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Home , Glucokinase, Glycerate kinase, Phosphofructokinase 2

Unusual pathways and of central in Archaea Bettina Siebers1 and Peter Scho¨ nheit2

Sugar-utilizing hyperthermophilic and halophilic Archaea are oxidized to 3-phosphoglycerate by way of phosphor- degrade and glucose polymers to acetate or to CO2 ylative glyceraldehyde-3-phosphate dehydrogenase and using O2, nitrate, sulfur or sulfate as electron acceptors. phosphoglycerate ; in the latter reaction, ATP is Comparative analyses of glycolytic pathways in these formed by level . 3-Phospho- organisms indicate a variety of differences from the classical glycerate is converted to phosphoenolpyruvate (PEP) by Emden–Meyerhof and Entner–Doudoroff pathways that are way of and . The con- operative in and Eukarya, respectively. The archaeal version of PEP to pyruvate is catalyzed by allosteric pathways are characterized by the presence of numerous novel regulated , and ATP is formed by sub- enzymes and families that catalyze, for example, strate level phosphorylation. The net ATP yield of the the phosphorylation of glucose and of 6-phosphate, EM pathway is 2 mol ATP/mol glucose. the isomerization of glucose 6-phosphate, the cleavage of fructose 1,6-bisphosphate, the oxidation of glyceraldehyde In the classical phosphorylative ED pathway, glucose-6- 3-phosphate and the conversion of acetyl-CoA to acetate. phosphate, which is formed by ATP-dependent glucoki- Recent major advances in deciphering the complexity of nase, is oxidized to 6-phosphogluconate by glucose-6- archaeal central were gained by phosphate dehydrogenase. Subsequent dehydration by combination of classical biochemical and genomic-based 6-phosphogluconate dehydratase yields 2-keto-3-deoxy- approaches. (6-phospho)-gluconate (KDPG), the characteristic inter- Addresses mediate of the pathway. KDPG cleavage by KDPG 1 Universita¨ t Duisburg-Essen, Campus Essen, FB Biologie und aldolase forms pyruvate and GAP, which is converted Geografie, Mikrobiologie, Universita¨ tsstr.5, D-45117 Essen, Germany to pyruvate by the enzymes also used in the EM pathway. 2 Christian–Albrechts–Universita¨ t Kiel, Institut fu¨ r Allgemeine The net ATP yield of ED pathway is 1 mol ATP/mol Mikrobiologie, Am Botanischen Garten 1-9, D-241118 Kiel, Germany gucose. Corresponding author: Scho¨ nheit, Peter ([email protected]) In the hyperthermophilic and the thermophilic aerobic Archaea (Thermoplasma acidophilum [1] and Sulfolobus solfataricus [2,3,4], respectively) glucose is metabolized Current Opinion in Microbiology 2005, 8:695–705 by way of modifications of the ED pathway, whereas the This review comes from a themed issue on hyperthermophilic fermentative anaerobes Pyrococcus fur- Growth and development iosus, Thermococcus species, Desulfurococcus amylolyticus, the Edited by John N Reeve and Ruth Schmitz sulfate reducer Archaeoglobus fulgidus strain 7324 and the Available online 26th October 2005 microaerophilic Pyrobaculum aerophilum use different modifications of the EM pathway ([5–8]; Reher et al. 1369-5274/$ – see front matter personal communication). To date, the only Archaeon # 2005 Elsevier Ltd. All rights reserved. known to use modifications of both the EM and ED DOI 10.1016/j.mib.2005.10.014 pathways in parallel for glucose degradation is the hyperthermophilic sulfur-dependent anaerobe Thermo- proteus tenax [4,6,9–11,12]. In aerobic halophilic Archaea Introduction (e.g. Haloarcula marismortui and Halobacterium saccharo- Comparative biochemical studies on central carbohydrate vorum), 13C-nuclear magnetic resonance (13C-NMR) and metabolism revealed that Archaea utilize modifications of enzymatic studies as well as DNA microarray analyses the classical Embden–Meyerhof (EM) and Entner–Dou- revealed that glucose is degraded only by way of a doroff (ED) pathways for (Figures 1–3). modified ‘semi-phosphorylative’ ED pathway [13–15], whereas fructose is almost completely metabolized by In the classical EM pathway, glucose is converted to way of a modified EM pathway (in Haloarcula marismortui fructose-1,6-bisphosphate (FBP), the central intermedi- [13] and Haloarcula vallismortis [16]). ate, by way of ATP-dependent /, phosphoglucose and ATP-dependent allosteric Degradation of pyuvate formed by the various glycolytic . Cleavage of FBP to dihydrox- pathways involves oxidation to acetyl-CoA, which is yacetone phosphate and glyceraldehyde-3-phosphate catalyzed in all Archaea by pyruvate-ferredoxin oxidor- (GAP) by FBP aldolase and the subsequent isomerization eductase. In anaerobic fermentative Archaea, acetyl-CoA by triosephosphate isomerase yields two mol GAP, which is further converted to acetate by an unusual prokaryotic www.sciencedirect.com Current Opinion in Microbiology 2005, 8:695–705 696 Growth and development

Figure 1

Pathways and enzymes of glucose degradation to acetate or to CO2 in Archaea. Pyrococcus furiosus, Thermococcus celer, Desulfurococcus 2 amylolyticus and Archaeoglobus fulgidus strain 7324 (+ SO4 ) convert glucose to generate acetate as a main . However, Pyrobaculum aerophilum (+ O2 or NO3 ), Thermoproteus tenax (+ S), Sulfolobus solfataricus (+ O2)andThermoplasma acidophilum (+ O2) completely oxidize glucose to CO2 using the external electron acceptors indicated. The aerobic Halobacterium saccharovorum and Haloarcula marismortui form significant amounts of acetate in addition to CO2. Glucose degradation to pyruvate proceeds either by modified Embden–Meyerhof pathways (Mod. EM) or by modified Entner–Doudoroff pathways (Mod. ED). The modifications of the EM and ED pathways are specified in Figure 2 and Figure 3, respectively. Pyruvate is converted to acetyl-CoA by pyruvate:ferredoxin (Pyr:Fd OR). The conversion of acetyl-CoA to acetate is catalyzed by ADP-forming acetyl-CoA synthetase (ADP-forming) (ACD) (acetyl-CoA + ADP + Pi = acetate + ATP + CoA). The 1 oxidation of acetyl-CoA to 2CO2 proceeds via the tricarboxylic acid cycle (TCA cycle). T. tenax and S. solfataricus use a ‘branched’ (non- and semi-phosphorylative) ED modification (see text). enzyme — ADP-forming acetyl-CoA synthetase (ACD) pathways, correspond to the classical glycolytic pathways, — whereas in O2-, nitrate- and sulfur-reducing Archaea, most of the respective archaeal enzymes show no acetyl-CoA is oxidized to 2CO2 through the tricarboxylic similarity to their ‘classical’ bacterial and eukaryal coun- acid cycle (Figure 1). terparts and therefore represent examples of non-homo- logous displacement. Furthermore, the great variety Analysis of metabolism in methanogenic Archaea, of alternative enzymes, often from different enzyme which are mostly lithoautotrophic H2/CO2- or acetate- families, identified in different Archaea (e.g. sugar utilizing organisms, mainly concerns . In , phosphoglucose and enzymes of gly- some Methanococcus species, the degradation of intracel- ceraldehyde-3-phosphate oxidation) reflects a great meta- lular seems to be performed by glycolysis that bolic diversity in this third domain of life, which exceeds uses enzymes of a modified EM pathway. that of Bacteria and Eukarya.

Although most of the catalyzed reactions, and thus the Recently, great advances were obtained in elucidation of intermediates of the modified archaeal EM and ED archaeal sugar metabolism for enzymes from (hyper)ther-

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Figure 2

Modifications of the Embden–Meyerhof (EM) pathway in Archaea. The modified archaeal EM pathways differ from the classical EM pathway as it has unusual enzymes for glucose phosphorylation, phosphoglucose isomerization, fructose 6-phosphate phosphorylation, fructose-1,6- bisphosphate cleavage, glyceraldehyde-3-phosphate oxidation and PEP conversion to pyruvate. For characterized archaeal enzymes, comparison to ‘classical’ EM enzymes and energy yield, see main body of text. Abbreviations: aFBA, archaeal class I FBA; cPGI, cupin PGI;

DHAP, dihydroxyacetone phosphate; FBA, fructose 1,6-bisphosphatae aldolase; F-1,6-BP, fructose 1,6-bisphosphate; Fdox and Fdred, oxidized and reduced ferredoxin; F-6-P, fructose-6-phosphate; GAP, glyceraldehyde-3-phosphate; GAPN, non-phosphorylative glyceraldehyde 3-phosphate dehydrogenase; GAPOR, glyceraldehyde-3 phosphate-ferredoxin oxidoreductase; GLK, glucokinase (ADP- or ATP-dependent); G-6-P, glucose-6-phosphate; PEP, phosphoenolpyruvate; PFK, 6-; 2-PG, 2-phosphoglycerate; 3-PG, 3-phosphoglycerate; PGI/PMI, bifunctional phosphoglucose/phosphomannose isomerase); PGI, phosphoglucose isomerase; PGM, phosphoglycerate mutase; PK, pyruvate kinase; TIM, triosephosphate isomerase. mophilic Archaea, because most can be expressed in the Unusual enzymes of modfied EM mesophilic host Escherichia coli and can subsequently be pathways in Archaea characterized as recombinant enzymes. Furthermore, the Glucose phosphorylation increased intrinsic rigidity of hyperthermophilic proteins As Archaea lack the bacterial PEP-dependent phopho- obviously favours crystallization and thus structural ana- system-like transport systems, the initial phos- lysis. However, in halophiles, the adaptation of proteins to phorylation of glucose is the first activation step in the high salt concentrations hampers respective develop- EM modifications. In Archaea, a great variety of enzymes, ments and therefore less information is available about which differ in specificity and their phosphoryl donor, is purified and crystallized enzymes. observed. In Euryarchaeota, ADP-dependent glucoki- nases, which exhibit high specificity for glucose, were In this review, we will present a survey of the archaeal identified and characterized (e.g. in P. furiosus [5,23], modifications of EM and ED pathways and of the bio- Thermococcus litoralis [24] and A. fulgidus strain 7324 chemistry and regulation of the unusual enzymes [25]). In addition, a bifunctional ADP-dependent gluco- involved. For previous reviews and review-like articles kinase/phosphofructokinase, which is active on both glu- on this topic, see [4,6,12,17,18,19,20–22]. cose and fructose 6-phosphate, was described in www.sciencedirect.com Current Opinion in Microbiology 2005, 8:695–705 698 Growth and development

Figure 3

Modifications of the Entner–Doudoroff (ED) pathway in Archaea. (a) The non-phosphorylative ED pathway (enzymes 1–7) is operative in Thermoplasma acidophilum. This pathway is not coupled with a net ATP yield (‘non-phosphorylative’). (b) The semi-phosphorylative ED pathway (enzymes 1, 2, 8, 3, 9–12, 6 and 7) is present in halophilic Archaea. Owing to the phosphorylative GAPDH/ enzyme couple, this ED modification yields one ATP. A branched ED (i.e. a combination of both non-phosphorylative [a] and semi-phosphorylative [b] ED pathways) is operative in S. solfataricus and T. tenax. Owing to non-phosphorylative GAPN, the net ATP yield is zero. Abbreviations: 1.3 BPG, 1,3-bisphosphoglycerate; Fdox and Fdred, oxidized and reduced ferredoxin; GA, glyceraldehyde; GAP, glyceraldehyde-3 phosphate; KDG, 2-keto-3-deoxy-gluconate; KDPG, 2-keto-3-deoxy-6-phosphogluconate; PEP, phosphoenolpyruvate; 2 PG, 2-phosphoglycerate; 3 PG, 3-phosphoglycerate. Enzymes are nnumbered as follows: 1, glucose dehydrogenase; 2, gluconate dehydratase; 3, KD(P)G aldolase; 4, glyceraldehyde dehydrogenase (poposed for T. acidophilum [12]), glyceraldehyde:ferredoxin oxidoreductase (proposed for T. tenax [76]) or glyceraldehyde oxidoreductase (proposed for S. acidocaldarius [101]); 5, ; 6, enolase; 7, pyruvate kinase; 8, KDG kinase; 9, GAPDH; 10, phosphoglycerate kinase; 11, GAPN; 12, phosphoglycerate mutase.

Methanococaldococcus jannaschii [26]. Structural analysis of Glucose 6-phosphate/fructose 6-phosphate the enzymes from T. litoralis [27] and Pyrococcus horikoshii isomerization [28] grouped the ADP-dependent kinases in the riboki- The isomerization of glucose 6-phosphate in Archaea is nase superfamily (SCOP; structural classification of pro- catalyzed by three different protein families. Homologs of teins). In Crenarchaeota (e.g. Aeropyrum pernix [29,30] and the classical phosphoglucose isomerase (PGI) superfam- T. tenax [31]), ATP-dependent glucokinases with broad ily, which comprise almost all PGIs in Eukarya and hexokinase-like substrate specificity (e.g. glucose, fruc- Bacteria, were identified in only three Archaea: in two tose, and 2-deoxyglucose) were identified. The halophiles (Haloarcula marismortui and Halobacterium ATP–dependent enzymes are members of the ROK NRC1) and in M. jannaschii. The enzyme from M. jan- family (repressor protein, open reading frame, sugar naschii was characterized [32]. kinase), which belong to the actin-ATPase superfamily (SCOP). No archaeal glucokinases exhibit allosteric prop- In the Euryarchaeota P. furiosus, Thermococcus litoralis, A. erties and thus differ from eukaryotic , which fulgidus and Methansosarcina mazei, a novel type of metal- constitute an allosteric control step in the classical EM dependent PGIs have been identified and characterized pathway. [33,34,35,36]. These PGIs belong to the cupin super-

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family (cPGI) and thus represent a convergent line of PGI Glyceraldehyde 3-phosphate oxidation evolution. The crystal structure of a cPGI from P. furiosus In Archaea, the oxidation of GAP in glucose degradation revealed a typical cupin fold [37–39], and a hydride is catalyzed by either glyceraldehyde-3-phosphate:ferre- mechanism of glucose 6-phosphate isomerization was doxin oxidoreductase (GAPOR; in P. furiosus [57,58], A. proposed [37]InA. pernix, P. aerophilum, T. acidophilum fulgidus strain 7324 and Pyrobaculum aerophilum; Reher [40,41] and T. tenax [12] an unusual PGI was described et al., personal communication) and/or non-phosphorylat- that differs from all knows PGIs; this catalyzes the iso- ing glyceraldehyde-3-phosphate dehydrogenase (GAPN; merization of both glucose-6-phosphate and mannose-6- in T. tenax [59] and S. solfataricus;[4], Ettema et al. phosphate at similar catalytic efficiency, defining the personal communication). Both enzymes catalyze the enzyme as bifunctional phosphoglucose/phosphoman- irreversible, non-phosphorylating oxidation of GAP to nose isomerase (PGI/PMI). PGI/PMIs represent a novel 3-phosphoglycerate using either ferredoxin or NAD(P)+ family within the PGI superfamily, as proven by the as electron acceptors. GAPOR belongs to the aldehyde crystal structure of the P. aerophilum enzyme [42]; a ferredoxin oxidoreductase superfamily. The archaeal structural basis for bifunctionality was proposed [43]. GAPN is a member of the aldehyde dehydrogenase superfamily, but the characterized enzymes of T. tenax Fructose 6-phosphate phosphorylation and S. solfataricus are unusual in respect to their allosteric The phosphorylation of fructose-6-phosphate is catalyzed properties ([4,59] Ettema et al. personal communication). by different enzymes that vary in respect to their phos- The T. tenax enzyme is controlled by the energy charge of phoryl donor PPi, ADP and ATP. Whereas the PPi- the and by early intermediates of the EM pathway as dependent phosphofructokinase is reversible (T. tenax well as by glycogen metabolism, suggesting a central role [12,44]), the ADP-dependent phosphofructokinases (in in the regulation of glycolysis. The crystal structure of the P. furiosus [5,45], Thermococcus zilligii [46], A. fulgidus 7324 T. tenax GAPN was solved [60]. The structural basis for [47] and glycogen-forming methanogenic Archaea [48]) the of the T. tenax enzyme was and the ATP-dependent 6-phophofructokinases (in deciphered and based on sequence comparisons allosteric Desulfurococcus amylolyticus [49] and A. pernix [50,51]) properties were predicted for the enzymes of Sulfolobus represent unidirectional glycolytic enzymes. tokodaii, S. solfataricus, A. pernix and P. furiosus [61].

Phylogenetic analysis revealed that the PPi-dependent All Archaea contain the classical type of glyceraldehyde- phophofructokinase is related to classical ATP-depen- 3-phosphate dehydrogenase (GAPDH), which catalyzes dent enzymes and is a member of the phosphofructoki- the reversible phosphorylating oxidation of GAP to yield nase A (PFK A) family [44]. ADP-dependent 1,3-bisphosphoglycerate. In Archaea, with the exception phosphofructokinases belong to the superfam- of glycolysis in halophilic species (Figure 3), GAPDH ily [27]. The archaeal ATP-dependent phosphofructoki- appears to be exclusively involved in gluconeogenesis. nases are members of PFK B family, which also belong to Enzymatic as well as transcript analyses in P. furiosus the ribokinase superfamily. The crystal structure of an [58,62,63] and T. tenax [4,12,64], which harbour all three archaeal PFK B homolog, an ATP-dependent nucleoside GAP-converting enzymes, suggest a catabolic function for kinase from Methanocaldococcus jannaschi, was solved [52]. GAPN and GAPOR and an anabolic function for the GAPDH/phosphoglycerate kinase enzyme couple. Strikingly, for all archaeal phosphofructokinases described to date, no allosteric regulation by classical effectors of 3-Phosphoglycerate/2-phosphoglycerate bacterial and eukaryal ATP-dependent phosphofructoki- interconversion nases was observed. This indicates that these enzymes do Phosphoglycerate mutase (PGM) catalyzes the intercon- notrepresentasiteofallostericcontrolinarchaealglycolysis. version of 3-phosphoglycerate and 2-phosphoglycerate. Two distinct PGM types have been described that differ Fructose 1,6-bisphosphate cleavage in their requirement for 2,3-bisphosphoglycerate (dPGM) FBP aldolase catalyzes the reversible cleavage of FBP to as the phosphoryl donor. In Archaea, distant homologues glyceraldehyde 3-phosphate and dihydroxyacetone phos- of -independent PGM (iPGM) and dPGM have phate. Archaeal FBP aldolases show no obvious sequence been identified. iPGM, which belongs to the alkaline similarity to the classical bacterial and eukaryal class I and (binuclear metalloenzyme) superfamily, was II FBP aldolases, but form a new family of archaeal-type characterized (in P. furiosus, M. jannaschii [65,66] and S. class I FBP aldolases (in T. tenax and P. furiosus [53]). solfataricus [67]). Structural analysis of the T. tenax enzyme revealed new insights in the evolution of (ba)8-barrel proteins [54] and Phosphoenolpyruvate conversion to pyruvate the reaction mechanism of Schiff base forming FBP Enolase catalyses the formation of phosphoenolpyruvate aldolases [55]. Isomerization of dihydroxyacetone phos- from 2-phosphoglycerate; this enzyme has been character- phate to glyceraldehydes 3-phosphate is catalyzed by ized in P. furiosus [68]. The conversion of phosphoenol- triosephosphate isomerases (see [56]). pyruvate to pyruvate in Archaea is catalyzed by two www.sciencedirect.com Current Opinion in Microbiology 2005, 8:695–705 700 Growth and development

different enzymes. Pyruvate kinase (PK; T. tenax [69], A. in S. solfataricus [3,18], whereas the pathway seems to be fulgidus, A. pernix and P. aerophilum [70]) catalyzes the specific for glucose in T. tenax [4](Figure 3). irreversible energy-yielding formation of pyruvate. In contrast to bacterial and eukaryal PKs, these archaeal Glucose oxidation PKs exhibit reduced regulatory potential, and thus another Glucose dehydrogenase catalyzes the oxidation of glucose important allosteric control point present in the classical to yield gluconate (in T. acidophilum [82], Haloferax med- EM pathway appears to be absent in archaeal modifica- iterranei [83], T. tenax [10], S. solfataricus [3,84,85] and tions. However, an AMP-stimulated PK was described in Picrophilus torridus [86]). According to pathway promis- T. acidophilum [71]. Pyruvate phosphate dikinase in T. cuity, the enzymes of S. solfataricus, P. torridus and T. tenax catalyzes the reversible interconversion of PEP acidophilum show high activities when using galactose as a and pyruvate (ATP + Pi + pyruvate $ AMP + PPi + substrate, whereas no significant activity with galactose PEP) (Tjaden et al., personal communication; [12]). was observed for the T. tenax enzyme. The structures of the glucose dehydrogenases of T. acidophilum [87] and of Pyruvate conversion to acetyl-CoA H. mediterranei [88] have been solved. All Archaea, both anaerobes and aerobes, convert pyru- vate to acetyl CoA by way of pyruvate:ferredoxin oxidor- Gluconate dehydration eductase (see in [17]). A functional pyruvate Gluconate dehydratase catalyzes the dehydration of the dehydrogenase complex, typical for Eukarya and Bac- respective sugar acid. For the enzyme from S. solfataricus teria, has not been described in Archaea to date, although promiscuity for both gluconate and galactonate was homologous were found in T. acidophilum and in reported by Lamble et al.[89] but Kim and Lee did not halophilic Archaea [72,73]. find that this promiscuity occurred [90]; the T. tenax enzyme was shown to be specific for gluconate [4]. The Acetyl-CoA conversion to acetate enzyme is a member of the enolase superfamily and shows Several anaerobic fermentative hyperthermophilic no similarity to the classical ED dehydratase [4,89,90]. Archaea and aerobic halophiles [74] generate significant amounts of acetate as a product of glucose fermentation 2-keto-3-deoxy gluconate/2-keto-3-deoxy- (Figure 1).It was found that in these Archaea, the formation (6-phospho)-gluconate cleavage of acetate from acetyl CoA is catalyzed by a novel prokar- KDG and KDPG generated in ED modifications of both yotic enzyme, acetyl-CoA-synthetase (ADP-forming) S. solfataricus and T. tenax are cleaved by bifunctional (ACD) (acetyl-CoA + ADP + Pi acetate + ATP + CoA) KD(P)G aldolase [4 ]. This enzyme catalyzes the rever- [75]. This represents the major energy-conserving reaction sible aldol cleavage of non-phosphorylated substrates in anaerobic sugar-fermenting hyperthermophiles. By con- (e.g. KDG and glyceraldehyde) [91] as well as of phos- trast, all Bacteria, including the hyperthermophile Thermo- phorylated substrates (e.g. KDPG and glyceraldehyde toga, convert acetyl-CoA to acetate by way of two enzymes: 3-phosphate) [4]. Furthermore, lack of facial selectivity phosphotransacetylase and [19]. ACDs from was demonstrated for the S. solfataricus enzyme in cata- several hyperthermophiles and from Haloarcula marismor- lyzing the cleavage of KDG as well as of 2-keto-3- tui have been characterized [76–81]. deoxygalactonate (KDgal), both of which yield glyceral- dehydes and pyruvate [3]. The enzyme is a member of Modified Entner–Doudoroff pathways in the N-acetyl-neuraminate superfamily and shows no Archaea similarity to the classical ED aldolase [4,91]. The crystal Initial studies in Archaea revealed the presence of the structure of the S. solfataricus KD(P)G aldolase was non-phosphorylative ED pathway, which involves 2- resolved and binding sites for the non-phosphorylated keto-3-deoxy gluconate (KDG) cleavage, glyceraldehyde substrates KDG, KDGal and glyceraldehyde were deter- oxidation and glycerate phosphorylation in the mined, providing a structural basis for the promiscuity of (hyper)thermophilic Archaea (S. solfataricus [2], T. acid- these substrates [92]. ophilum [1] and T. tenax [6,9–11]). The semi-phosphor- ylative ED pathway, which involves KDG kinase, KDPG 2-keto-3-deoxy gluconate phosphorylation cleavage and GAP oxidation by GAPDH, was identified KDG kinase is a member of the ribokinase superfamily as a catabolic route for glucose in halophiles [13,14]. and catalyzes the ATP-dependent phosphorylation of However, a more recent comparative genomics-based KDG to yield KDPG. KDG kinase represents the key approach indicates the presence of a ‘branched’ (i.e. a enzyme in the semi-phosphorylative ED modifications in non- and semi-phosphorylative) ED modification that halophilic Archaea and in T. tenax and S. solfataricus [4]. involves KDG kinase, a bifunctional KD(P)G aldolase and GAPN in the hyperthermophiles S. solfataricus and Energetics of modified Embden–Meyerhof T. tenax [4,12]. The non-phosphorylative ED pathway and Entner–Doudoroff pathways was recently shown to be promiscuous and represents The net ATP yields of the classical EM and ED pathway an equivalent route for glucose and galactose catabolism are 2 mol and 1 mol ATP per mol glucose, respectively.

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The formal net ATP yield of the modified EM pathways unusual pathways that are significantly different to the that involve non-phosphorylative GAPOR or GAPN is classical EM and ED pathways. In particular, differences zero (or <1 ATP in T. tenax, assuming that the anabolic- in sugar-phosphorylating and -isomerizing enzymes and formed PPi, a waste product of the cell, is recycled by PPi- in GAP-oxidizing enzymes were found. The biochemical, dependent PFK; Figure 2). For Pyrococcus, an additional phylogenetic and structural analysis of these novel site of ATP formation has been proposed to occur by way archaeal enzymes contributes, for example, to the under- of electron transport phosphorylation coupled to H2 for- standing of the complexity of enzyme superfamilies. mation via ferredoxin-dependent hydrogenase [93]or via reversal of PEP synthetase [22]. Formally, the net Increasing archaeal genome sequence information, and ATP yields of non-phosphorylative ED (as proposed for thus comparative and functional genomic approaches T. acidophilum [4]) and of the branched ED variants (non- [4,12,20,21,63], allowed predictions with respect to and semi-phosphorylative) of T. tenax and S. solfataricus reconstruction of archaeal carbohydrate metabolism and that involve non-phosphorylative GAPN are zero. The — together with classical biochemical methods — the semi-phosphorylative ED pathway of halophilic Archaea, identification of the unusual glycolytic pathways and which involves phosphorylating GAPDH and phospho- enzymes. Several novel enzymes (e.g sugar isomerases) glycerate kinase, yields one ATP (Figure 3). and their encoding genes were identified after initial biochemical characterization. Gluconeogenesis in Archaea Gluconeogenesis (i.e. glucose 6-phosphate formation from Although the routes of catabolism have been pyruvate) proceeds in lithoautotrophic (e.g. methanogens) unraveled in several Archaea, the regulation as well as and organonotrophic Archaea, as in Bacteria and Eukarya, energetics of the archaeal glycolytic pathways are still not by way of the reversible reactions of the EM pathway. well understood. In view of the apparent absence of Accordingly, the irreversible reactions of the modified EM classical allosteric sites, a primary regulation of glycolytic pathway in Archaea (i.e. ADP- and ATP-dependent PFKs, fluxes in Archaea might proceed at the level of gene GAPOR and GAPN, and PKs) are reversed by different expression [21]. Current analyses hint that there might enzymes: fructose-1,6-bisphosphatase (FBPase), classical be control points at the level of glyceraldehyde-3-phos- GAPDH/phosphoglycerate kinase and phosphoenolpyru- phate, which also includes allosteric control of GAPN. vate synthetases (PEPS), respectively. Furthermore, to date, the pathways of pentose degrada- tion [99] and of hexose/pentose conversions have not Enzymatic and mutational analysis in Thermococcus koda- been studied in detail in Archaea [100]. karaensis revealed that the FBPase class V represents the functional FBPase in Archaea [21,94]. In T. tenax, rever- Clearly, future functional genomics studies combined sible PPi-dependent PFK substitutes for FBPase in glu- with biochemical characterization of enzymes will pro- coneogenesis. vide further new insights and will extend our current understanding of central carbohydrate metabolism and its The formation of GAP from 3-phosphoglycerate in regulation in Archaea. Archaea in the course of gluconeogenesis, which counter- acts the irreversible GAPOR and GAPN reactions, is References and recommended reading catalyzed by the NADP+-dependent GAPDH and the Papers of particular interest, published within the annual period of review, have been highlighted as: phosphoglycerate kinase enzyme couple (for references see in [20]). Both enzymes are kinetically regulated in the of special interest gluconeogenetic direction (as shown for P. furiosus [62] of outstanding interest and T. tenax [64]). In halophilic Archaea, GAPDH and phosphoglycerate kinase have a glycolytic function in the 1. Budgen N, Danson MJ: Metabolism of glucose via a modified Entner-Doudoroff pathway in the thermoacidophilic semi-phosphorylative ED pathway. The structure of archaebacterium Thermoplasma acidophilum. FEBS Lett 1986, GAPDH from S. solfataricus [95] and from M. fervidus 196:207-210. [96] has been solved. 2. De Rosa M, Gambacorta A, Nicolaus B, Giardina P, Poerio E, Buonocore V: Glucose metabolism in the extreme thermoacidophilic archaebacterium Sulfolobus solfataricus. PEPS counteracts the PK reaction. PEPS of T. tenax is a Biochem J 1984, 224:407-414. true anabolic enzyme (Tjaden et al., personal commu- 3. Lamble HJ, Heyer NI, Bull SD, Hough DW, Danson MJ: Metabolic nication, [12]), whereas a function in both glycolysis and pathway promiscuity in the archaeon Sulfolobus solfataricus revealed by studies on glucose dehydrogenase and 2-keto-3- gluconeogenesis was proposed for PEPS of P. furiosus deoxygluconate aldolase. J Biol Chem 2003, 278:34066-34072. [97,98]. 4. Ahmed H, Ettema TJ, Tjaden B, Geerling AC, van der OJ, Siebers B: The semi-phosphorylative Entner-Doudoroff pathway in Conclusions hyperthermophilic archaea — a re-evaluation. Biochem J 2005, 390:529-540. 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