Maltose fermentation to acetate, CO2 and H2 in the anaerobic hyperthermophilic archaeon Pyrococcus furiosus: evidence for the operation of a novel sugar fermentation pathway

Sulfide dehydrogenase from the hyperthermophilic archaeon Pyrococcus furiosus: a new multifunctional enzyme involved in the reduction of elemental sulfur

Pyrococcus furiosus is an anaerobic archaeon that grows optimally at 100 degrees C by the fermentation of carbohydrates yielding acetate, CO2, and H2 as the primary products. If elemental sulfur (S0) or polysulfide is added to the growth medium, H2S is also produced. The cytoplasmic hydrogenase of P. furiosus, which is responsible for H2 production with ferredoxin as the electron donor, has been shown to also catalyze the reduction of polysulfide to H2S (K. Ma, R. N. Schicho, R. M. Kelly, and M. W. W. Adams, Proc. Natl. Acad. Sci. USA 90:5341-5344, 1993). From the cytoplasm of this organism, we have now purified an enzyme, sulfide dehydrogenase (SuDH), which catalyzes the reduction of polysulfide to H2S with NADPH as the electron donor. SuDH is a heterodimer with subunits of 52,000 and 29,000 Da. SuDH contains flavin and approximately 11 iron and 6 acid-labile sulfide atoms per mol, but no other metals were detected. Analysis of the enzyme by electron paramagnetic resonance spectroscopy indicated the presence of four iron-sulfur centers, one of which was specifically reduced by NADPH. SuDH has a half-life at 95 degrees C of about 12 h and shows a 50% increase in activity after 12 h at 82 degrees C. The pure enzyme has a specific activity of 7 mumol of H2S produced.min-1.mg of protein-1 at 80 degrees C with polysulfide (1.2 mM) and NADPH (0.4 mM) as substrates. The apparent Km values were 1.25 mM and 11 microM, respectively. NADH was not utilized as an electron donor for polysulfide reduction. P. furiosus rubredoxin (K(m) = 1.6 microM) also functioned as an electron acceptor for SuDH, and SuDH catalyzed the reduction of NADP with reduced P. furiosus ferredoxin (K(m) = 0.7 microM) as an electron donor. The multiple activities of SuDH and its proposed role in the metabolism of S(o) and polysulfide are discussed.

Isolation of maltose-regulated genes from the hyperthermophilic archaeum, Pyrococcus furiosus, by subtractive hybridization

The hyperthermophilic archaeum, Pyrococcus furiosus, utilizes maltose as a preferred carbon source for growth. 32P-labeled complementary DNA (cDNA) probes representing maltose-regulated genes were obtained by a subtractive hybridization procedure that minimized retrieval of ribosomal RNA (rRNA) sequences during screening. Genomic DNA clones were isolated by positive hybridization to these probes. Genes whose expression varied both in the level of transcription, relative to rRNA, as well as in the degree of regulation were obtained; the extent of regulation varied over a wide range, from as little as fivefold to as high as 50-100-fold. DNA sequence analysis of several of these regulated genes indicated that the subtraction library included gene products required for maltose utilization (e.g., pyruvate dikinase), as well as growth-rate-related genes such as those encoding ribosomal proteins and RNA polymerase subunits. Our approach is applicable to studying gene regulation in organisms that are not amenable to classical genetic techniques.

Biochemical diversity among sulfur-dependent, hyperthermophilic microorganisms

Hyperthermophiles are a recently discovered group of microorganisms that grow at and above 90 degrees C. They currently comprise over 20 different genera, and except for two novel bacteria, all are classified as Archaea. The majority of these organisms are obligately anaerobic heterotrophs that reduce elemental sulfur (S degree) to H2S. The best studied from a biochemical perspective are the archaeon, Pyrococcus furiosus, and the bacterium, Thermotoga maritima, both of which are saccharolytic. P. furiosus is thought to contain a new type of Entner-Doudoroff pathway for the conversion of carbohydrates ultimately to acetate, H2 and CO2. The pathway is independent of nicotinamide nucleotides and involves novel types of ferredoxin-linked oxidoreductases, one of which has tungsten, a rarely used element, as a prosthetic group. The only site of energy conservation is at the level of acetyl CoA, which is the presence of ADP and phosphate is converted to acetate and ATP in a single step. In contrast, T. maritima utilizes a conventional Embden-Meyerhof pathway for sugar oxidation. P. furiosus also utilizes peptides as a sole carbon and energy source. Amino acid oxidation is thought to involve glutamate dehydrogenase together with at least three types of novel ferredoxin-linked oxidoreductases which catalyze the oxidation of 2-ketoglutarate, aryl pyruvates and formaldehyde. One of these enzymes also utilizes tungsten. In P. furiosus, virtually all of the reductant that is generated during the catabolism of both carbohydrates and peptides is channeled to a cytoplasmic hydrogenase. This enzyme is now termed sulhydrogenase, as it reduces both protons to H2 and S degrees (or polysulfide) to H2S. S degrees reduction appears to lead to the conservation of energy in P. furiosus but not in T. maritima, although the mechanism by which this occurs is not known.

Properties of a thermostable 4Fe-ferredoxin from the hyperthermophilic bacterium Thermotoga maritima

A ferredoxin has been purified from one of the most ancient and most thermophilic bacteria known, Thermotoga maritima, which grows up to 90 degrees C. The reduced protein (M(r) approx. 6300) contains a single S = 1/2 [4Fe-4S]1+ cluster with complete cysteinyl ligation, and was unaffected after incubation at 95 degrees C for 12 h. It functioned as an electron carrier for T. maritima pyruvate oxidoreductase. Remarkably, the properties and amino acid sequence of this hyperthermophilic bacterial protein are much more similar to those of ferredoxins from hyperthermophilic archaea, rather than ferredoxins from mesophilic and moderately thermophilic bacteria.

Thermostability and thermoactivity of enzymes from hyperthermophilic Archaea

Enzymes from hyperthermophilic microorganisms are characteristically thermostable and thermoactive at extremely high temperatures. Information about the basis for the structure and function of these novel proteins is beginning to emerge. However, there are very few generalizations that can be drawn at this point that can be derived from the limited number of studies that have focused on biocatalysis and thermostability at extremely high temperatures.

Characterization of aromatic aminotransferases from the hyperthermophilic archaeon Thermococcus litoralis

The hyperthermophilic archaeon (formerly archaebacterium) Thermococcus litoralis grows at temperatures up to 98 degrees C using peptides and proteins as the sole sources of carbon and nitrogen. Cell-free extracts of the organism contained two distinct types of aromatic aminotransferases (EC 2.6.1.57) which were separated and purified to electrophoretic homogeneity. Both enzymes are homodimers with subunit masses of approximately 47 kDa and 45 kDa. Using 2-oxoglutarate as the amino acceptor, each catalyzed the pyridoxal-5'-phosphate-dependent transamination of the three aromatic amino acids but showed virtually no activity towards aspartic acid, alanine, valine or isoleucine. From the determination of Km and kcat values using 2-oxoglutarate, phenylalanine, tyrosine and tryptophan as substrates, both enzymes were shown to be highly efficient at transaminating phenylalanine (kcat/Km approximately 400 s-1 mM-1); the 47-kDa enzyme showed more activity towards tyrosine and tryptophan compared to the 45-kDa one. Kinetic analyses indicated a two-step mechanism with a pyridoxamine intermediate. Both enzymes were virtually inactive at 30 degrees C and exhibited maximal activity between 95-100 degrees C. They showed no N-terminal sequence similarity with each other (approximately 30 residues), nor with the complete amino acid sequences of aromatic aminotransferases from Escherichia coli and rat liver. The catalytic properties of the two enzymes are distinct from bacterial aminotransferases, which have broad substrate specificities, but are analogous to two aromatic aminotransferases which play a biosynthetic role in a methanogenic archaeon. In contrast, it is proposed that one or both play a catabolic role in proteolytic T. litoralis in which they generate glutamate and an arylpyruvate. These serve as substrates for glutamate dehydrogenase and indolepyruvate ferredoxin oxidoreductase in a novel pathway for the utilization of aromatic amino acids.

Purification and characterization of NADP-specific alcohol dehydrogenase and glutamate dehydrogenase from the hyperthermophilic archaeon Thermococcus litoralis

Thermococcus litoralis is a strictly anaerobic archaeon that grows at temperatures up to 98 degrees C by fermenting peptides. Little is known about the primary metabolic pathways of this organism and, in particular, the role of enzymes that are dependent on thermolabile nicotinamide nucleotides. In this paper we show that the cytoplasmic fraction of cell extracts contained NADP-specific glutamate dehydrogenase (GDH) and NADP-specific alcohol dehydrogenase (ADH) activities, neither of which utilized NAD as a cofactor. The GDH is composed of identical subunits having an M(r) of 45,000 and had an optimal pH and optimal temperature for glutamate oxidation of 8.0 and > 95 degrees C, respectively. Potassium phosphate (60 mM), KCl (300 mM), and NaCl (300 mM) each stimulated the rate of glutamate oxidation activity between two- and threefold. For glutamate oxidation the apparent Km values at 80 degrees C for glutamate and NADP were 0.22 and 0.029 mM, respectively, and for 2-ketoglutarate reduction the apparent Km values for 2-ketoglutarate, NADPH, and NH4+ were 0.16, 0.14, and 0.63 mM, respectively. This enzyme is the first NADP-specific GDH purified form a hyperthermophilic organism. T. litoralis ADH is a tetrameric protein composed of identical subunits having an M(r) of 48,000; the optimal pH and optimal temperature for ethanol oxidation were 8.8 and 80 degrees C, respectively. In contrast to GDH activity, potassium phosphate (60 mM), KCl (0.1 M), and NaCl (0.3 M) inhibited ADH activity, whereas (NH4)2SO4 (0.1 M) had a slight stimulating effect. This enzyme exhibited broad substrate specificity for primary alcohols, but secondary alcohols were not oxidized.(ABSTRACT TRUNCATED AT 250 WORDS)

Pathway of glycogen metabolism in Methanococcus maripaludis

Methanococcus maripaludis, a facultatively autotrophic archaebacterium that grows with H2 or formate as the electron donor, does not assimilate sugars and other complex organic substrates. However, glycogen is biosynthesized intracellularly and commonly reaches values of 0.34% of the cellular dry weight in the early stationary phase. To determine the pathway of glycogen catabolism, specific enzymes of sugar metabolism were assayed in cell extracts. The following enzymes were found (specific activity in milliunits per milligram of protein): glycogen phosphorylase, 4.4; phosphoglucomutase, 10; glucose-6-phosphate isomerase, 9; 6-phosphofructokinase, 5.6, fructose-1,6-bisphosphatase, 10; fructose-1,6-bisphosphate aldolase, 4.2; triosephosphate isomerase, 44; glyceraldehyde-3-phosphate dehydrogenase, 26; phosphoglycerate kinase, 20; phosphoglycerate mutase, 78; enolase, 107; and pyruvate kinase, 4.0. Glyceraldehyde-3-phosphate dehydrogenase was NADP+ dependent, and the pyruvate kinase required MnCl2. The 6-phosphofructokinase had an unusually low pH optimum of 6.0. Four nonoxidative pentose-biosynthetic enzymes were found (specific activity in milliunits per milligram of protein): transketolase, 12; transaldolase, 24; ribulose-5-phosphate-3-epimerase, 55; and ribulose-5-phosphate isomerase, 100. However, the key enzymes of the oxidative pentose phosphate pathway, the reductive pentose phosphate pathway, and the classical and modified Entner-Duodoroff pathways were not detected. Thus, glycogen appears to be catabolized by the Embden-Meyerhoff-Parnas pathway. This result is in striking contrast to the nonmethanogenic archaebacteria that have been examined, among which the Entner-Doudoroff pathway is common. A dithiothreitol-specific NADP(+)-reducing activity was also found (8.5 mU/mg of protein). Other thiol compounds, such as cysteine hydrochloride, reduced glutathione, and 2-mercaptoethanesulfonic acid, did not replace dithiothreitol for this activity. The physiological significance of this activity is not known.

Metabolism in hyperthermophilic microorganisms

Hyperthermophilic microorganisms grow at temperatures of 90 degrees C and above and are a recent discovery in the microbial world. They are considered to be the most ancient of all extant life forms, and have been isolated mainly from near shallow and deep sea hydrothermal vents. All but two of the nearly twenty known genera are classified as Archaea (formerly archaebacteria). Virtually all of them are strict anaerobes. The majority are obligate heterotrophs that utilize proteinaceous materials as carbon and energy sources, although a few species are also saccharolytic. Most also depend on the reduction of elemental sulfur to hydrogen sulfide (H2S) for significant growth. Peptide fermentation involves transaminases and glutamate dehydrogenase, together with several unusual ferredoxin-linked oxidoreductases not found in mesophilic organisms. Similarly, a novel pathway based on a partially non-phosphorylated Entner-Doudoroff scheme has been postulated to convert carbohydrates to acetate, H2 and CO2, although a more conventional Embden-Meyerhof pathway has also been identified in one saccharolytic species. The few hypethermophiles known that can assimilate CO2 do so via a reductive citric acid cycle. Two S(o)-reducing enzymes termed sulfhydrogenase and sulfide dehydrogenase have been purified from the cytoplasm of a hyperthermophile that is able to grow either with or without S(o). A scheme for electron flow during the oxidation of carbohydrates and peptides and the reduction of S(o) has been proposed. However, the mechanisms by which S(o) reduction is coupled to energy conservation in this organism and in obligate S(o)-reducing hyperthermophiles is not known.

The glutamate dehydrogenase-encoding gene of the hyperthermophilic archaeon Pyrococcus furiosus: sequence, transcription and analysis of the deduced amino acid sequence

Glutamate dehydrogenase (GDH) from the hyperthermophilic archaeon, Pyrococcus woesei, has been isolated, characterized and found to be very similar if not identical to the recently purified GDH from P. furiosus. Using a polymerase chain reaction, based on the N-terminal amino acid sequences of GDH, the P. furiosus gdh gene was identified, cloned into Escherichia coli and sequenced. The transcription start point of gdh has been mapped 1 nucleotide upstream from the ribosome-binding site. Using antiserum raised against purified GDH, expression of gdh was observed in E. coli. The deduced primary sequence of the P. furiosus GDH has been compared to various bacterial, archaeal and eukaryal GDHs and showed a high degree of similarity (32-52%).

Enzymes from high-temperature microorganisms

Enzymes derived from microorganisms growing at extreme temperatures are of biotechnological use as highly thermostable biocatalysts and should provide insight into the intrinsic basis of protein stability. So far, only DNA polymerases from these organisms have been put to commercial use, although the application of other classes of highly thermostable enzymes is being considered. Problems in the cultivation of high-temperature microorganisms and in the production of their enzymes still hampers progress in this field.

Purification and characterization of an extremely thermostable beta-glucosidase from the hyperthermophilic archaeon Pyrococcus furiosus

Cell-free extracts of cellobiose-grown cells of the hyperthermophile Pyrococcus furiosus contain very high activities (19.8 U/mg) of a beta-glucosidase. The cytoplasmic enzyme was purified 22-fold to apparent homogeneity, indicating that the enzyme comprises nearly 5% of the total cell protein. The native beta-glucosidase has a molecular mass of 230 +/- 20 kDa, composed of 58 +/- 2-kDa subunits. The enzyme has a pI of 4.40. Thiol groups are not essential for activity, nor is the enzyme dependent on divalent cations or a high ionic strength. The enzyme shows optimum activity at pH 5.0 and 102-105 degrees C. From Lineweaver-Burk plots, Vmax values of 470 U/mg and 700 U/mg were found for cellobiose (Km = 20 mM) and p-nitrophenyl-beta-D-glucopyranoside (Km = 0.15 mM), respectively. The purified enzyme also exhibits high beta-galactosidase activity and beta-xylosidase activity, but shows no activity towards alpha-linked disaccharides or beta-linked polymers, like cellulose. The purified beta-glucosidase shows a remarkable thermostability with a half life of 85 h at 100 degrees C and 13 h at 110 degrees C.