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Journal articles on the topic 'Entner doudoroff pathway'

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Published: 4 June 2021

Last updated: 7 February 2022

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1

Mendz, G. L., S. L. Hazell, and B. P. Burns. "The Entner-Doudoroff Pathway in Helicobacter pylori." Archives of Biochemistry and Biophysics 312, no. 2 (August 1994): 349–56. http://dx.doi.org/10.1006/abbi.1994.1319.

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2

Held, Gary, and Manuel Goldman. "Pathways of glucose catabolism in the smut fungus Ustilago violacea." Canadian Journal of Microbiology 32, no. 1 (January 1, 1986): 56–61. http://dx.doi.org/10.1139/m86-011.

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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.

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3

Conway, Tyrrell. "The Entner-Doudoroff pathway: history, physiology and molecular biology." FEMS Microbiology Letters 103, no. 1 (September 1992): 1–28. http://dx.doi.org/10.1111/j.1574-6968.1992.tb05822.x.

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4

Ahmed, H., B. Tjaden, R. Hensel, and B. Siebers. "Embden–Meyerhof–Parnas and Entner–Doudoroff pathways in Thermoproteus tenax: metabolic parallelism or specific adaptation?" Biochemical Society Transactions 32, no. 2 (April 1, 2004): 303–4. http://dx.doi.org/10.1042/bst0320303.

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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.

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5

Felux, Ann-Katrin, Dieter Spiteller, Janosch Klebensberger, and David Schleheck. "Entner–Doudoroff pathway for sulfoquinovose degradation in Pseudomonas putida SQ1." Proceedings of the National Academy of Sciences 112, no. 31 (July 20, 2015): E4298—E4305. http://dx.doi.org/10.1073/pnas.1507049112.

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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.

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6

Lamble, Henry J., Christine C. Milburn, Garry L. Taylor, David W. Hough, and Michael J. Danson. "Gluconate dehydratase from the promiscuous Entner-Doudoroff pathway inSulfolobus solfataricus." FEBS Letters 576, no. 1-2 (September 15, 2004): 133–36. http://dx.doi.org/10.1016/j.febslet.2004.08.074.

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7

Chen, Xi, Karoline Schreiber, Jens Appel, Alexander Makowka, Berit Fähnrich, Mayo Roettger, Mohammad R. Hajirezaei, et al. "The Entner–Doudoroff pathway is an overlooked glycolytic route in cyanobacteria and plants." Proceedings of the National Academy of Sciences 113, no. 19 (April 25, 2016): 5441–46. http://dx.doi.org/10.1073/pnas.1521916113.

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Glucose degradation pathways are central for energy and carbon metabolism throughout all domains of life. They provide ATP, NAD(P)H, and biosynthetic precursors for amino acids, nucleotides, and fatty acids. It is general knowledge that cyanobacteria and plants oxidize carbohydrates via glycolysis [the Embden–Meyerhof–Parnas (EMP) pathway] and the oxidative pentose phosphate (OPP) pathway. However, we found that both possess a third, previously overlooked pathway of glucose breakdown: the Entner–Doudoroff (ED) pathway. Its key enzyme, 2-keto-3-deoxygluconate-6-phosphate (KDPG) aldolase, is widespread in cyanobacteria, moss, fern, algae, and plants and is even more common among cyanobacteria than phosphofructokinase (PFK), the key enzyme of the EMP pathway. Active KDPG aldolases from the cyanobacterium Synechocystis and the plant barley (Hordeum vulgare) were biochemically characterized in vitro. KDPG, a metabolite unique to the ED pathway, was detected in both in vivo, indicating an active ED pathway. Phylogenetic analyses revealed that photosynthetic eukaryotes acquired KDPG aldolase from the cyanobacterial ancestors of plastids via endosymbiotic gene transfer. Several Synechocystis mutants in which key enzymes of all three glucose degradation pathways were knocked out indicate that the ED pathway is physiologically significant, especially under mixotrophic conditions (light and glucose) and under autotrophic conditions in a day/night cycle, which is probably the most common condition encountered in nature. The ED pathway has lower protein costs and ATP yields than the EMP pathway, in line with the observation that oxygenic photosynthesizers are nutrient-limited, rather than ATP-limited. Furthermore, the ED pathway does not generate futile cycles in organisms that fix CO2 via the Calvin–Benson cycle.

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8

Ahmed, Hatim, Thijs J. G. Ettema, Britta Tjaden, Ans C. M. Geerling, John van der Oost, and Bettina Siebers. "The semi-phosphorylative Entner–Doudoroff pathway in hyperthermophilic archaea: a re-evaluation." Biochemical Journal 390, no. 2 (August 23, 2005): 529–40. http://dx.doi.org/10.1042/bj20041711.

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Biochemical studies have suggested that, in hyperthermophilic archaea, the metabolic conversion of glucose via the ED (Entner–Doudoroff) pathway generally proceeds via a non-phosphorylative variant. A key enzyme of the non-phosphorylating ED pathway of Sulfolobus solfataricus, KDG (2-keto-3-deoxygluconate) aldolase, has been cloned and characterized previously. In the present study, a comparative genomics analysis is described that reveals conserved ED gene clusters in both Thermoproteus tenax and S. solfataricus. The corresponding ED proteins from both archaea have been expressed in Escherichia coli and their specificity has been identified, revealing: (i) a novel type of gluconate dehydratase (gad gene), (ii) a bifunctional 2-keto-3-deoxy-(6-phospho)-gluconate aldolase (kdgA gene), (iii) a 2-keto-3-deoxygluconate kinase (kdgK gene) and, in S. solfataricus, (iv) a GAPN (non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase; gapN gene). Extensive in vivo and in vitro enzymatic analyses indicate the operation of both the semi-phosphorylative and the non-phosphorylative ED pathway in T. tenax and S. solfataricus. The existence of this branched ED pathway is yet another example of the versatility and flexibility of the central carbohydrate metabolic pathways in the archaeal domain.

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9

Kresge, Nicole, Robert D. Simoni, and Robert L. Hill. "The Entner-Doudoroff Pathway for Glucose Degradation: the Work of MichaelDoudoroff." Journal of Biological Chemistry 280, no. 27 (July 2005): e24-e25. http://dx.doi.org/10.1016/s0021-9258(20)61415-6.

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10

Sutter, Jan-Moritz, Julia-Beate Tästensen, Ulrike Johnsen, Jörg Soppa, and Peter Schönheit. "Key Enzymes of the Semiphosphorylative Entner-Doudoroff Pathway in the Haloarchaeon Haloferax volcanii: Characterization of Glucose Dehydrogenase, Gluconate Dehydratase, and 2-Keto-3-Deoxy-6-Phosphogluconate Aldolase." Journal of Bacteriology 198, no. 16 (June 13, 2016): 2251–62. http://dx.doi.org/10.1128/jb.00286-16.

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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.

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11

Ponce, Elizabeth, Mauricio García, and Ma Enriqueta Muñoz. "Participation of the Entner–Doudoroff pathway inEscherichia colistrains with an inactive phosphotransferase system (PTS–Glc+) in gluconate and glucose batch cultures." Canadian Journal of Microbiology 51, no. 11 (November 1, 2005): 975–82. http://dx.doi.org/10.1139/w05-101.

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The activity of the enzymes of the central metabolic pathways has been the subject of intensive analysis; however, the Entner–Doudoroff (ED) pathway has only recently begun to attract attention. The metabolic response to edd gene knockout in Escherichia coli JM101 and PTS–Glc+was investigated in gluconate and glucose batch cultures and compared with other pyruvate kinase and PTS mutants previously constructed. Even though the specific growth rates between the strain carrying the edd gene knockout and its parent JM101 and PTS–Glc+edd and its parent PTS–Glc+were very similar, reproducible changes in the specific consumption rates and biomass yields were obtained when grown on glucose. These results support the participation of the ED pathway not only on gluconate metabolism but on other metabolic and biochemical processes in E. coli. Despite that gluconate is a non-PTS carbohydrate, the PTS–Glc+and derived strains showed important reductions in the specific growth and gluconate consumption rates. Moreover, the overall activity of the ED pathway on gluconate resulted in important increments in PTS–Glc+and PTS-Glc+pykF mutants. Additional results obtained with the pykA pykF mutant indicate the important contribution of the pyruvate kinase enzymes to pyruvate synthesis and energy production in both carbon sources.Key words: Escherichia coli, gluconate metabolism, Entner-Doudoroff pathway, PT system, pyruvate kinase isoenzymes.

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12

Holten, Eirik. "6-PHOSPHOGLUCONATE DEHYDROGENASE AND ENZYMES OF THE ENTNER-DOUDOROFF PATHWAY IN NEISSERIA." Acta Pathologica Microbiologica Scandinavica Section B Microbiology and Immunology 82B, no. 2 (August 15, 2009): 207–13. http://dx.doi.org/10.1111/j.1699-0463.1974.tb02313.x.

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13

Figueiredo, Ana Sofia, Theresa Kouril, Dominik Esser, Patrick Haferkamp, Patricia Wieloch, Dietmar Schomburg, Peter Ruoff, Bettina Siebers, and Jörg Schaber. "Systems biology of the modified branched Entner-Doudoroff pathway in Sulfolobus solfataricus." PLOS ONE 12, no. 7 (July 10, 2017): e0180331. http://dx.doi.org/10.1371/journal.pone.0180331.

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14

Gunnarsson, Nina, Uffe H. Mortensen, Margherita Sosio, and Jens Nielsen. "Identification of the Entner-Doudoroff pathway in an antibiotic-producing actinomycete species." Molecular Microbiology 52, no. 3 (April 1, 2004): 895–902. http://dx.doi.org/10.1111/j.1365-2958.2004.04028.x.

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15

Okano, Kenji, Qianqin Zhu, and Kohsuke Honda. "In vitro reconstitution of non-phosphorylative Entner–Doudoroff pathway for lactate production." Journal of Bioscience and Bioengineering 129, no. 3 (March 2020): 269–75. http://dx.doi.org/10.1016/j.jbiosc.2019.09.010.

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16

Lamble, Henry J., Alex Theodossis, Christine C. Milburn, Garry L. Taylor, Steven D. Bull, David W. Hough, and Michael J. Danson. "Promiscuity in the part-phosphorylative Entner-Doudoroff pathway of the archaeonSulfolobus solfataricus." FEBS Letters 579, no. 30 (December 1, 2005): 6865–69. http://dx.doi.org/10.1016/j.febslet.2005.11.028.

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17

Waligora, E. A., C. R. Fisher, N. J. Hanovice, A. Rodou, E. E. Wyckoff, and S. M. Payne. "Role of Intracellular Carbon Metabolism Pathways in Shigella flexneri Virulence." Infection and Immunity 82, no. 7 (April 14, 2014): 2746–55. http://dx.doi.org/10.1128/iai.01575-13.

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ABSTRACTShigella flexneri, which replicates in the cytoplasm of intestinal epithelial cells, can use the Embden-Meyerhof-Parnas, Entner-Doudoroff, or pentose phosphate pathway for glycolytic carbon metabolism. To determine which of these pathways is used by intracellularS. flexneri, mutants were constructed and tested in a plaque assay for the ability to invade, replicate intracellularly, and spread to adjacent epithelial cells. Mutants blocked in the Embden-Meyerhof-Parnas pathway (pfkABandpykAFmutants) invaded the cells but formed very small plaques. Loss of the Entner-Doudoroff pathway geneedaresulted in small plaques, but the doubleeda eddmutant formed normal-size plaques. This suggested that the plaque defect of theedamutant was due to buildup of the toxic intermediate 2-keto-3-deoxy-6-phosphogluconic acid rather than a specific requirement for this pathway. Loss of the pentose phosphate pathway had no effect on plaque formation, indicating that it is not critical for intracellularS. flexneri. Supplementation of the epithelial cell culture medium with pyruvate allowed the glycolysis mutants to form larger plaques than those observed with unsupplemented medium, consistent with data from phenotypic microarrays (Biolog) indicating that pyruvate metabolism was not disrupted in these mutants. Interestingly, the wild-typeS. flexnerialso formed larger plaques in the presence of supplemental pyruvate or glucose, with pyruvate yielding the largest plaques. Analysis of the metabolites in the cultured cells showed increased intracellular levels of the added compound. Pyruvate increased the growth rate ofS. flexneriin vitro, suggesting that it may be a preferred carbon source inside host cells.

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18

Borodina, Irina, Charlotte Schöller, Anna Eliasson, and Jens Nielsen. "Metabolic Network Analysis of Streptomyces tenebrarius, a Streptomyces Species with an Active Entner-Doudoroff Pathway." Applied and Environmental Microbiology 71, no. 5 (May 2005): 2294–302. http://dx.doi.org/10.1128/aem.71.5.2294-2302.2005.

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ABSTRACT Streptomyces tenebrarius is an industrially important microorganism, producing an antibiotic complex that mainly consists of the aminoglycosides apramycin, tobramycin carbamate, and kanamycin B carbamate. When S. tenebrarius is used for industrial tobramycin production, kanamycin B carbamate is an unwanted by-product. The two compounds differ only by one hydroxyl group, which is present in kanamycin carbamate but is reduced during biosynthesis of tobramycin. 13C metabolic flux analysis was used for elucidating connections between the primary carbon metabolism and the composition of the antibiotic complex. Metabolic flux maps were constructed for the cells grown on minimal medium with glucose or with a glucose-glycerol mixture as the carbon source. The addition of glycerol, which is more reduced than glucose, led to a three-times-greater reduction of the kanamycin portion of the antibiotic complex. The labeling indicated an active Entner-Doudoroff (ED) pathway, which was previously considered to be nonfunctional in Streptomyces. The activity of the pentose phosphate (PP) pathway was low (10 to 20% of the glucose uptake rate). The fluxes through Embden-Meyerhof-Parnas (EMP) and ED pathways were almost evenly distributed during the exponential growth on glucose. During the transition from growth phase to production phase, a metabolic shift was observed, characterized by a decreased flux through the ED pathway and increased fluxes through the EMP and PP pathways. Higher specific NADH and NADPH production rates were calculated in the cultivation on glucose-glycerol, which was associated with a lower percentage of nonreduced antibiotic kanamycin B carbamate.

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19

Goldbourt, Amir, Loren A. Day, and Ann E. McDermott. "Assignment of congested NMR spectra: Carbonyl backbone enrichment via the Entner–Doudoroff pathway." Journal of Magnetic Resonance 189, no. 2 (December 2007): 157–65. http://dx.doi.org/10.1016/j.jmr.2007.07.011.

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20

Wanken, Amy E., Tyrrell Conway, and Kathryn A. Eaton. "The Entner-Doudoroff Pathway Has Little Effect on Helicobacter pylori Colonization of Mice." Infection and Immunity 71, no. 5 (May 2003): 2920–23. http://dx.doi.org/10.1128/iai.71.5.2920-2923.2003.

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ABSTRACT Helicobacter pylori mutants deficient in 6-phosphogluconate dehydratase (6PGD) were constructed. Colonization densities were lower and minimum infectious doses were higher for mutant strains than for wild-type strains. In spite of better colonization, however, wild-type strains did not displace the mutant in cocolonization experiments. Loss of 6PGD diminishes the fitness of H. pylori in vivo, but the pathway is nonessential for colonization.

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21

ISHIKAWA, Kohei, Yoshiya GUNJI, Hisashi YASUEDA, and Kozo ASANO. "Improvement ofL-Lysine Production byMethylophilus methylotrophusfrom Methanolviathe Entner-Doudoroff Pathway, Originating inEscherichia coli." Bioscience, Biotechnology, and Biochemistry 72, no. 10 (October 23, 2008): 2535–42. http://dx.doi.org/10.1271/bbb.80183.

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22

Fabris, Michele, Michiel Matthijs, Stephane Rombauts, Wim Vyverman, Alain Goossens, and Gino J. E. Baart. "The metabolic blueprint of Phaeodactylum tricornutum reveals a eukaryotic Entner-Doudoroff glycolytic pathway." Plant Journal 70, no. 6 (March 31, 2012): 1004–14. http://dx.doi.org/10.1111/j.1365-313x.2012.04941.x.

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23

Dhatt, Sharmistha, Shrabani Sen, and Pinaki Chaudhury. "Entner-Doudoroff glycolysis pathway as quadratic-cubic mixed autocatalytic network: A kinetic assay." Chemical Physics 528 (January 2020): 110531. http://dx.doi.org/10.1016/j.chemphys.2019.110531.

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24

Olavarria, Karel, Marina Pupke Marone, Henrique da Costa Oliveira, Juan Camilo Roncallo, Fernanda Nogales da Costa Vasconcelos, Luiziana Ferreira da Silva, and José Gregório Cabrera Gomez. "Quantifying NAD(P)H production in the upper Entner-Doudoroff pathway fromPseudomonas putidaKT2440." FEBS Open Bio 5, no. 1 (January 1, 2015): 908–15. http://dx.doi.org/10.1016/j.fob.2015.11.002.

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25

DANDEKAR, Thomas, Stefan SCHUSTER, Berend SNEL, Martijn HUYNEN, and Peer BORK. "Pathway alignment: application to the comparative analysis of glycolytic enzymes." Biochemical Journal 343, no. 1 (September 24, 1999): 115–24. http://dx.doi.org/10.1042/bj3430115.

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Comparative analysis of metabolic pathways in different genomes yields important information on their evolution, on pharmacological targets and on biotechnological applications. In this study on glycolysis, three alternative ways of comparing biochemical pathways are combined: (1) analysis and comparison of biochemical data, (2) pathway analysis based on the concept of elementary modes, and (3) a comparative genome analysis of 17 completely sequenced genomes. The analysis reveals a surprising plasticity of the glycolytic pathway. Isoenzymes in different species are identified and compared; deviations from the textbook standard are detailed. Several potential pharmacological targets and by-passes (such as the Entner-Doudoroff pathway) to glycolysis are examined and compared in the different species. Archaean, bacterial and parasite specific adaptations are identified and described.

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Hager, Paul W., M. Worth Calfee, and Paul V. Phibbs. "The Pseudomonas aeruginosa devB/SOL Homolog,pgl, Is a Member of the hex Regulon and Encodes 6-Phosphogluconolactonase." Journal of Bacteriology 182, no. 14 (July 15, 2000): 3934–41. http://dx.doi.org/10.1128/jb.182.14.3934-3941.2000.

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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.

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27

Ng, Chiam Yu, Iman Farasat, Costas D. Maranas, and Howard M. Salis. "Rational design of a synthetic Entner–Doudoroff pathway for improved and controllable NADPH regeneration." Metabolic Engineering 29 (May 2015): 86–96. http://dx.doi.org/10.1016/j.ymben.2015.03.001.

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28

Liu, Huaiwei, Yuanzhang Sun, Kristine Rose M. Ramos, Grace M. Nisola, Kris Niño G. Valdehuesa, Won–Keun Lee, Si Jae Park, and Wook-Jin Chung. "Combination of Entner-Doudoroff Pathway with MEP Increases Isoprene Production in Engineered Escherichia coli." PLoS ONE 8, no. 12 (December 20, 2013): e83290. http://dx.doi.org/10.1371/journal.pone.0083290.

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Chavarría, Max, Pablo I. Nikel, Danilo Pérez-Pantoja, and Víctor de Lorenzo. "The Entner-Doudoroff pathway empowersPseudomonas putida KT2440 with a high tolerance to oxidative stress." Environmental Microbiology 15, no. 6 (January 10, 2013): 1772–85. http://dx.doi.org/10.1111/1462-2920.12069.

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30

Rutkis, Reinis, Uldis Kalnenieks, Egils Stalidzans, and David A. Fell. "Kinetic modelling of the Zymomonas mobilis Entner–Doudoroff pathway: insights into control and functionality." Microbiology 159, Pt_12 (December 1, 2013): 2674–89. http://dx.doi.org/10.1099/mic.0.071340-0.

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31

Roy, Alexander B., Michael J. E. Hewlins, Andrew J. Ellis, John L. Harwood, and Graham F. White. "Glycolytic Breakdown of Sulfoquinovose in Bacteria: a Missing Link in the Sulfur Cycle." Applied and Environmental Microbiology 69, no. 11 (November 2003): 6434–41. http://dx.doi.org/10.1128/aem.69.11.6434-6441.2003.

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ABSTRACT Sulfoquinovose (6-deoxy-6-sulfo-d-glucopyranose), formed by the hydrolysis of the plant sulfolipid, is a major component of the biological sulfur cycle. However, pathways for its catabolism are poorly delineated. We examined the hypothesis that mineralization of sulfoquinovose to inorganic sulfate is initiated by reactions of the glycolytic and/or Entner-Doudoroff pathways in bacteria. Metabolites of [U-13C]sulfoquinovose were identified by 13C-nuclear magnetic resonance (NMR) in strains of Klebsiella and Agrobacterium previously isolated for their ability to utilize sulfoquinovose as a sole source of carbon and energy for growth, and cell extracts were analyzed for enzymes diagnostic for the respective pathways. Klebsiella sp. strain ABR11 grew rapidly on sulfoquinovose, with major accumulations of sulfopropandiol (2,3-dihydroxypropanesulfonate) but no detectable release of sulfate. Later, when sulfoquinovose was exhausted and growth was very slow, sulfopropandiol disappeared and inorganic sulfate and small amounts of sulfolactate (2-hydroxy-3-sulfopropionate) were formed. In Agrobacterium sp. strain ABR2, growth and sulfoquinovose disappearance were again coincident, though slower than that in Klebsiella sp. Release of sulfate was still late but was faster than that in Klebsiella sp., and no metabolites were detected by 13C-NMR. Extracts of both strains grown on sulfoquinovose contained phosphofructokinase activities that remained unchanged when fructose 6-phosphate was replaced in the assay mixture with either glucose 6-phosphate or sulfoquinovose. The results were consistent with the operation of the Embden-Meyerhoff-Parnas (glycolysis) pathway for catabolism of sulfoquinovose. Extracts of Klebsiella but not Agrobacterium also contained an NAD+-dependent sulfoquinovose dehydrogenase activity, indicating that the Entner-Doudoroff pathway might also contribute to catabolism of sulfoquinovose.

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Klingner, Arne, Annekathrin Bartsch, Marco Dogs, Irene Wagner-Döbler, Dieter Jahn, Meinhard Simon, Thorsten Brinkhoff, Judith Becker, and Christoph Wittmann. "Large-Scale13C Flux Profiling Reveals Conservation of the Entner-Doudoroff Pathway as a Glycolytic Strategy among Marine Bacteria That Use Glucose." Applied and Environmental Microbiology 81, no. 7 (January 23, 2015): 2408–22. http://dx.doi.org/10.1128/aem.03157-14.

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ABSTRACTMarine bacteria form one of the largest living surfaces on Earth, and their metabolic activity is of fundamental importance for global nutrient cycling. Here, we explored the largely unknown intracellular pathways in 25 microbes representing different classes of marine bacteria that use glucose:Alphaproteobacteria,Gammaproteobacteria, andFlavobacteriiaof theBacteriodetesphylum. We used13C isotope experiments to infer metabolic fluxes through their carbon core pathways. Notably, 90% of all strains studied use the Entner-Doudoroff (ED) pathway for glucose catabolism, whereas only 10% rely on the Embden-Meyerhof-Parnas (EMP) pathway. This result differed dramatically from the terrestrial model strains studied, which preferentially used the EMP pathway yielding high levels of ATP. Strains using the ED pathway exhibited a more robust resistance against the oxidative stress typically found in this environment. An important feature contributing to the preferential use of the ED pathway in the oceans could therefore be enhanced supply of NADPH through this pathway. The marine bacteria studied did not specifically rely on a distinct anaplerotic route, but the carboxylation of phosphoenolpyruvate (PEP) or pyruvate for fueling of the tricarboxylic acid (TCA) cycle was evenly distributed. The marine isolates studied belong to clades that dominate the uptake of glucose, a major carbon source for bacteria in seawater. Therefore, the ED pathway may play a significant role in the cycling of mono- and polysaccharides by bacterial communities in marine ecosystems.

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KIM, Seonghun, and Sun Bok LEE. "Characterization ofSulfolobus solfataricus2-Keto-3-deoxy-D-gluconate Kinase in the Modified Entner-Doudoroff Pathway." Bioscience, Biotechnology, and Biochemistry 70, no. 6 (June 23, 2006): 1308–16. http://dx.doi.org/10.1271/bbb.50566.

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Rutkis, Reinis, Inese Strazdina, Elina Balodite, Zane Lasa, Nina Galinina, and Uldis Kalnenieks. "The Low Energy-Coupling Respiration in Zymomonas mobilis Accelerates Flux in the Entner-Doudoroff Pathway." PLOS ONE 11, no. 4 (April 21, 2016): e0153866. http://dx.doi.org/10.1371/journal.pone.0153866.

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35

Budgen, Nigel, and Michael J. Danson. "Metabolism of glucose via a modified Entner-Doudoroff pathway in the thermoacidophilic archaebacterium Thermoplasma acidophilum." FEBS Letters 196, no. 2 (February 17, 1986): 207–10. http://dx.doi.org/10.1016/0014-5793(86)80247-2.

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Richhardt, Janine, Stephanie Bringer, and Michael Bott. "Role of the pentose phosphate pathway and the Entner–Doudoroff pathway in glucose metabolism of Gluconobacter oxydans 621H." Applied Microbiology and Biotechnology 97, no. 10 (January 25, 2013): 4315–23. http://dx.doi.org/10.1007/s00253-013-4707-2.

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Maleki, Susan, Mali Mærk, Svein Valla, and Helga Ertesvåg. "Mutational Analyses of Glucose Dehydrogenase and Glucose-6-Phosphate Dehydrogenase Genes in Pseudomonas fluorescens Reveal Their Effects on Growth and Alginate Production." Applied and Environmental Microbiology 81, no. 10 (March 6, 2015): 3349–56. http://dx.doi.org/10.1128/aem.03653-14.

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ABSTRACTThe biosynthesis of alginate has been studied extensively due to the importance of this polymer in medicine and industry. Alginate is synthesized from fructose-6-phosphate and thus competes with the central carbon metabolism for this metabolite. The alginate-producing bacteriumPseudomonas fluorescensrelies on the Entner-Doudoroff and pentose phosphate pathways for glucose metabolism, and these pathways are also important for the metabolism of fructose and glycerol. In the present study, the impact of key carbohydrate metabolism enzymes on growth and alginate synthesis was investigated inP. fluorescens. Mutants defective in glucose-6-phosphate dehydrogenase isoenzymes (Zwf-1 and Zwf-2) or glucose dehydrogenase (Gcd) were evaluated using media containing glucose, fructose, or glycerol. Zwf-1 was shown to be the most important glucose-6-phosphate dehydrogenase for catabolism. Both Zwf enzymes preferred NADP as a coenzyme, although NAD was also accepted. Only Zwf-2 was active in the presence of 3 mM ATP, and then only with NADP as a coenzyme, indicating an anabolic role for this isoenzyme. Disruption ofzwf-1resulted in increased alginate production when glycerol was used as the carbon source, possibly due to decreased flux through the Entner-Doudoroff pathway rendering more fructose-6-phosphate available for alginate biosynthesis. In alginate-producing cells grown on glucose, disruption ofgcdincreased both cell numbers and alginate production levels, while this mutation had no positive effect on growth in a non-alginate-producing strain. A possible explanation is that alginate synthesis might function as a sink for surplus hexose phosphates that could otherwise be detrimental to the cell.

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Haferkamp, Patrick, Simone Kutschki, Jenny Treichel, Hatim Hemeda, Karsten Sewczyk, Daniel Hoffmann, Melanie Zaparty, and Bettina Siebers. "An additional glucose dehydrogenase from Sulfolobus solfataricus: fine-tuning of sugar degradation?" Biochemical Society Transactions 39, no. 1 (January 19, 2011): 77–81. http://dx.doi.org/10.1042/bst0390077.

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Within the SulfoSYS (Sulfolobus Systems Biology) project, the effect of temperature on a metabolic network is investigated at the systems level. Sulfolobus solfataricus utilizes an unusual branched ED (Entner–Doudoroff) pathway for sugar degradation that is promiscuous for glucose and galactose. In the course of metabolic pathway reconstruction, a glucose dehydrogenase isoenzyme (GDH-2, SSO3204) was identified. GDH-2 exhibits high similarity to the previously characterized GDH-1 (SSO3003, 61% amino acid identity), but possesses different enzymatic properties, particularly regarding substrate specificity and catalytic efficiency. In contrast with GDH-1, which exhibits broad substrate specificity for C5 and C6 sugars, GDH-2 is absolutely specific for glucose. The comparison of kinetic parameters suggests that GDH-2 might represent the major player in glucose catabolism via the branched ED pathway, whereas GDH-1 might have a dominant role in galactose degradation via the same pathway as well as in different sugar-degradation pathways.

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Taha, T. S. M., and T. L. Deits. "Detection of Metabolites of the Entner-Doudoroff Pathway by HPLC with Pulsed Amperometry: Application to Assays for Pathway Enzymes." Analytical Biochemistry 219, no. 1 (May 1994): 115–20. http://dx.doi.org/10.1006/abio.1994.1239.

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40

del Castillo, Teresa, Juan L. Ramos, José J. Rodríguez-Herva, Tobias Fuhrer, Uwe Sauer, and Estrella Duque. "Convergent Peripheral Pathways Catalyze Initial Glucose Catabolism in Pseudomonas putida: Genomic and Flux Analysis." Journal of Bacteriology 189, no. 14 (May 4, 2007): 5142–52. http://dx.doi.org/10.1128/jb.00203-07.

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ABSTRACT In this study, we show that glucose catabolism in Pseudomonas putida occurs through the simultaneous operation of three pathways that converge at the level of 6-phosphogluconate, which is metabolized by the Edd and Eda Entner/Doudoroff enzymes to central metabolites. When glucose enters the periplasmic space through specific OprB porins, it can either be internalized into the cytoplasm or be oxidized to gluconate. Glucose is transported to the cytoplasm in a process mediated by an ABC uptake system encoded by open reading frames PP1015 to PP1018 and is then phosphorylated by glucokinase (encoded by the glk gene) and converted by glucose-6-phosphate dehydrogenase (encoded by the zwf genes) to 6-phosphogluconate. Gluconate in the periplasm can be transported into the cytoplasm and subsequently phosphorylated by gluconokinase to 6-phosphogluconate or oxidized to 2-ketogluconate, which is transported to the cytoplasm, and subsequently phosphorylated and reduced to 6-phosphogluconate. In the wild-type strain, glucose was consumed at a rate of around 6 mmol g−1 h−1, which allowed a growth rate of 0.58 h−1 and a biomass yield of 0.44 g/g carbon used. Flux analysis of 13C-labeled glucose revealed that, in the Krebs cycle, most of the oxalacetate fraction was produced by the pyruvate shunt rather than by the direct oxidation of malate by malate dehydrogenase. Enzymatic and microarray assays revealed that the enzymes, regulators, and transport systems of the three peripheral glucose pathways were induced in response to glucose in the outer medium. We generated a series of isogenic mutants in one or more of the steps of all three pathways and found that, although all three functioned simultaneously, the glucokinase pathway and the 2-ketogluconate loop were quantitatively more important than the direct phosphorylation of gluconate. In physical terms, glucose catabolism genes were organized in a series of clusters scattered along the chromosome. Within each of the clusters, genes encoding porins, transporters, enzymes, and regulators formed operons, suggesting that genes in each cluster coevolved. The glk gene encoding glucokinase was located in an operon with the edd gene, whereas the zwf-1 gene, encoding glucose-6-phosphate dehydrogenase, formed an operon with the eda gene. Therefore, the enzymes of the glucokinase pathway and those of the Entner-Doudoroff pathway are physically linked and induced simultaneously. It can therefore be concluded that the glucokinase pathway is a sine qua non condition for P. putida to grow with glucose.

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Refaeli, Bosmat, and Amir Goldbourt. "Protein expression and isotopic enrichment based on induction of the Entner–Doudoroff pathway in Escherichia coli." Biochemical and Biophysical Research Communications 427, no. 1 (October 2012): 154–58. http://dx.doi.org/10.1016/j.bbrc.2012.09.031.

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42

Carter, A. T., B. M. Pearson, J. R. Dickinson, and W. E. Lancashire. "Sequence of the Escherichia coli K-12 edd and eda genes of the Entner-Doudoroff pathway." Gene 130, no. 1 (August 1993): 155–56. http://dx.doi.org/10.1016/0378-1119(93)90362-7.

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43

Harada, Eiji, Ken-Ichiro Iida, Susumu Shiota, Hiroaki Nakayama, and Shin-Ichi Yoshida. "Glucose Metabolism in Legionella pneumophila: Dependence on the Entner-Doudoroff Pathway and Connection with Intracellular Bacterial Growth." Journal of Bacteriology 192, no. 11 (April 2, 2010): 2892–99. http://dx.doi.org/10.1128/jb.01535-09.

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ABSTRACT Glucose metabolism in Legionella pneumophila was studied by focusing on the Entner-Doudoroff (ED) pathway with a combined genetic and biochemical approach. The bacterium utilized exogenous glucose for synthesis of acid-insoluble cell components but manifested no discernible increase in the growth rate. Assays with permeabilized cell preparations revealed the activities of three enzymes involved in the pathway, i.e., glucokinase, phosphogluconate dehydratase, and 2-dehydro-3-deoxy-phosphogluconate aldolase, presumed to be encoded by the glk, edd, and eda genes, respectively. Gene-disrupted mutants for the three genes and the ywtG gene encoding a putative sugar transporter were devoid of the ability to metabolize exogenous glucose, indicating that the pathway is almost exclusively responsible for glucose metabolism and that the ywtG gene product is the glucose transporter. It was also established that these four genes formed part of an operon in which the gene order was edd-glk-eda-ywtG, as predicted by genomic information. Intriguingly, while the mutants exhibited no appreciable change in growth characteristics in vitro, they were defective in multiplication within eukaryotic cells, strongly indicating that the ED pathway must be functional for the intracellular growth of the bacterium to occur. Curiously, while the deficient glucose metabolism of the ywtG mutant was successfully complemented by the ywtG + gene supplied in trans via plasmid, its defect in intracellular growth was not. However, the latter defect was also manifested in wild-type cells when a plasmid carrying the mutant ywtG gene was introduced. This phenomenon, resembling so-called dominant negativity, awaits further investigation.

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44

Velázquez, Francisco, Ilaria di Bartolo, and Víctor de Lorenzo. "Genetic Evidence that Catabolites of the Entner-Doudoroff Pathway Signal C Source Repression of the σ54Pu Promoter of Pseudomonas putida." Journal of Bacteriology 186, no. 24 (December 15, 2004): 8267–75. http://dx.doi.org/10.1128/jb.186.24.8267-8275.2004.

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ABSTRACT Glucose and other C sources exert an atypical form of catabolic repression on the σ54-dependent promoter Pu, which drives transcription of an operon for m-xylene degradation encoded by the TOL plasmid pWW0 in Pseudomonas putida. We have used a genetic approach to identify the catabolite(s) shared by all known repressive C sources that appears to act as the intracellular signal that triggers downregulation of Pu. To this end, we reconstructed from genomic data the pathways for metabolism of repressor (glucose, gluconate) and nonrepressor (fructose) C sources. Since P. putida lacks fructose-6-phosphate kinase, glucose and gluconate appear to be metabolized exclusively by the Entner-Doudoroff (ED) pathway, while fructose can be channeled through the Embden-Meyerhof (EM) route. An insertion in the gene fda (encoding fructose-1,6-bisphosphatase) that forces fructose metabolism to be routed exclusively to the ED pathway makes this sugar inhibitory for Pu. On the contrary, a crc mutation known to stimulate expression of the ED enzymes causes the promoter to be less sensitive to glucose. Interrupting the ED pathway by knocking out eda (encoding 2-dehydro-3-deoxyphosphogluconate aldolase) exacerbates the inhibitory effect of glucose in Pu. These observations pinpoint the key catabolites of the ED route, 6-phosphogluconate and/or 2-dehydro-3-deoxyphosphogluconate, as the intermediates that signal Pu repression. This notion is strengthened by the observation that 2-ketogluconate, which enters the ED pathway by conversion into these compounds, is a strong repressor of the Pu promoter.

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45

KIM, Seonghun, and Sun Bok LEE. "Identification and characterization of Sulfolobus solfataricusD-gluconate dehydratase: a key enzyme in the non-phosphorylated Entner–Doudoroff pathway." Biochemical Journal 387, no. 1 (March 22, 2005): 271–80. http://dx.doi.org/10.1042/bj20041053.

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The extremely thermoacidophilic archaeon Sulfolobus solfataricus utilizes D-glucose as a sole carbon and energy source through the non-phosphorylated Entner–Doudoroff pathway. It has been suggested that this micro-organism metabolizes D-gluconate, the oxidized form of D-glucose, to pyruvate and D-glyceraldehyde by using two unique enzymes, D-gluconate dehydratase and 2-keto-3-deoxy-D-gluconate aldolase. In the present study, we report the purification and characterization of D-gluconate dehydratase from S. solfataricus, which catalyses the conversion of D-gluconate into 2-keto-3-deoxy-D-gluconate. D-Gluconate dehydratase was purified 400-fold from extracts of S. solfataricus by ammonium sulphate fractionation and chromatography on DEAE-Sepharose, Q-Sepharose, phenyl-Sepharose and Mono Q. The native protein showed a molecular mass of 350 kDa by gel filtration, whereas SDS/PAGE analysis provided a molecular mass of 44 kDa, indicating that D-gluconate dehydratase is an octameric protein. The enzyme showed maximal activity at temperatures between 80 and 90 °C and pH values between 6.5 and 7.5, and a half-life of 40 min at 100 °C. Bivalent metal ions such as Co2+, Mg2+, Mn2+ and Ni2+ activated, whereas EDTA inhibited the enzyme. A metal analysis of the purified protein revealed the presence of one Co2+ ion per enzyme monomer. Of the 22 aldonic acids tested, only D-gluconate served as a substrate, with Km=0.45 mM and Vmax=0.15 unit/mg of enzyme. From N-terminal sequences of the purified enzyme, it was found that the gene product of SSO3198 in the S. solfataricus genome database corresponded to D-gluconate dehydratase (gnaD). We also found that the D-gluconate dehydratase of S. solfataricus is a phosphoprotein and that its catalytic activity is regulated by a phosphorylation–dephosphorylation mechanism. This is the first report on biochemical and genetic characterization of D-gluconate dehydratase involved in the non-phosphorylated Entner–Doudoroff pathway.

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46

Theodossis, Alex, Christine C. Milburn, Narinder I. Heyer, Henry J. Lamble, David W. Hough, Michael J. Danson, and Garry L. Taylor. "Preliminary crystallographic studies of glucose dehydrogenase from the promiscuous Entner–Doudoroff pathway in the hyperthermophilic archaeonSulfolobus solfataricus." Acta Crystallographica Section F Structural Biology and Crystallization Communications 61, no. 1 (December 24, 2004): 112–15. http://dx.doi.org/10.1107/s174430910403101x.

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47

Patra, T., H. Koley, T. Ramamurthy, A. C. Ghose, and R. K. Nandy. "The Entner-Doudoroff Pathway Is Obligatory for Gluconate Utilization and Contributes to the Pathogenicity of Vibrio cholerae." Journal of Bacteriology 194, no. 13 (April 27, 2012): 3377–85. http://dx.doi.org/10.1128/jb.06379-11.

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48

Liang, Shaoxiong, Hong Chen, Jiao Liu, and Jianping Wen. "Rational design of a synthetic Entner–Doudoroff pathway for enhancing glucose transformation to isobutanol in Escherichia coli." Journal of Industrial Microbiology & Biotechnology 45, no. 3 (January 30, 2018): 187–99. http://dx.doi.org/10.1007/s10295-018-2017-5.

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49

Reher, Matthias, Tobias Fuhrer, Michael Bott, and Peter Schönheit. "The Nonphosphorylative Entner-Doudoroff Pathway in the Thermoacidophilic Euryarchaeon Picrophilus torridus Involves a Novel 2-Keto-3-Deoxygluconate- Specific Aldolase." Journal of Bacteriology 192, no. 4 (December 18, 2009): 964–74. http://dx.doi.org/10.1128/jb.01281-09.

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ABSTRACT The pathway of glucose degradation in the thermoacidophilic euryarchaeon Picrophilus torridus has been studied by in vivo labeling experiments and enzyme analyses. After growth of P. torridus in the presence of [1-13C]- and [3-13C]glucose, the label was found only in the C-1 and C-3 positions, respectively, of the proteinogenic amino acid alanine, indicating the exclusive operation of an Entner-Doudoroff (ED)-type pathway in vivo. Cell extracts of P. torridus contained all enzyme activities of a nonphosphorylative ED pathway, which were not induced by glucose. Two key enzymes, gluconate dehydratase (GAD) and a novel 2-keto-3-deoxygluconate (KDG)-specific aldolase (KDGA), were characterized. GAD is a homooctamer of 44-kDa subunits, encoded by Pto0485. KDG aldolase, KDGA, is a homotetramer of 32-kDa subunits. This enzyme was highly specific for KDG with up to 2,000-fold-higher catalytic efficiency compared to 2-keto-3-deoxy-6-phosphogluconate (KDPG) and thus differs from the bifunctional KDG/KDPG aldolase, KD(P)GA of crenarchaea catalyzing the conversion of both KDG and KDPG with a preference for KDPG. The KDGA-encoding gene, kdgA, was identified by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) as Pto1279, and the correct translation start codon, an ATG 24 bp upstream of the annotated start codon of Pto1279, was determined by N-terminal amino acid analysis. The kdgA gene was functionally overexpressed in Escherichia coli. Phylogenetic analysis revealed that KDGA is only distantly related to KD(P)GA, both enzymes forming separate families within the dihydrodipicolinate synthase superfamily. From the data we conclude that P. torridus degrades glucose via a strictly nonphosphorylative ED pathway with a novel KDG-specific aldolase, thus excluding the operation of the branched ED pathway involving a bifunctional KD(P)GA as a key enzyme.

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50

Liu, Shuang, Pei Kang, Zhenzhen Cui, Zhiwen Wang, and Tao Chen. "Increased riboflavin production by knockout of 6-phosphofructokinase I and blocking the Entner–Doudoroff pathway in Escherichia coli." Biotechnology Letters 38, no. 8 (April 12, 2016): 1307–14. http://dx.doi.org/10.1007/s10529-016-2104-5.

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