d-Xylose Degradation Pathway in the Halophilic Archaeon Haloferax volcanii

Johnsen, Ulrike; Dambeck, Michael; Zaiss, Henning; Fuhrer, Tobias; Soppa, Jörg; Sauer, Uwe; Schönheit, Peter

doi:10.1074/jbc.m109.003814

Cited by 95 publications

(102 citation statements)

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“…brasilense and Cau. crescentus, was identified as part of the xylose degradation gene cluster, which is upregulated during growth on D-xylose (287). Although the enzyme activity was not confirmed, nor was an in-frame deletion mutant constructed, to confirm that this enzyme is essential for D-xylose degradation.…”

Section: Bacteria Eukaryamentioning

confidence: 96%

“…Also, glycolaldehyde is shuttled into the CAC after oxidation to glycoxylate via glycolate and further conversion to malate via malate synthase. In Archaea, pentose utilization has been reported for some aerobic halophiles and for Sulfolobus species (14,283,287,291,343,345). For other Archaea, including hyperthermophiles from the orders Thermococcales, Archaeoglobales, Thermoproteales, Desulfurococcales, and Pyrodictyales, no growth on pentoses has been reported, although many of these organisms are able to grow with hexoses or hexose polymers as carbon and energy sources (14).…”

Section: Pentose Degradation Pathways In Archaeamentioning

confidence: 99%

“…volcanii, this pathway was also proposed for the halophiles Har. marismortui, Haloterrigena turkmenica, and Haloterrigena lacusprofundi based on comparative genome analysis, although growth of the latter two organisms on D-xylose has not yet been described (287,346). Conversely, in Halorhabdus utahensis, the presence of the classical xylose degradation pathway via xylose isomerase and xylulokinase, as known, e.g., for E. coli, has been proposed (346)(347)(348).…”

Section: Pentose Degradation Pathways In Archaeamentioning

confidence: 99%

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Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Bräsen

Esser

Rauch

et al. 2014

Microbiol Mol Biol Rev

279

294

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SUMMARY The metabolism of Archaea , the third domain of life, resembles in its complexity those of Bacteria and lower Eukarya . However, this metabolic complexity in Archaea is accompanied by the absence of many “classical” pathways, particularly in central carbohydrate metabolism. Instead, Archaea are characterized by the presence of unique, modified variants of classical pathways such as the Embden-Meyerhof-Parnas (EMP) pathway and the Entner-Doudoroff (ED) pathway. The pentose phosphate pathway is only partly present (if at all), and pentose degradation also significantly differs from that known for bacterial model organisms. These modifications are accompanied by the invention of “new,” unusual enzymes which cause fundamental consequences for the underlying regulatory principles, and classical allosteric regulation sites well established in Bacteria and Eukarya are lost. The aim of this review is to present the current understanding of central carbohydrate metabolic pathways and their regulation in Archaea . In order to give an overview of their complexity, pathway modifications are discussed with respect to unusual archaeal biocatalysts, their structural and mechanistic characteristics, and their regulatory properties in comparison to their classic counterparts from Bacteria and Eukarya . Furthermore, an overview focusing on hexose metabolic, i.e., glycolytic as well as gluconeogenic, pathways identified in archaeal model organisms is given. Their energy gain is discussed, and new insights into different levels of regulation that have been observed so far, including the transcript and protein levels (e.g., gene regulation, known transcription regulators, and posttranslational modification via reversible protein phosphorylation), are presented.

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Section: Bacteria Eukaryamentioning

confidence: 96%

Section: Pentose Degradation Pathways In Archaeamentioning

confidence: 99%

Section: Pentose Degradation Pathways In Archaeamentioning

confidence: 99%

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Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Bräsen

Esser

Rauch

et al. 2014

Microbiol Mol Biol Rev

279

294

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“…In Haloferax volcanii, for example, D-xylose is metabolized via the pathway leading directly to 2-oxoglutarate, not utilizing the branch involving aldol cleavage of 2-keto-3-deoxy-D-xylonate and subsequent conversion to malate (26). Furthermore, the xylose dehydrogenase of H. volcanii is highly specific; D-glucose was used at a 130-fold lower catalytic efficiency than D-xylose, and no significant activity was measured with L-arabinose.…”

Section: A Proposed Catabolic Pathway For D-xylose and L-arabinose-mentioning

confidence: 99%

Metabolism of Pentose Sugars in the Hyperthermophilic Archaea Sulfolobus solfataricus and Sulfolobus acidocaldarius

Nunn

Johnsen

Schönheit

et al. 2010

Journal of Biological Chemistry

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We have previously shown that the hyperthermophilic archaeon, Sulfolobus solfataricus, catabolizes D-glucose and D-galactose to pyruvate and glyceraldehyde via a non-phosphorylative version of the Entner-Doudoroff pathway. At each step, one enzyme is active with both C6 epimers, leading to a metabolically promiscuous pathway. On further investigation, the catalytic promiscuity of the first enzyme in this pathway, glucose dehydrogenase, has been shown to extend to the C5 sugars, D-xylose and L-arabinose. In the current paper we establish that this promiscuity for C6 and C5 metabolites is also exhibited by the third enzyme in the pathway, 2-keto-3-deoxygluconate aldolase, but that the second step requires a specific C5-dehydratase, the gluconate dehydratase being active only with C6 metabolites. The products of this pathway for the catabolism of D-xylose and L-arabinose are pyruvate and glycolaldehyde, pyruvate entering the citric acid cycle after oxidative decarboxylation to acetyl-coenzyme A. We have identified and characterized the enzymes, both native and recombinant, that catalyze the conversion of glycolaldehyde to glycolate and then to glyoxylate, which can enter the citric acid cycle via the action of malate synthase. Evidence is also presented that similar enzymes for this pentose sugar pathway are present in Sulfolobus acidocaldarius, and metabolic tracer studies in this archaeon demonstrate its in vivo operation in parallel with a route involving no aldol cleavage of the 2-keto-3-deoxy-pentanoates but direct conversion to the citric acid cycle C5-metabolite, 2-oxoglutarate.Sulfolobus solfataricus and Sulfolobus acidocaldarius are hyperthermophilic archaea that grow optimally at 78 -85°C, pH 2-4, and are able to utilize a variety of carbon sources, including the four most-commonly occurring sugars in nature, D-glucose, D-galactose, D-xylose, and L-arabinose (1).Metabolism of glucose in S. solfataricus and S. acidocaldarius proceeds via a non-phosphorylative variant of the Entner-Doudoroff pathway, which generates pyruvate with no net production of ATP (Fig. 1) (2-5). Glucose dehydrogenase catalyzes the conversion of glucose to gluconate, which is then dehydrated to 2-keto-3-deoxygluconate (KD-gluconate) 4 by gluconate dehydratase. KD-gluconate in turn is cleaved to pyruvate and glyceraldehyde via 2-keto-3-deoxygluconate aldolase (KDG-aldolase), the glyceraldehyde generating a second molecule of pyruvate via the actions of glyceraldehyde oxidoreductase, glycerate kinase, enolase, and pyruvate kinase.In vitro kinetic analyses of glucose dehydrogenase, gluconate dehydratase, and KDG-aldolase from S. solfataricus showed these enzymes are also capable of catalyzing the catabolism of galactose, the C4 epimer of glucose, to pyruvate and glyceraldehyde, leading to the suggestion that the pathway exhibits a metabolic promiscuity toward these two hexose sugars (5-7). Because recombinantly produced glucose dehydrogenase has good activity with the pentose sugars D-xylose and L-arabinose (6) and KDG-aldolase catalyze...

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“…Initially, the microarray was used to analyze the metabolic changes following a switch from casamino acids to glucose, 34 since then it has been successfully used e.g., to identify the genes involved in xylose metabolism, to discover a tryptophan-inducible promoter, to study translational regulation, and to compare the transcriptomes of deletion mutants with that of the wild-type. 35,39,46,47 The inclusion of a probe in the microarray and the detection of a signal in microarray analyses are listed. * 2 It is shown if the sRNA was detected by hTS and/or northern blot analysis.…”

confidence: 99%

Bioinformatic prediction and experimental verification of sRNAs in the haloarchaeonHaloferax volcanii

Babski¹,

Tjaden²,

Voss³

et al. 2011

RNA Biology

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d-Xylose Degradation Pathway in the Halophilic Archaeon Haloferax volcanii

Abstract: The pathway of D-xylose degradation in archaea is unknown. In a previous study we identified in Haloarcula marismortui the first enzyme of xylose degradation, an inducible xylose dehydrogenase (Johnsen, U., and Schönheit, P.

Cited by 95 publications

References 28 publications

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Metabolism of Pentose Sugars in the Hyperthermophilic Archaea Sulfolobus solfataricus and Sulfolobus acidocaldarius

Bioinformatic prediction and experimental verification of sRNAs in the haloarchaeonHaloferax volcanii

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