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.

The hyperthermophilic, facultatively heterotrophic crenarchaeum Thermoproteus tenax was analyzed using a low-coverage shotgun-sequencing approach. A total of 1.81 Mbp (representing 98.5% of the total genome), with an average gap size of 100 bp and 5.3-fold coverage, are reported, giving insights into the genome of T. tenax. Genome analysis and biochemical studies enabled us to reconstruct its central carbohydrate metabolism. T. tenax uses a variant of the reversible Embden-Meyerhof-Parnas (EMP) pathway and two different variants of the Entner-Doudoroff (ED) pathway (a nonphosphorylative variant and a semiphosphorylative variant) for carbohydrate catabolism. For the EMP pathway some new, unexpected enzymes were identified. The semiphosphorylative ED pathway, hitherto supposed to be active only in halophiles, is found in T. tenax. No evidence for a functional pentose phosphate pathway, which is essential for the generation of pentoses and NADPH for anabolic purposes in bacteria and eucarya, is found in T. tenax. Most genes involved in the reversible citric acid cycle were identified, suggesting the presence of a functional oxidative cycle under heterotrophic growth conditions and a reductive cycle for CO 2 fixation under autotrophic growth conditions. Almost all genes necessary for glycogen and trehalose metabolism were identified in the T. tenax genome.Archaea were recognized as a distinct phylogenetic group more than 25 years ago (75). Their importance as the third major evolutionary line is well established, but our knowledge of their physiological capabilities remains limited. Central metabolic pathways within these organisms are far from fully understood (43,47,72).Thermoproteus tenax was the first hyperthermophilic archaeum described (76). It is able to grow chemolithoautotrophically on H 2 , CO 2 , and S o as well as chemoorganoheterotrophically in the presence of S o and various organic substrates such as glucose, starch, amylose, glycerate, glycerol, ethanol, and malate (12, 76). Physiological and biochemical studies revealed T. tenax as a physiologically versatile organism with numerous archaeon-specific metabolic capabilities, regulation, and thermoadaptive traits.Comparative studies of carbohydrate metabolism in hyperthermophilic archaea indicate that sugars are generally metabolized by variants of the Entner-Doudoroff (ED) and Embden-Meyerhof-Parnas (EMP) pathways. The so-called nonphosphorylative ED pathway (phosphorylation takes place only at the stage of glycerate) is the only pathway that has been identified for sugar degradation in the aerobes Sulfolobus solfataricus (9) and Thermoplasma acidophilum (7), whereas the anaerobes Pyrococcus furiosus (27,28,31,66,69), Thermococcus spp. (31,44,50), Desulfurococcus amylolyticus (20), and Archaeoglobus fulgidus (33) use modified versions of the EMP pathway. In contrast to findings for other hyperthermophilic archaea, T. tenax uses both variants-the ED and EMP pathways-for glucose metabolism, as shown by in vitro studies identifying specific intermediates...

Archaea utilize a branched modification of the classical Entner-Doudoroff (ED) pathway for sugar degradation. The semi-phosphorylative branch merges at the level of glyceraldehyde 3-phosphate (GAP) with the lower common shunt of the Emden-Meyerhof-Parnas pathway. In Sulfolobus solfataricus two different GAP converting enzymes-classical phosphorylating GAP dehydrogenase (GAPDH) and the non-phosphorylating GAPDH (GAPN)-were identified. In Sulfolobales the GAPN encoding gene is found adjacent to the ED gene cluster suggesting a function in the regulation of the semi-phosphorylative ED branch. The biochemical characterization of the recombinant GAPN of S. solfataricus revealed that-like the well-characterized GAPN from Thermoproteus tenax-the enzyme of S. solfataricus exhibits allosteric properties. However, both enzymes show some unexpected differences in co-substrate specificity as well as regulatory fine-tuning, which seem to reflect an adaptation to the different lifestyles of both organisms. Phylogenetic analyses and database searches in Archaea indicated a preferred distribution of GAPN (and/or GAP oxidoreductase) in hyperthermophilic Archaea supporting the previously suggested role of GAPN in metabolic thermoadaptation. This work suggests an important role of GAPN in the regulation of carbon degradation via modifications of the EMP and the branched ED pathway in hyperthermophilic Archaea.Keywords Glyceraldehyde-3-phosphate Á Non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase Á GAPN Á Aldehyde dehydrogenase superfamily Á Branched Entner-Doudoroff pathway Á Carbohydrate metabolism Á Archaea Abbreviations EDEntner-Doudoroff sp Semi-phosphorylative np Non-phosphorylative EMP Embden-Meyerhof-Parnas G1P

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Background: The presence of the branched Entner-Doudoroff (ED) pathway in two hyperthermophilic Crenarchaea, the anaerobe Thermoproteus tenax and the aerobe Sulfolobus solfataricus, was suggested. However, so far no enzymatic information of the non-phosphorylative ED branch and especially its key enzyme -glycerate kinase -was available. In the T. tenax genome, a gene homolog with similarity to putative hydroxypyruvate reductase/glycerate dehydrogenase and glycerate kinase was identified.