Seventeen species of facultative anaerobic bacteria belonging to three genera (Serratia, Cellulomonas, and Corynebacterium) were screened for the production of xylitol; a sugar alcohol used as a sweetener in the pharmaceutical and food industries. A chromogenic assay of both solid and liquid cultures showed that 10 of the 17 species screened could grow on D-xylose and produce detectable quantities of xylitol during 24-96 h of fermentation. The ten bacterial species were studied for the effect of environmental factors, such as temperature, concentration of D-xylose, and aeration, on xylitol production. Under most conditions, Corynebacterium sp. NRRL B 4247 produced the highest amount of xylitol. The xylitol produced by Corynebacterium sp. NRRL B 4247 was confirmed by mass spectrometry. Corynebacterium sp. NRRL B 4247 was studied for the effect of initial D-xylose concentration, glucose, glyceraldehyde, and gluconate, aeration, and growth medium. Corynebacterium sp. NRRL B 4247 produced xylitol only in the presence of xylose, and did not produce xylitol when gluconate or glucose was the substrate. The highest yield of xylitol produced in 24 h (0.57 g/g xylose) was using an initial D-xylose concentration of 75 g/l. Under aerobic conditions the highest xylitol yield was 0.55 g/g while under anaerobic conditions the highest yield was 0.2 g/g. Glyceraldehyde in concentrations greater than 1 g/l inhibited Corynebacterium sp. B 4247 growth and xylitol production. Corynebacterium sp. NRRL B 4247 culture grown in the presence of potassium gluconate (96 g/l) for 48 h and on addition of D-xylose to the media increased accumulation to 10.1 g/l of xylitol after 150 h. Corynebacterium sp. NRRL B 4247 exhibited both NADH and NADPH-dependent xylose reductase activity in cell-free extracts. The NADPH-dependent activity was substrate dependent. The activity was 2.2-fold higher when DL-glyceraldehyde was used as substrate than with D-xylose. In cell-free extracts the difference in xylose reductase and xylitol dehydrogenase activity was highest at 24 h, whereas for cell cultures that were grown in gluconate and xylose, the difference in the reductase and dehydrogenase activities was highest at 12 h after xylose addition. The NAD+ dependent xylitol dehydrogenase activity was low compared to the cells grown without gluconate. The molecular weight of NADPH-dependent xylose reductase protein obtained by gel filtration chromatography was 58 kDa. Initial purification was performed on a DE-52 anion exchange column. Purification using Red Sepharose affinity column resulted in a 58 kDa protein on the SDS PAGE gel and was further purified on a Mono-Q column. The activity stained band on the native gel yielded 58, 49, 39 and 30 kDa bands on the denaturing gel. The peptides of the 58 kDa protein of Corynebacterium sp. B 4247 sequenced by mass spectrometry, identified with E2 and E3 (Bacillus subtilis) components of multi-enzyme system consisting of pyruvate dehydrogenase complex, 2-oxoglutarate dehydrogenase complex and oxo-acid dehydrogenase complex. A 75% match was shown by the peptide "QMSSLVTR" with E-value of 8e-04 to the Saccharomyces cerevisiae protein that was capable of reducing xylose to xylitol. The peptide "LLNDPQLILMEA" had conserved match "LL + DP" over several aldose reductases. The xylose reductase of the yeast Candida tropicalis ATCC 96745 was also purified. The molecular weight of the yeast NADPH-dependent xylose reductase was about 37 kDa on an SDS PAGE / Ph. D.

<p>U radu je ostvarena vi&scaron;efazna transformacija D-ksiloze u pogodno funkcionalizovane derivate koji su kuplovanjem sa siliranim timinom selektivno dali nukleozide sa beta-konfiguracijom na anomernom centru. Takođe, u cilju sinteze nukleozida L-serije, ispitana je mogućnost izomerizacije nekih derivata D-&scaron;ečera u odgovarajuće L-stereoizomere.</p> / <p>Muitistep transformation of D-xylose to suitabte functional derivatives were achieved. Coupling of these derivatives with silylated thymine gave the nucleosides with beta-configuration on anomeric centre. In order to synthesis nucleosides of L-series, the possibility for isomerization of some kinds D-sugar derivatives in corresponding L-stereisomeric compounds, were investigatet, too.</p>

Au cours de ce projet de recherche, nous nous sommes intéressés à la synthèse de motifs hétérospiraniques énantioenrichis. De ce fait, notre équipe a pu élaborer une nouvelle voie synthétique pouvant conduire à la synthèse de molécules possédant des structures bicycliques spiraniques diverses. Cette voie de synthèse inédite est articulée sur une réaction de nitroso Diels-Alder. Le contrôle de la stéréosélectivité ainsi que le contrôle de la régiosélectivité, peu décrit dans la littérature, ont été spécifiquement étudiés lors de ces travaux. Nos différentes études ont permis de mieux appréhender ces aspects de la réaction de nitroso Diels-Alder. Deux approches différentes ont d’ailleurs été développées au cours de ces travaux. Celles-ci ont toutes deux conduit a un contrôle total de la régiosélectivité de cette cycloaddition. Les cycloadditions réalisées par une réaction utilisant un diénophile de type nitrosopyridine et catalysées par une source de cuivre chiral ont conduit aux cycloadduits précurseurs d’azaspirobicycles avec une énantiosélectivité modeste. D’autres cycloadditions utilisant un dienophile chiral de type chloronitroso dérivé du D-xylose ont permis la synthèse de précurseurs de bicycles oxaspiraniques avec des excès énantiomériques supérieurs à 95%. Cette dernière approche a permis la synthèse de spiroethers par une réaction d’ouverture de liaison N-O ainsi qu’une réaction de substitution nucléophile intramoléculaire, tandis que des spirolactones ont été obtenus par oxydation du diol résultant de l’ouverture de la liaison N-O. La fonctionnalisation de ces structures a été possible en engageant leur fonction vinyl triflate dans des couplages de Suzuki. Il a ainsi été possible de synthétiser 9 structures différentes oaxaspiraniques dont 5 de façons énantiosélectives. / During this research, we were interested in the synthesis of enantiopur heterospiranic bicycles. We therefore developed a new synthetic route towards the synthesis of molecules with different spirocyclic structures. This novel synthetic route features a nitroso Diels-Alder cycloaddition as key step. The total control of the stereoselectivity and the regioselectivity of the reaction, rarely described in the literature, have been specifically studied during this work. This study allows us to have a better understanding of this reaction. Two different approaches have been developed in this work. They both led to total control of the regioselectivity of this cycloaddition. Cycloadditions performed by reactions using a nitrosopyridine dienophile and catalyzed by a chiral source of copper allows the synthesis of cycloadducts precursor of azaspirocycles with a modest enantioselectivity. Cycloadditions using a chloronitroso chiral dienophile derived from xylose allowed the synthesis of oxaspiraniques precursors with enantioselective excess of at least 95%. The last approach was finally validated by the synthesis of various spiroethers and spirolactones through N-O bond cleavage an intramolecular cyclizations. Finally, the vinyl triflate function of the spirolactones and spiroethers was engaged in Suzuki couplings to introduce molecular diversity at a late stage allowing the synthesis of 9 different spiranic structures including 5 enantioenriched.

A parede celular vegetal, estrutura essencial para as plantas, é extremamente importante para a economia humana, já que apresenta diversas utilidades, como por exemplo, fabricação de papel, fibras de vestuário, construção civil, entre outras. A maior parte da parede celular vegetal primária (aproximadamente 90%), é formada por polissacarídeos como celulose, hemiceluloses e pectinas. Os monossacarídeos, unidades formadoras dos polissacarídeos, são sintetizados, nas plantas, a partir de diferentes açúcares nucleotídeos, sendo que, o suprimento desses, pode afetar a biossíntese dos polissacarídeos da parede celular. Visando analisar o impacto da alteração do fluxo metabólico do carbono na composição da parede celular, o presente projeto de pesquisa teve como objetivo alterar a composição dos polissacarídeos da parede celular de Nicotiana tabcum, através da modulação da expressão do gene uxs, responsável pela codificação da enzima UDP-D-glucuronato descarboxilase (UDPGlcADC, EC 4.1.1.35) que converte UDP-D-glucuronato em UDP-D-xilose, importante açúcar nucleotídeo, precursor do monossacarídeo xilose. Para isso, após a clonagem do gene uxs de ervilha, foram obtidas plantas transgênicas de tabaco superexpressando esse gene. Diversas análises foram realizadas para determinação da composição química da parede celular primária e secundária dessas plantas. Pela análise de FTIR da parede celular primária, verificou-se que três linhagens transgênicas apresentaram espectrotipos consistentes, indicando uma redução na quantidade de pectinas e ligações ésteres carboxílica nessas linhagens transgênicas. Apesar de não terem sido detectadas alterações na proporção dos monossacarídeos ramnose, xilose, arabinose, manose e galactose, e na quantidade de celulose, na parede celular primária das plantas transgênicas, foram observadas diferenças na proporção de galactose não esterificada, nas linhagens que apresentaram espectrotipo. Com relação à parede celular secundária, observou-se que algumas linhagens transgênicas apresentaram maior concentração de lignina solúvel relacionada a uma redução no conteúdo de lignina insolúvel. / The plant cell wall is not only an essential structure for plants, but also an extremely important raw material in human economy. The plant cell wall has diverse utilities, for example, papermaking, textile fiber, civil construction. Polysaccharides, such as cellulose, hemicelluloses and pectins, are the major components of the primary plant cell wall (approximately 90%). These polysaccharides are formed by monosaccharides, which are synthesized in the plant from different nucleotide sugars. The suppliment of the nucleotide sugars can affect plant cell wall polysaccharides biosynthesis. Aiming at analyzing the impact of the alteration in the metabolic carbon flux on cell wall composition, the objective of this research project was to alterate the plant cell wall polysaccharides composition by the modulation of the uxs gene. This gene encodes the UDP-D-glucuronic acid decarboxylase enzyme (UDPGlcADC, EC 4.1.1.35) that promotes the conversion of UDP-D-glucuronic acid to UDP-D-xylose, an important sugar nucleotide precursor of xylose monosaccharide. To achieve this goal, the pea uxs gene was cloned and transgenic tobacco plants overexpressing this gene were obtained. Several analyses were performed to determinate the primary and secondary cell wall composition of those transgenic plants. The primary cell wall analysis by FTIR identified three transgenic lines that show different spectrotypes compared to wild type and those transgenic spectrotypes had the same features. The results indicate a reduction of pectin and ester carbonyl binding in the transgenic plants. No alterations were detected in the monosaccharide (rhamnose, xylose, arabinose, manose and galactose) proportions and the amount of cellulose in the primary cell wall of the transgenic plants. Nevertheless, differences in the proportion of unesterified galactose were observed in the same transgenic lines that showed spectrotypes. With regard to secondary cell wall, some transgenic lines showed an increase in soluble lignin which is related to a reduction in insoluble lignin.

A parede celular vegetal, estrutura essencial para as plantas, é extremamente importante para a economia humana, já que apresenta diversas utilidades, como por exemplo, fabricação de papel, fibras de vestuário, construção civil, entre outras. A maior parte da parede celular vegetal primária (aproximadamente 90%), é formada por polissacarídeos como celulose, hemiceluloses e pectinas. Os monossacarídeos, unidades formadoras dos polissacarídeos, são sintetizados, nas plantas, a partir de diferentes açúcares nucleotídeos, sendo que, o suprimento desses, pode afetar a biossíntese dos polissacarídeos da parede celular. Visando analisar o impacto da alteração do fluxo metabólico do carbono na composição da parede celular, o presente projeto de pesquisa teve como objetivo alterar a composição dos polissacarídeos da parede celular de Nicotiana tabcum, através da modulação da expressão do gene uxs, responsável pela codificação da enzima UDP-D-glucuronato descarboxilase (UDPGlcADC, EC 4.1.1.35) que converte UDP-D-glucuronato em UDP-D-xilose, importante açúcar nucleotídeo, precursor do monossacarídeo xilose. Para isso, após a clonagem do gene uxs de ervilha, foram obtidas plantas transgênicas de tabaco superexpressando esse gene. Diversas análises foram realizadas para determinação da composição química da parede celular primária e secundária dessas plantas. Pela análise de FTIR da parede celular primária, verificou-se que três linhagens transgênicas apresentaram espectrotipos consistentes, indicando uma redução na quantidade de pectinas e ligações ésteres carboxílica nessas linhagens transgênicas. Apesar de não terem sido detectadas alterações na proporção dos monossacarídeos ramnose, xilose, arabinose, manose e galactose, e na quantidade de celulose, na parede celular primária das plantas transgênicas, foram observadas diferenças na proporção de galactose não esterificada, nas linhagens que apresentaram espectrotipo. Com relação à parede celular secundária, observou-se que algumas linhagens transgênicas apresentaram maior concentração de lignina solúvel relacionada a uma redução no conteúdo de lignina insolúvel. / The plant cell wall is not only an essential structure for plants, but also an extremely important raw material in human economy. The plant cell wall has diverse utilities, for example, papermaking, textile fiber, civil construction. Polysaccharides, such as cellulose, hemicelluloses and pectins, are the major components of the primary plant cell wall (approximately 90%). These polysaccharides are formed by monosaccharides, which are synthesized in the plant from different nucleotide sugars. The suppliment of the nucleotide sugars can affect plant cell wall polysaccharides biosynthesis. Aiming at analyzing the impact of the alteration in the metabolic carbon flux on cell wall composition, the objective of this research project was to alterate the plant cell wall polysaccharides composition by the modulation of the uxs gene. This gene encodes the UDP-D-glucuronic acid decarboxylase enzyme (UDPGlcADC, EC 4.1.1.35) that promotes the conversion of UDP-D-glucuronic acid to UDP-D-xylose, an important sugar nucleotide precursor of xylose monosaccharide. To achieve this goal, the pea uxs gene was cloned and transgenic tobacco plants overexpressing this gene were obtained. Several analyses were performed to determinate the primary and secondary cell wall composition of those transgenic plants. The primary cell wall analysis by FTIR identified three transgenic lines that show different spectrotypes compared to wild type and those transgenic spectrotypes had the same features. The results indicate a reduction of pectin and ester carbonyl binding in the transgenic plants. No alterations were detected in the monosaccharide (rhamnose, xylose, arabinose, manose and galactose) proportions and the amount of cellulose in the primary cell wall of the transgenic plants. Nevertheless, differences in the proportion of unesterified galactose were observed in the same transgenic lines that showed spectrotypes. With regard to secondary cell wall, some transgenic lines showed an increase in soluble lignin which is related to a reduction in insoluble lignin.

In order to decrease our dependence on non-renewable petrochemical resources, it is urgently required to establish sustainable biomass-based biorefineries. Replacing fossil fuels with renewable biomass as a raw feedstock for the production of chemicals and biofuels is a main driving force of biorefinering. Almost all kinds of biomass can be converted to biochemicals, biomaterials and biofuels via continuing advances on conversion technologies. In vitro synthetic biology is an emergent biomanufacturing platform that circumvents cellular constraints so that it can implement some biotransformations better than whole-cell fermentation, which spends a fraction of energy and carbon sources for cellular duplication and side-product formation. In this work, the in vitro synthetic (enzymatic) biosystem is used to produce a future carbon-neutral transportation fuel, hydrogen, and two high-value chemicals, a sugar phosphate and a highly marketable sweetener, representing a new portfolio for new biorefineries. Hydrogen gas is a promising future energy carrier as a transportation fuel, offering a high energy conversion efficiency via fuel cells, nearly zero pollutants produced to end users, and high mass-specific and volumetric energy densities compared to rechargeable batteries. Distributed production of cost-competitive green hydrogen from renewable biomass will be vital to the hydrogen economy. Substrate costs contribute to a major portion of the production cost for low-value bulk biocommodities, such as hydrogen. The reconstitution of 17 thermophilic enzymes enabled to construct an artificial enzymatic pathway converting all glucose units of starch, regardless of the branched and linear contents, to hydrogen gas at a theoretic yield (i.e., 12 H2 per glucose), three times of the theoretical yield from dark microbial fermentation. Using a biomimetic electron transport chain, a maximum volumetric productivity was increased by more than 200-fold to 90.2 mmol of H2/L/h at a high starch concentration from the original study in 2007. In order to promote economics of biorefineries, the production of a sugar phosphate and a fourth-generation sweetener is under development. D-xylulose 5-phosphate (Xu5P), which cannot be prepared efficiently by regular fermentation due to the negatively charged and hydrophilic phosphate groups, was synthesized from D-xylose and polyphosphate via a minimized two-enzyme system using a promiscuous activity of xylulose kinase. Under the optimized condition, 32 mM Xu5P was produced from 50 mM xylose and polyphosphate, achieving a 64% conversion yield, after 36 h at 45 °C. L-arabinose, a FDA-approved zero-calorie sweetener, was produced from D-xylose via a novel enzymatic pathway consisting of xylose isomerase, L-arabinose isomerase and xylulose 4-epimerase (Xu4E). Promiscuous activity of Xu4E, a monosaccharide C4-epimerase, was discovered for the first time. Directed evolution of Xu4E enabled to increase the catalytic function of C4-epimerization on D-xylulose as a substrate by more than 29-fold from the wild-type enzyme. Together, these results demonstrate that the in vitro synthetic biosystem as a feasible biomanufacturing platform has great engineering, and can be used to convert renewable biomass resources to a spectrum of marketable products and renewable energy. As future efforts are addressed to overcome remaining challenges, for example, decreasing enzyme production costs, prolonging enzyme lifetime, engineering biomimetic coenzymes to replace natural coenzymes, and so on. This in vitro synthetic biology platform would become a cornerstone technology for biorefinery industries and advanced biomanufacturing (Biomanufacturing 4.0). / Ph. D. / The carbon cycle is the circulation and transformation of carbon back and forth between living things and the environment. With the fixed amount of carbon dioxide in the atmosphere, the carbon cycle has been in the balance of exchanges between living things and the environment. As we evolve with increasing demand on crude oil, however, significant amounts of carbon are being released into the atmosphere much faster than they would have been released naturally. This rapid release is the primary cause of currently observed global warming. In order to decrease our dependence on petrochemical products, the biorefinery was introduced as the sustainable processing of biomass into a spectrum of alternatives to products from petrochemical refineries. Almost all kinds of biomass can be converted to biochemicals, biomaterials and biofuels via continuing advances on conversion technologies. In vitro synthetic biology is an emergent biomanufacturing platform that circumvents whole cell’s constraints, so that it can implement some biotransformations better than whole-cell fermentation spending a significant fraction of energy and carbon sources for cellular duplication and side-product formation. In this work, the in vitro synthetic (enzymatic) biosystem is used to produce a future carbon-neutral transportation fuel, hydrogen gas, and two high-value chemicals, a sugar phosphate and a highly marketable sweetener, representing a new portfolio for new biorefineries. Hydrogen gas is a promising energy carrier as a transportation fuel, offering a high energy conversion efficiency via fuel cells, nearly zero pollutants produced to end users, and high mass-specific and volumetric energy densities compared to rechargeable batteries. Distributed production of cost-competitive green hydrogen will be vital to the hydrogen economy. We demonstrated an in vitro 17-thermophilic enzyme pathway that can convert all glucose units of starch to hydrogen a theoretic yield, which is three times of the theoretical yield from dark microbial fermentation. D-xylulose 5-phosphate (Xu5P), which cannot be prepared efficiently by regular fermentation due to the negatively charged and hydrophilic phosphate groups, was synthesized from D-xylose and polyphosphate via a minimized two-enzyme system using a promiscuous activity of xylulose kinase. This minimal in vitro enzymatic pathway was optimized for improved conversion yield and productivity. L-arabinose, a FDA-approved zero-calorie sweetener, was also produced from D-xylose via a novel enzymatic pathway consisting of xylose isomerase, L-arabinose isomerase and hypothetical enzyme xylulose 4-epimerase (Xu4E), a monosaccharide 4-epimerase that can convert D-xylulose to L-ribulose. Xu4E activities due to substrate promiscuity of some natural 4-epimerases were discovered for the first time. Three rounds of directed evolution have been conducted to increase the catalytic function of carbon 4-epimerization on D-xylulose. As the result, the catalytic activity of Xu4E was improved by more than 29-fold from the wild-type enzyme.

<p>U radu je ostvarena sinteza četiri prirodna proizvoda, goniobutenolida A i B,<br />krasalaktona D i 3-deoksi-kardiobutanolida i 32 derivata i analoga polazeći iz<br />D-glukoze. Sinteza prirodnog stiril-laktona, kardiobutanolida&nbsp; i njegova 4<br />derivata je izvedena polazeći iz&nbsp; D-ksiloze.&nbsp; Ispitan je uticaj sintetizovanih<br />jedinjenja&nbsp; na inhibiciju rasta 10 tumorskih i jedne zdrave ćelijske linije.<br />Uspostavljene su i&nbsp; korelacije izmedju strukture i antiproliferativne aktivnosti&nbsp;(SAR) i ispitan je mehanzam antitumorskog dejstva.</p> / <p>Synthesis of four natural products: goniobutenolide A and B,&nbsp;crassalactone D, 3-deoxy-cardiobutanolide and their 32 analogues&nbsp;and derivatives is accomplished starting from&nbsp; D-glucose. Synthesis of natural styryl lactone cardiobutanolide and its four derivatives is &nbsp;achieved&nbsp; starting&nbsp; from&nbsp; D-xylose.&nbsp; Synthesized natural lactones, their analogues and derivatives were evaluated for their antiproliferative activity against ten malignant cell lines&nbsp; as well as against a single normal cell line. Influence of functional groups on antitumour activity was established by correlating structures of synthesized compounds&nbsp; with&nbsp; their&nbsp; biological&nbsp; activity (SAR).&nbsp; Also, mechanism of antitumour action was investigated.</p>