the prevalence of SNPs in the SI gene in different populations. The mammalian α-glucosidases are compared to the 3 Å structure of CfXyl31, a Family 31 glycoside hydrolase from Cellulomonas fimi. Comparison to Family 31 glycoside hydrolases of known structure gives rise to possible mutations proposed to mimic ntMGAM α-glucosidase activity. Through inhibitor studies, homology models, examining mutations found in disease states such as congenital sucrase isomaltase deficiency, and investigating a bacterial family 31 glycoside hydrolase from Cellulomonas fimi, the active site characteristics and substrate specificities of SI and MGAM are better understood.

As sessile organisms, plants are unable to escape from attack by herbivorous insects. To cope with this pressure, plants have evolved several defense strategies, including the production of secondary metabolites, specialized chemicals with ecological functions. Most studies have focused on the role of secondary metabolites in plant defense against chewing insects. Little is known about what compounds are present in phloem sap and how they affect phloem feeding insects. Therefore, I investigated the effects of phenolic compounds on phloem feeders, using Chaitophorus aphids in bioassays with wildtype and transgenic poplar overexpressing the transcription factor MYB 134, which results in elevated levels of tannins and reduced levels of phenolic glycosides. Aphids produced significantly more offspring on MYB 134 plants but showed a significant preference for lower tannin leaf tissue. Analysis of poplar phloem exudates and aphid extracts provides direct evidence that the phenolic glycosides salicin, salicortin and tremulacin are present in poplar phloem and are ingested by aphids. These results are discussed in relation to what is driving the differences in aphid fecundity and choice between plant types. / Graduate / 0309 / 0307 / 0329 / alphareghanwong@gmail.com

The use of 4-acetoxy-2,2-dimethylbutanoyl protecting group for the C2-hydroxyl allows the selective formation of β-glycosides without producing α-glycosides. This very bulky protecting group can be removed under mild conditions.

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