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

Bräsen, Christopher; Esser, Dominik; Rauch, Bernadette; Siebers, Bettina

doi:10.1128/mmbr.00041-13

Cited by 280 publications

(307 citation statements)

References 576 publications

(1,228 reference statements)

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“…Thorarchaeota appear to have the ability to convert glucose-6-phosphate partially or completely to phosphoenol pyruvate (Figure 4). Pyruvate kinase was not identified in any of the Thorarchaeota and instead pyruvate appears to be generated using phosphoenolpyruvate synthase (Brasen et al, 2014). All three genomes contain the genes necessary to convert pyruvate to acetyl-CoA including both the E1 (PDHA) and E2 (PDHB) units of pyruvate dehydrogenase and all the subunits of pyruvate ferredoxin oxioreductase (porABDG).…”

Section: Smtz-1 Bin 83mentioning

confidence: 99%

Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction

Seitz¹,

et al. 2016

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Marine and estuary sediments contain a variety of uncultured archaea whose metabolic and ecological roles are unknown. De novo assembly and binning of high-throughput metagenomic sequences from the sulfate-methane transition zone in estuary sediments resulted in the reconstruction of three partial to near-complete (2.4-3.9 Mb) genomes belonging to a previously unrecognized archaeal group. Phylogenetic analyses of ribosomal RNA genes and ribosomal proteins revealed that this group is distinct from any previously characterized archaea. For this group, found in the White Oak River estuary, and previously registered in sedimentary samples, we propose the name 'Thorarchaeota'. The Thorarchaeota appear to be capable of acetate production from the degradation of proteins. Interestingly, they also have elemental sulfur and thiosulfate reduction genes suggesting they have an important role in intermediate sulfur cycling. The reconstruction of these genomes from a deeply branched, widespread group expands our understanding of sediment biogeochemistry and the evolutionary history of Archaea.

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Section: Smtz-1 Bin 83mentioning

confidence: 99%

Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction

Seitz¹,

et al. 2016

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“…They generate ATP, NAD(P)H, and biosynthetic precursors for amino acids, nucleotides, and fatty acids. Prokaryotes, in contrast, exhibit a broad diversity in sugar oxidation pathways (3)(4)(5). These routes differ in ATP yield, in the enzymes and cofactors involved, and in the chemical intermediates of the pathways.…”

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confidence: 99%

The Entner–Doudoroff pathway is an overlooked glycolytic route in cyanobacteria and plants

Chen

Schreiber

Appel

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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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 CO 2 via the Calvin-Benson cycle. T he breakdown of glucose is central for energy and biosynthetic metabolism throughout all domains of life. The Embden-Meyerhof-Parnas (EMP) pathway (glycolysis) and the oxidative pentose phosphate (OPP) pathway are the backbones of eukaryotic carbon and energy metabolism (1, 2). They generate ATP, NAD(P)H, and biosynthetic precursors for amino acids, nucleotides, and fatty acids. Prokaryotes, in contrast, exhibit a broad diversity in sugar oxidation pathways (3-5). These routes differ in ATP yield, in the enzymes and cofactors involved, and in the chemical intermediates of the pathways. The most common glycolytic routes in prokaryotes are the EMP, ED, and OPP pathways (Fig. 1). The key enzyme unique to the ED pathway is 2-keto-3-deoxygluconate-6-phosphate (KDPG) aldolase (Eda), whereas phosphofructokinase (PFK) is unique to the EMP pathway in the catabolic direction (3, 6). KDPG as a metabolite is exclusively found in the ED pathway (Fig. 1). The first two steps of the OPP pathway are catalyzed by glucose 6-phosphate-dehydrogenase (Zwf) and 6-phosphogluconate dehydrogenase (Gnd). As the pentose phosphate pathway can either run in its oxidative mode (OPP pathway) to oxidize carbohydrates or in its reductive mode ...

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“…In the second branch, KDG is phosphorylated by KDG kinase (KDGK) to generate 2-keto-3-deoxy-6-phosphogluconate (KDPG), which is cleaved to pyruvate and glyceraldehyde-3-phosphate (GAP) by a bifunctional KDG/ KDPG aldolase (KDPGA) that catalyzes the cleavage of both KDG and KDPG. Further conversion of GAP to pyruvate involves nonphosphorylative GAP dehydrogenase (GAPN), phosphoglycerate mutase, enolase, and pyruvate kinase (1,2). As indicated for the npED pathway of P. torridus, the branched ED pathway of S. solfataricus was also described to be promiscuous for the degradation of both D-glucose and D-galactose (5)(6)(7).…”

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confidence: 99%

“…Accordingly, the enzymes GDH, GAD, KDGK, and KDG/KDPG aldolase catalyzed the conversion of glucose and galactose and the corresponding subsequent intermediates at similar catalytic efficiencies (7,8). A modified ED pathway similar to the branched ED pathway of S. solfataricus has been proposed for the hyperthermophilic archaeon Thermoproteus tenax (1).…”

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confidence: 99%

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

et al. 2016

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The halophilic archaeon Haloferax volcanii has 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 C 4 epimers 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 from H. 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 ⌬gad mutant 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 the in vivo operation of the spED pathway for glucose degradation in H. 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 haloarchaeon Haloferax volcanii. The functional involvement of the three enzymes was proven by analyses of the corresponding knockout mutants. These results provide evidence for the in vivo operation of the semiphosphorylative Entner-Doudoroff pathway in haloarchaea and thus expand our understanding of the unusual sugar degradation pathways in the domain Archaea. Glucose degradation in thermoacidophilic and halophilic archaea has been proposed to proceed via modified versions of the classical Entner-Doudoroff (ED) pathway of bacteria (1, 2) (Fig. 1). For the thermoacidophilic euryarchaeon Picrophilus torridus, a nonphosphorylative ED (npED) pathway was reported (3). Accordingly, glucose is converted to 2-keto-3-deoxygluconate (KDG) via glucose dehydrogenase (GDH) and gluconate dehydratase (GAD). KDG is then cleaved by a KDG aldolase to pyruvate and glyceraldehyde (GA), which is converted to a second molecule of pyruvate via glyceraldehyde dehydrogenase, 2-phosphoglycerate forming glycerate kinase, enolase, and pyruvate kinase. The pathway was proposed to be promiscuous, being involved in the degradation of both D-glucose and its C 4 epimer ...

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

Cited by 280 publications

References 576 publications

Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction

Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction

The Entner–Doudoroff pathway is an overlooked glycolytic route in cyanobacteria and plants

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

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