Academic literature on the topic 'Entner-Doudoroff'

The pathways of glucose catabolism were examined in haploid and diploid strains of the smut fungus Ustilago violacea. Radiorespirometric studies indicated that both of the haploid mating types and diploid strains of this basidiomycete catabolized glucose through the Embden–Meyerhof and hexose monophosphate shunt pathways. The Entner–Doudoroff pathway was not utilized by any of the strains examined. Radiorespirometric data also suggested functioning of an active tricarboxylic acid cycle. In vitro enzyme assays established the presence in this organism of all the enzymes integral to the operative pathways plus the presence of the enzymes of the glyoxylate cycle. Enzyme activities specific to the Entner–Doudoroff pathway were not detected. No major differences in the routes of glucose dissimilation were found between the two haploid mating types or between haploid and diploid forms of this organism.

ABSTRACT A cyclic version of the Entner-Doudoroff pathway is used byPseudomonas aeruginosa to metabolize carbohydrates. Genes encoding the enzymes that catabolize intracellular glucose to pyruvate and glyceraldehyde 3-phosphate are coordinately regulated, clustered at 39 min on the chromosome, and collectively form thehex regulon. Within the hex cluster is an open reading frame (ORF) with homology to the devB/SOLfamily of unidentified proteins. This ORF encodes a protein of either 243 or 238 amino acids; it overlaps the 5′ end of zwf (encodes glucose-6-phosphate dehydrogenase) and is followed immediately by eda (encodes the Entner-Doudoroff aldolase). The devB/SOL homolog was inactivated in P. aeruginosa PAO1 by recombination with a suicide plasmid containing an interrupted copy of the gene, creating mutant strain PAO8029. PAO8029 grows at 9% of the wild-type rate using mannitol as the carbon source and at 50% of the wild-type rate using gluconate as the carbon source. Cell extracts of PAO8029 were specifically deficient in 6-phosphogluconolactonase (Pgl) activity. The cloned devB/SOL homolog complemented PAO8029 to restore normal growth on mannitol and gluconate and restored Pgl activity. Hence, we have identified this gene as pgland propose that the devB/SOL family members encode 6-phosphogluconolactonases. Interestingly, three eukaryotic glucose-6-phosphate dehydrogenase (G6PDH) isozymes, from human, rabbit, and Plasmodium falciparum, contain Pgl domains, suggesting that the sequential reactions of G6PDH and Pgl are incorporated in a single protein. 6-Phosphogluconolactonase activity is induced in P. aeruginosa PAO1 by growth on mannitol and repressed by growth on succinate, and it is expressed constitutively in P. aeruginosa PAO8026 (hexR). Taken together, these results establish that Pgl is an essential enzyme of the cyclic Entner-Doudoroff pathway encoded by pgl, a structural gene of the hex regulon.

Sulfoquinovose (SQ; 6-deoxy-6-sulfoglucose) is the polar head group of the plant sulfolipid SQ-diacylglycerol, and SQ comprises a major proportion of the organosulfur in nature, where it is degraded by bacteria. A first degradation pathway for SQ has been demonstrated recently, a “sulfoglycolytic” pathway, in addition to the classical glycolytic (Embden–Meyerhof) pathway in Escherichia coli K-12; half of the carbon of SQ is abstracted as dihydroxyacetonephosphate (DHAP) and used for growth, whereas a C3-organosulfonate, 2,3-dihydroxypropane sulfonate (DHPS), is excreted. The environmental isolate Pseudomonas putida SQ1 is also able to use SQ for growth, and excretes a different C3-organosulfonate, 3-sulfolactate (SL). In this study, we revealed the catabolic pathway for SQ in P. putida SQ1 through differential proteomics and transcriptional analyses, by in vitro reconstitution of the complete pathway by five heterologously produced enzymes, and by identification of all four organosulfonate intermediates. The pathway follows a reaction sequence analogous to the Entner–Doudoroff pathway for glucose-6-phosphate: It involves an NAD+-dependent SQ dehydrogenase, 6-deoxy-6-sulfogluconolactone (SGL) lactonase, 6-deoxy-6-sulfogluconate (SG) dehydratase, and 2-keto-3,6-dideoxy-6-sulfogluconate (KDSG) aldolase. The aldolase reaction yields pyruvate, which supports growth of P. putida, and 3-sulfolactaldehyde (SLA), which is oxidized to SL by an NAD(P)+-dependent SLA dehydrogenase. All five enzymes are encoded in a single gene cluster that includes, for example, genes for transport and regulation. Homologous gene clusters were found in genomes of other P. putida strains, in other gamma-Proteobacteria, and in beta- and alpha-Proteobacteria, for example, in genomes of Enterobacteria, Vibrio, and Halomonas species, and in typical soil bacteria, such as Burkholderia, Herbaspirillum, and Rhizobium.

ABSTRACTThe halophilic archaeonHaloferax volcaniihas been proposed to degrade glucose via the semiphosphorylative Entner-Doudoroff (spED) pathway. So far, the key enzymes of this pathway, glucose dehydrogenase (GDH), gluconate dehydratase (GAD), and 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase (KDPGA), have not been characterized, and their functional involvement in glucose degradation has not been demonstrated. Here we report that the genes HVO_1083 and HVO_0950 encode GDH and KDPGA, respectively. The recombinant enzymes show high specificity for glucose and KDPG and did not convert the corresponding C4epimers galactose and 2-keto-3-deoxy-6-phosphogalactonate at significant rates. Growth studies of knockout mutants indicate the functional involvement of both GDH and KDPGA in glucose degradation. GAD was purified fromH. volcanii, and the encoding gene,gad, was identified as HVO_1488. GAD catalyzed the specific dehydration of gluconate and did not utilize galactonate at significant rates. A knockout mutant of GAD lost the ability to grow on glucose, indicating the essential involvement of GAD in glucose degradation. However, following a prolonged incubation period, growth of the Δgadmutant on glucose was recovered. Evidence is presented that under these conditions, GAD was functionally replaced by xylonate dehydratase (XAD), which uses both xylonate and gluconate as substrates. Together, the characterization of key enzymes and analyses of the respective knockout mutants present conclusive evidence for thein vivooperation of the spED pathway for glucose degradation inH. volcanii.IMPORTANCEThe work presented here describes the identification and characterization of the key enzymes glucose dehydrogenase, gluconate dehydratase, and 2-keto-3-deoxy-6-phosphogluconate aldolase and their encoding genes of the proposed semiphosphorylative Entner-Doudoroff pathway in the haloarchaeonHaloferax volcanii. The functional involvement of the three enzymes was proven by analyses of the corresponding knockout mutants. These results provide evidence for thein vivooperation of the semiphosphorylative Entner-Doudoroff pathway in haloarchaea and thus expand our understanding of the unusual sugar degradation pathways in the domainArchaea.

Genome data as well as biochemical studies have indicated that – as a peculiarity within hyperthermophilic Archaea – Thermoproteus tenax uses three different pathways for glucose metabolism, a variant of the reversible EMP (Embden–Meyerhof–Parnas) pathway and two different modifications of the ED (Entner–Doudoroff) pathway, a non-phosphorylative and a semi-phosphorylative version. An overview of the three different pathways is presented and the physiological function of the variants is discussed.

Thesis (MSc)--Stellenbosch University, 2014.
ENGLISH ABSTRACT: Metabolic networks of cellular systems are complex, in that there are numerous components with multiple non-linear interactions. To understand how these networks work they are often split into manageable pieces and studied individually. However, an individual part is unable to account for the complex properties of systems. In order to study these interactions the eld of systems biology has developed. Systems biology makes use of computers to construct models as a method to describe aspects of living systems. Using cellular pathways, kinetic models of metabolic pathways can be constructed and used as a tool to study the biological systems and provide a quantitative description. This thesis describes the quantitative analysis of a bacterium using a systems biology approach. Zymomonas mobilis is a rod shaped, Gram-negative, non-mobile facultative anaerobe and has one of the fastest observed fermentations, yet least energy e cient extractions found in nature. Furthermore it is the only known micro-organism to use the Entner-Doudoro (2-keto-3-deoxy-6- phosphogluconate) pathway anaerobically. The low energy yield of fermentation in Z. mobilis is a result of the usage of the Entner-Doudoro glycolytic pathway, which has half the energy yield per mol substrate compared to the well known Embden-Meyerhof-Parnas glycolytic pathway. The work presented in this thesis forms part of a larger project to compare glycolytic regulation in di erent micro-organisms Z. mobilis, Escherichia coli, Saccharomyces cerevisiae and Lactococcus lactis. These organisms were chosen based on their usage of di erent glycolytic mechanisms. Kinetic models are suitable tools to draw a comparison between these organisms. The emphasis here is on the construction of a kinetic model of the Entner-Doudoroff glycolytic pathway as it occurs in Z. mobilis. The aim of this thesis was to characterise as many of the Entner-Doudoro pathway enzymes as possible, under standard conditions. This was done using enzyme assays, to obtain the kinetic parameters of each of the enzymes. Microtitre plate assays were used to characterise most of the enzymes of the Entner-Doudoro pathway. However, not all characterisations could be done using plate assay methods, as some intermediates were not commercially available to perform coupled assays. Nuclear magnetic resonance (NMR) spectroscopy was used to characterise these enzymes. These experimentally obtained parameters were then incorporated in a mathematical framework. Time simulations on the initial model were unable to reach a steady-state, with a build up of metabolic intermediates. A secondary model was constructed (using calculated maximal activities) which allowed us to identify discrepancies in the initial model. This showed that the experimentally determined maximal activities of three enzymes in lower glycolysis were unrealistically low, which might be due to protein denaturation by sonication. A nal model was constructed which incorporated a correction factor for these three enzymes. The models' predicted output (steady-state concentrations and ux) was compared to that of either literature or experimentally determined values, as a method to validate the model. The model output compared well to literature values. The constructed and partially validated kinetic model was then used as an analytical tool to identify points of control and regulation of glycolysis in Z. mobilis. The model presented in this work was also compared to published models. Our model relies much less on literature obtained values, and uses kinetic parameters experimentally determined under the same conditions. The parameters of the published models were obtained from the literature and in many instances, the assay conditions for these parameters were set-up to yield the maximum activity under non-physiological conditions. Furthermore, the number of excluded or assumed parameters is much less in our model. However, introduction of a milder, more predictable extraction technique for preparing cell lysates, should be considered for future work, to obtain the parameters that was not determined during this study. The published models do include reactions not included in our model (e.g ATP metabolism), which should be considered for inclusion, as we strive to construct a detailed kinetic model of glycolysis in Z. mobilis in the future.
AFRIKAANSE OPSOMMING: Sellul^ere metaboliese netwerke is komplekse stelsels, omdat hulle bestaan uit talle komponente met verskeie nie-lineêre interaksies. Om die funksionering van hierdie netwerke te verstaan, word hulle dikwels in hanteerbare stukke verdeel en individueel bestudeer. 'n Enkele komponent is egter nie in staat om die komplekse eienskappe van sulke stelsels te verklaar nie. Die veld van sisteembiologie het ontwikkel met die doel om sulke stelsels te bestudeer. Sisteembiologie maak gebruik van rekenaarmodelle as 'n metode om aspekte van lewende sisteme te beskryf. Kinetiese modelle van metaboliese paaie word gebou en gebruik as gereedskap om die biologiese stelsels te bestudeer en 'n kwantitatiewe beskrywing te bekom. Hierdie tesis beskryf die kwantitatiewe ontleding van 'n bakterie deur middel van 'n sisteembiologiese benadering. Zymomonas Mobilis is 'n staafvormige, Gram-negatiewe, nie-mobiele fakultatiewe ana erobe, en het een van die vinnigste waargenome fermentasies, maar met die minste energie-doeltre ende ekstraksie wat in die natuur aangetref word. Verder is dit die enigste bekende mikro-organisme wat die Entner-Doudoro (2-keto-3-dioksi-6-fosfoglukonaat) pad ana erobies gebruik. Die lae-energieopbrengs van fermentasie in Z. mobilis is 'n gevolg van die gebruik van die Entner-Doudoro metaboliese pad, wat die helfte van die energie-opbrengs per mol substraat lewer, in vergelyking met die bekende Embden-Meyerhof-Parnas pad. Die werk wat in hierdie tesis aangebied word, vorm deel van 'n groter projek om glikolitiese regulering in verskillende mikro-organismes te vergelyk, naamlik Z. mobilis, Escherichia coli, Sac- charomyces en Lactococcus lactis. Hierdie organismes is gekies op grond van hul gebruik van verskillende glikolitiese meganismes. Kinetiese modellering is 'n handige metode om 'n vergelyking tussen hierdie organismes te trek. Hierdie werk fokus op die bou van 'n kinetiese model van die Entner-Doudoro glikolitiese metaboliese pad soos dit in Z. mobilis voorkom. Die doel van hierdie tesis was om so veel moontlik van die Entner-Doudoro ensieme onder standaard-toestande te karakteriseer. Die kinetiese parameters van elk van die ensieme is met behulp van ensimatiese essai's bepaal. Vir die meeste essai's is 96-put mikrotiterplate gebruik, maar nie al die karakteriserings kon met behulp van hierdie metode gedoen word nie, omdat sommige intermediate nie kommersieel beskikbaar was om gekoppelde essai's mee uit te voer nie. Kernmagnetiese resonansie (KMR) spektroskopie is gebruik om hierdie ensieme te karakteriseer. Die eksperimenteel bepaalde parameters is opgeneem in 'n wiskundige raamwerk. Tydsimulasies op die aanvanklike model was nie in staat om 'n bestendige toestand te bereik nie, omdat metaboliete opgebou het. 'n Sekond^ere model is gebou (met behulp van berekende maksimale aktiwiteite) wat ons toegelaat om teenstrydighede in die aanvanklike model te identi seer. Dit het getoon dat die eksperimenteel bepaalde maksimale aktiwiteite van drie ensieme in die laer gedeelte van glikolise te laag was, waarskynlik as gevolg van prote en denaturering tydens die ultrasoniese disintegrasieproses. 'n Finale model is gebou waarin 'n korreksiefaktor vir hierdie drie ensieme opgeneem is. Die modelle se voorspelde uitset (bestendige toestand konsentrasies en uksie) is vergelyk met waardes uit die literatuur of wat ons self bepaal het, as 'n metode om die model te valideer. Die model uitset was in goeie ooreenstemming met hierdie waardes. Die gedeeltelik gevalideerde kinetiese model is voorts gebruik as 'n analitiese instrument om beheer en regulering van glikolise in Z. mobilis te ondersoek. Die model wat in hierdie werk ontwikkel is, is ook vergelyk met die vorige gepubliseerde modelle. Ons model berus baie minder op waardes uit die wetenskaplike literatuur, en maak gebruik van parameters wat eksperimenteel bepaal is, onder identiese toestande. Die parameters van die gepubliseerde modelle is meesal verkry uit die literatuur, en in baie gevalle was die eksperimentele kondisies vir hierdie analises opgestel om die maksimale aktiwiteit te lewer onder nie- siologiese toestande. Verder bevat ons model minder parameters wat of uitgesluit is of wie se waardes aangeneem moes word. In toekomstige werk sal daar egter klem gel^e moet word op 'n minder wisselvallige ekstraksietegniek vir die verkryging van selekstrakte, om sodoende parameters te identi seer wat nie in hierdie werk bepaal kon word nie. Die gepubliseerde modelle sluit ook reaksies in wat nie ingesluit is in ons model nie (bv. ATP metabolisme). Hierdie sou in ag geneem moet word vir insluiting in 'n toekomstige uitgebreide model, om daarna te streef om 'n gedetailleerde kinetiese model van glikolise in Z. mobilis te bou.

Thesis (Ph. D.)--Ohio State University, 2003.
Title from first page of PDF file. Document formatted into pages; contains xiii, 145 p.; also includes graphics (some col.). Includes abstract and vita. Advisor: Kathryn Eaton, Dept. of Veterinary Biosciences. Includes bibliographical references (p. 130-145).

The fossil energy resources decrease and climate changes, caused by carbon dioxide (CO2) emissions, have led most industrialized countries to undertake policies aimed at the development and use of renewable energy sources. Among the renewable energies, vegetal biomasses play a key role because widely available and potentially able to cover up to 200% of the global energy demand. Vegetal biomasses can be used mainly as raw materials for the production of chemicals, biofuels and energy, in the increasingly important green economy concept based on biorefineries creation. Although the vegetal biomasses result widely available, rising costs of food raw material such as wheat, corn and sugar beet have raised a serious ethical problem using these resources. To avoid the use of such raw materials, the exploitation of lignocellulosic biomasses plays a fundamental role in the industry. However, for an efficient utilization of lignocellulosic biomasses, new technologies are required in order to transform the starting biomass into simple molecules, such as pentoses and hexoses sugars, more easily to use by the microrganism, which will have the task of producing both fine chemicals and bulk chemicals in an economically and environmentally sustainable processes. In this regard, industrial biotechnologies should be able to develop new microrganisms capable to face the harsh environmental conditions that occur during an industrial production process. For many of these productions the yeast Saccharomyces cerevisiae is largely used, not only because of its naturally ability to produce large ethanol amount, but also is widely known both at genetic and metabolic level, outlining a good starting point for the development of producers strains with high tolerance against different stresses occur during an industrial process. This is the view adopted by NEMO project (Novel high performance Enzymes and Microrganisms for conversion of lignocellulosic biomass to ethanol), belonging to the European Union seventh framework program, where it become of primary importance the development of microrganisms, especially S.cerevisiae, for the second generation ethanol production. Microrganisms must be, on the one hand able to efficiently utilize all the sugars released from lignocellulosic biomass pre-treatment, on the other hand should be more tolerant against process conditons, such as inhibitory compounds and environmental stresses. A point of relevant importance is the ability to utilize pentose sugars, like D-xylose, released in large amount after lignocellulose pre-treatment. Currently, worldwide researches are focused on the development of yeast strains engineered with xylose degradation pathways involving the pentose phosphate pathway. In fact the fungal pathway exploits xylose reductase and the xylitol dehydrogenase while the bacterial pathway exploits xylose isomerase; both pathways degrade D-xylose into D-xylulose, which will enter into pentose phosphate pathway. In addition to these two pathways studied since the ‘80s of the last century, there also two other poorly known metabolisms, described for the first time in the ‘70s, which produce alpha-ketoglutarate or pyruvate and glycolaldehyde through an oxidative xylose degradation. These pathways are composed of 5 enzymatic reactions by the Weimberg’s pathway and of 4 enzymatic reactions by the Dahms’ pathway, however they share the first 3 enzymatic reactions. After bioinformatics we were identified the presence of Weimberg’s pathway into Burkholderia xenovorans, while the reaction that characterizes the Dahms’ pathway has been identified in Escherichia coli. The encoding genes for these enzymatic activities were expressed in S.cerevisiae, and the capacity to grow on D-xylose as carbon source are evaluated. The reconstruction of these two pathways showed a poorly growth capacity on xylose. Such growth limitation seems to be related to several factors: the presence of bottlenecks associated to enzymes functionality, like D-xylonate dehydratase activity; the yeast ability to internalize xylose efficiently; the involved genes optimization. Another important aspect is the yeast ability to face and overcome environmental stresses encountered during an industrial process. The cytoplasmic membrane plays a key role in cellular homeostasis, being at the interface between the cell and the external environment, and reacting at environmental changes. The plant membrane protein TIL gives particular strength to the yeast cells when these are subjected to environmental stresses of industrial relevance, such as the presence of oxidative agents or during temperature changes. However, when TIL is expressed in an industrial and/or in an engineered laboratory strains, for industrial use, the protective effect against prolonged stress exposure and process conditions disappear. Finally, a further important aspect during an industrial process is the S.cerevisiae ability to tolerate the growth inhibitory compounds presence into pre-treated lignocellulose. In fact has been largely described how chemical compounds like aldehydes, organic acids and phenolic compounds, released during lignocellulose pre-treatment process, are toxic at certain concentration, inhibiting S.cerevisiae growth or causing yeast death. The growth performance of different wild type or engineered yeast strains are evaluated on spruce and giant cane lignocellulose pre-treated: in addition the same strains were tested on minimal formulated medium according to the spruce pre-treated composition. The results showed that the combination of low pH and the presence of organic acids, especially acetic acid and formic acid, are dramatically harmful for growth of both industrial strain, naturally more tolerant, and engineered strain, for the production and recycle of L-ascorbic acid. However, the behavior of engineered strain for production and recycle of L-ascorbic acid is interesting at low pH, because showed higher tolerance than other strains in terms of growth rate and ethanol production and productivity. Despite the positive results obtained by engineering microrganisms, especially S.cerevisiae, in laboratory, their industrial uses still remain limited. Therefore, appears extremely important the construction of more robustness strains, able to withstand different environmental conditions along an entire industrial process, with consequent influence on yields, production and productivity. For these reasons, the research is aimed to combine these aspects to provide the best microrganism possible to industry productions.

Polyuronic acids are an important constituent of seaweed and plants, and therefore represent a significant part of global biomass, providing an abundant carbon source for both terrestrial and marine heterotrophic bacteria. Through the action of polysaccharide lyases, polyuronic acids are degraded into unsaturated monouronic acid units, which are fed into the Entner-Doudoroff pathway where they are converted into pyruvate and glyceraldehyde-3-phosphate. The first step of this pathway was thought to occur non- enzymatically. A highly conserved sequence, kdgF was found in alginate and pectin utilization loci in a diverse range of prokaryotes, in proximity to well established enzymes catalyzing steps downstream in the Entner-Doudoroff pathway and I hypothesized that KdgF was involved in the catalysis of the first step of this pathway. The kdgF genes from both Yersinia enterocolitica and a locally acquired Halomonas sp. were expressed in Escherichia coli and their activity was examined using unsaturated galacturonic acid depletion activity assays. To gain perspective on the general structure of KdgF, x-ray crystallography was used to obtain a crystal structure of both HaKdgF and YeKdgF. These crystal structures provided insight into the molecular details of catalysis by the KdgF proteins, including their putative catalytic residues and a coordinated metal binding site for substrate recognition. To elucidate amino acids that may be involved in binding and/or catalysis, mutants were created in HaKdgF, and lack of activity was observed in four mutants (Asp102A, Phe104A, Arg108A, and Gln55A). The research done in this study suggests that KdgF proteins use a metal binding site coordinated by three histidines and several additional residues to cause a change in monouronic acid, thereby, affecting the unsaturated double bond. This suggests that KdgF is involved in the first step in the Entner-Doudoroff pathway, which is the linearization of unsaturated monouronic acids.
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