Archaeal Fructose-1,6-bisphosphate Aldolases Constitute a New Family of Archaeal Type Class I Aldolase

Siebers, Bettina; Brinkmann, Henner; Dörr, Christine; Tjaden, Britta; Lilie, Hauke; Oost, John van der; Verhees, Corné H.

doi:10.1074/jbc.m103447200

Cited by 101 publications

(121 citation statements)

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“…Separate transcription start sites for the internal kdgA and kdgK genes could not be detected (data not shown). The assignment of crenarchaeal consensus promoter sequences in front of the first gene of an operon (gad) and in front of downstream located single genes (gapN), the absence of Shine-Dalgarno sequences upstream of the first gene and subsequent translation via leaderless transcripts is in good agreement with previous studies in S. solfataricus (Condo et al 1999;Tolstrup et al 2000) and other Crenarchaea [T. tenax (Schramm et al 2000;Siebers et al 2001Siebers et al , 2004, Pyrobaculum aerophilum (Slupska et al 2001)]. The transcription start points were confirmed by analysis of RNA samples derived from cultures grown on different carbon sources (S. solfataricus cells grown on D-glucose, D-arabinose and tryptone; data not shown).…”

Section: Resultssupporting

confidence: 89%

The non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN) of Sulfolobus solfataricus: a key-enzyme of the semi-phosphorylative branch of the Entner–Doudoroff pathway

et al. 2007

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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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Section: Resultssupporting

confidence: 89%

The non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN) of Sulfolobus solfataricus: a key-enzyme of the semi-phosphorylative branch of the Entner–Doudoroff pathway

et al. 2007

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“…Active site penetration by C terminus Tyr 259 to promote ␣-proton exchange during iminium-enamine interconversion, as in muscle aldolase, would resolve the apparent mechanistic conflict of the same water molecule participating in two competing reactions. Finally, it is intriguing that in archaeal FBP aldolases, which do not have a mobile C terminus tyrosine catalyst, the cleavage reaction rate is 2 orders of magnitude lower compared with mammalian FBP aldolases (47).…”

Section: Discussionmentioning

confidence: 99%

Stereospecific Proton Transfer by a Mobile Catalyst in Mammalian Fructose-1,6-bisphosphate Aldolase

St-Jean¹,

Sygusch

2007

Journal of Biological Chemistry

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Class I fructose-1,6-bisphosphate aldolases catalyze the interconversion between the enamine and iminium covalent enzymatic intermediates by stereospecific exchange of the pro(S) proton of the dihydroxyacetone-phosphate C3 carbon, an obligatory reaction step during substrate cleavage. To investigate the mechanism of stereospecific proton exchange, high resolution crystal structures of native and a mutant Lys 146 Stereospecificity is one of the hallmarks of enzyme catalysis. Aldolases, which are abundant and ubiquitous enzymes, catalyze stereospecific carbon-carbon bond formation, one of the most important transformations in living organisms. Their role is best known in glycolysis where fructose-1,6-bis(phosphate) (FBP) 3 aldolases (EC 4.1.2.13) promote the cleavage of FBP to triose phosphates, D-glyceraldehyde-3-phosphate (G3P), and dihydroxyacetone phosphate (DHAP). A common feature to class I enzymes is the use of a covalent mechanism for catalysis implicating iminium (protonated Schiff base) formation between a lysine residue on the enzyme and a ketose substrate (1) that entails stereospecific proton exchange in the covalent intermediate (2). Of the three aldolase isozymes found in vertebrates (3), the catalytic mechanism has been extensively studied using class I aldolase A from rabbit muscle and key intermediates are depicted in reaction Scheme 1.In the condensation direction, the reaction involves covalent intermediate formation with the keto triose phosphate DHAP followed by condensation with the aldehyde G3P to form the ketose of the acyclic FBP substrate (4, 5). To form the C3-C4 bond of FBP, the enzyme stereospecifically abstracts the pro(S) C3 proton of the trigonal iminium 1 (6, 7) that is formed from the Michaelis complex with DHAP thereby generating via the enamine 2 (2) the carbanionic character at C3 of DHAP for the aldol reaction. The nascent carbon-carbon bond has the same orientation as the pro(S) ␣-hydrogen initially abstracted from the DHAP imine intermediate. The overall retention of configuration at C3 requires that proton abstraction from 1 to yield the enamine 2 and condensation with aldehyde in 3 must take place from the same direction on the enzyme (8). The iminium intermediate formed is then hydrolyzed and FBP is released by the inverse reaction sequence shown in Scheme 1.A distinguishing mechanistic feature of class I aldolases is the relative stability of the iminium 1 and enamine 2 forms, which is a consequence of the catalytic requirements. The enzyme must stabilize the enamine 2 and/or the preceding iminium 1 such that no decomposition occurs prior to reaction with the aldehyde as shown in 3. This stability is reflected in solution where the enzymatic populations 1 and 2 represent 20 and 60%, respectively, of bound DHAP on the muscle enzyme under equilibrium conditions (9). The interconversion between the two forms implicates the conserved C-terminal Tyr 363 residue whose proteolysis inhibits the stereospecific proton exchange step, making it rate-limiting (10), whereas the pen...

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“…Note that the eukaryotic sequences are much more similar to their eubacterial homologues. sequence similarity to eukaryotic or eubacterial PFK but is related to archaebacterial ADP-dependent GK instead (Tuininga et al 1999); (iii) an aldolase that shares no sequence similarity with either of the typical eubacterial enzymes (Siebers et al 2001); and (iv) a TPI that shares only residual (ca. 20%) amino-acid sequence similarity to the eubacterial enzyme (Kohlhoff et al 1996).…”

Section: Commonalities and Differences Lead Quickly To Deeper Problemsmentioning

confidence: 99%

On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells

Martin

Russell

2003

Phil. Trans. R. Soc. Lond. B

730

621

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All life is organized as cells. Physical compartmentation from the environment and self-organization of self-contained redox reactions are the most conserved attributes of living things, hence inorganic matter with such attributes would be life's most likely forebear. We propose that life evolved in structured iron monosulphide precipitates in a seepage site hydrothermal mound at a redox, pH and temperature gradient between sulphide-rich hydrothermal fluid and iron(II)-containing waters of the Hadean ocean floor. The naturally arising, three-dimensional compartmentation observed within fossilized seepage-site metal sulphide precipitates indicates that these inorganic compartments were the precursors of cell walls and membranes found in free-living prokaryotes. The known capability of FeS and NiS to catalyse the synthesis of the acetyl-methylsulphide from carbon monoxide and methylsulphide, constituents of hydrothermal fluid, indicates that pre-biotic syntheses occurred at the inner surfaces of these metal-sulphide-walled compartments, which furthermore restrained reacted products from diffusion into the ocean, providing sufficient concentrations of reactants to forge the transition from geochemistry to biochemistry. The chemistry of what is known as the RNA-world could have taken place within these naturally forming, catalyticwalled compartments to give rise to replicating systems. Sufficient concentrations of precursors to support replication would have been synthesized in situ geochemically and biogeochemically, with FeS (and NiS) centres playing the central catalytic role. The universal ancestor we infer was not a free-living cell, but rather was confined to the naturally chemiosmotic, FeS compartments within which the synthesis of its constituents occurred. The first free-living cells are suggested to have been eubacterial and archaebacterial chemoautotrophs that emerged more than 3.8 Gyr ago from their inorganic confines. We propose that the emergence of these prokaryotic lineages from inorganic confines occurred independently, facilitated by the independent origins of membrane-lipid biosynthesis: isoprenoid ether membranes in the archaebacterial and fatty acid ester membranes in the eubacterial lineage. The eukaryotes, all of which are ancestrally heterotrophs and possess eubacterial lipids, are suggested to have arisen ca. 2 Gyr ago through symbiosis involving an autotrophic archaebacterial host and a heterotrophic eubacterial symbiont, the common ancestor of mitochondria and hydrogenosomes. The attributes shared by all prokaryotes are viewed as inheritances from their confined universal ancestor. The attributes that distinguish eubacteria and archaebacteria, yet are uniform within the groups, are viewed as relics of their phase of differentiation after divergence from the non-free-living universal ancestor and before the origin of the free-living chemoautotrophic lifestyle. The attributes shared by eukaryotes with eubacteria and archaebacteria, respectively, are viewed as inheritances via symbiosis. The ...

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Archaeal Fructose-1,6-bisphosphate Aldolases Constitute a New Family of Archaeal Type Class I Aldolase

Cited by 101 publications

References 55 publications

The non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN) of Sulfolobus solfataricus: a key-enzyme of the semi-phosphorylative branch of the Entner–Doudoroff pathway

The non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN) of Sulfolobus solfataricus: a key-enzyme of the semi-phosphorylative branch of the Entner–Doudoroff pathway

Stereospecific Proton Transfer by a Mobile Catalyst in Mammalian Fructose-1,6-bisphosphate Aldolase

On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells

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