Gene cloning and characterization of fructose-1,6-bisphosphate aldolase from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1

The fructose-1,6-bisphosphate (FBP) aldolase gene from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 was cloned. The gene encoding FBP aldolase (Tk-Fba) was expressed in Escherichia coli and the purified recombinant protein was characterized at high temperature. Tk-Fba is a homodecamer with a subunit molecular mass of 31,283 Da. The amino acid sequence, decameric conformation, formation of a Schiff-base intermediate, and stimulation (286%) of FBP cleavage activity by citrate suggested that Tk-Fba belonged to Class IA, a subtype of the classical Class I aldolases. The specific activity for the FBP cleavage reaction was 18.9 U/mg, which was much higher than those of other Class IA type FBP aldolases. Tk-Fba was extremely thermostable since the optimum temperature seemed to be above 100 degrees C. The optimum pH for Tk-Fba was determined to be 5.0 in the absence of citrate, while it shifted to around 7.0 in the presence of citrate. Tk-Fba accepted FBP and fructose-1-phosphate as substrates and K(m) values were determined to be 0.063 mM and 4.37 mM, respectively. In addition to citrate, phosphoenolpyruvate and pyrophosphate were also found to be potent activators of Tk-Fba, enhancing activities up to 346% and 201%, respectively. Erythrose-4-phosphate acted as an inhibitor and caused a decrease in the activity to 49%. Tk-Fba also catalyzed the condensation reaction with a similar activity level (14.9 U/mg) to that for FBP cleavage. However, none of the above compounds seemed to have a significant effect on the condensation reaction by Tk-Fba. These results suggest a regulatory function of Tk-Fba toward the catabolic direction of sugar metabolism in T. kodakaraensis KOD1.     

Gene analysis and enzymatic properties of thermostable beta-glycosidase from Pyrococcus kodakaraensis KOD1

A beta-glycosidase with broad substrate specificity was identified from a hyperthermophilic archaeon, Pyrococcus kodakaraensis KOD1. The gene encoding beta-glycosidase (Pk-gly) consists of 1449 nucleotides corresponding to a polypeptide of 483 amino acids. The protein showed similarity with other beta-glycosidases from family-1 glycosyl hydrolases, in particular, it showed high identity to beta-mannosidase from P. furiosus (55.7%), beta-glycosidase from Sulfolobus solfataricus (42.7%) and beta-glucosidase from P. furiosus (41.9%). The cloned gene was expressed in Escherichia coli and the recombinant protein was purified. The beta-glycosidase showed optimal activity at pH 6.5 and at an extremely high temperature of 100 degrees C, and had a half-life of 18 h at 90 degrees C. The beta-glycosidase hydrolyzed various pNp-beta-glycopyranosides, with kcat K(m) values in the order of pNp-beta-glucopyranoside = pNp-beta-mannopyranoside > pNp-beta-galactopyranoside > pNp-beta-xylopyranoside. pNp-beta-mannopyranoside was the substrate exhibiting the lowest K(m) value [0.254 mM] with a kcat K(m) ratio comparable to that of pNp-beta-glucopyranoside. This substrate specificity was distinct from previously reported beta-glycosidases. We observed that the region in PK-Gly corresponding to the fifth alpha-helix and beta-strand region of beta-glycosidase from S. solfataricus, which constitutes a large portion of the channel for substrate incorporation, displayed a chimeric structure, with the N-terminal region similar to beta-glycosidases and the C-terminal region similar to beta-mannosidases. An exo-type hydrolytic activity and transglycosylation activity were also observed towards cellooligomers.     

Acceptor specificity of 4-alpha-glucanotransferase from Pyrococcus kodakaraensis KOD1, and synthesis of cycloamylose

4-Alpha-glucanotransferase from a hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1 showed a broad acceptor specificity to various saccharides in an intermolecular transglycosylation reaction. In particular, the enzyme produced large amounts of transfer products of various acceptors such as D-glucose, methyl-alpha-D-glucoside, phenyl-alpha-D-glucoside, and D-xylose. It is suggested that the requirement for an effective acceptor in the intermolecular transglycosylation reaction catalyzed by this enzyme is the pyranose structure with the same configurations of the free C2-, C3-, and C4-hydroxyl groups as d-glucopyranose, like cyclomaltodextrin glucanotransferase (CGTase). However, the enzyme showed some acceptor specificities unlike those of CGTase. Analysis of the action of 4-alpha-glucanotransferase indicated that the enzyme catalyzes an intramolecular trans-glycosylation (cyclization) reaction of amylose to produce cyclic alpha-1,4-glucan (cycloamylose). The yield of cycloamylose reached 67%, and the degree of polymerization was found to range from 16 to above 55.     

Characterization of prolyl oligopeptidase from hyperthermophilic archaeon Thermococcus sp. NA1

The prolyl oligopeptidase TNA1_POP was found to be encoded in the genome of the hyperthermophilic archaeon Thermococcus sp. NA1 and showed high similarities to its archaeal homologs (76-83%). The enzyme was found to be a single polypeptide composed of 616 amino acids with conserved signature domains. A recombinant TNA1_POP expressed in Escherichia coli was capable of hydrolyzing succinyl-Ala-Pro-p-nitroanilide (Suc-Ala-Pro-pNA) with temperature and pH optimums of 80 degrees C and 7, respectively. TNA1_POP activity appeared to be significantly activated by pre-incubation at 80 degrees C and 90 degrees C with the optimum temperature unchanged. The heat-activated enzyme exhibited a k(cat) approximately twofold higher than that of the unheated enzyme, however, both enzymes showed the same K(m). TNA1_POP was thermostable at 80 degrees C retaining 80% of its heat-activated activity even after 23 h, but it lost its enzymatic activity at 90 degrees C with a half-life of 3 h. The loss of the enzymatic activity at 90 degrees C seemed to be caused by the autodegradation of the enzyme, not by thermal denaturation, as supported by circular dichroism spectropolarimetry. Autodegradation fragments ranging from 2 to 18 kDa were mapped by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry.     

Inhibitory effect of acetic acid on growth of hyperthermophilic archaeon Pyrococcus furiosus

The growth inhibition of Pyrococcus furiosus by acetic acid was stronger than that by hydrogen and could be described by a non-competitive inhibition model in which the inhibition constants of undissociated acetic acid, K(p) and n, were estimated to be 0.69 mM (25 mM total acetic acid at pH 6.5; pKa=4.96; 98 degrees C) and 1.0, respectively. In order to reduce the acetic acid inhibition, repeated-batch culturing was performed using a filtration module. This yielded 0.49 g of dry cells l(-1) after growth for 12 h after inoculation. It became impossible, however, to continue repeated-batch culturing manually because the time intervals for medium replacement became too short. In order to automatically maintain a low concentration of acetic acid, a perfusion culture was carried out in which medium feeding coupled to a pH-auxostat was performed. In this perfusion culture, it was possible to maintain the acetic acid concentration below 7.6 mM during exponential growth of P. furiosus, resulting in 1.8 g of dry cells l(-1) at 15 h after inoculation.     

Unique nucleoid structure during cell division of Thermococcus kodakaraensis KOD1

The nucleoid structure and the partition in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 were observed by a combination of phase-contrast microscopy and fluorescence microscopy. The nucleoids occurred as rounded fluorescent foci centrally located in the cells and as differences in fluorescence intensity between exponential and stationary phases. The cellular space occupied by the nucleoid in the stationary phase was larger than that in the exponential phase. Various shapes of nucleoid in the exponential-phase cells were observed, indicating that nucleoid separation was processed under cell cycle control. The number of cells which showed distinctive division stages was counted and the proportions of dividing cells were determined. About half of the observed cells were in the replication stage. More than 40% of the counted cells possessed a fully replicated but not separated form of nucleoid. Only 8% of the total cells clearly showed visible constriction. These results suggested that the post-replication period before cell division was relatively as long as the eucaryal gap period (G2); however, the period of visible cell constriction was almost the same as that of the bacteria.     

Biochemical characterization of deblocking aminopeptidase from hyperthermophilic archaeon Thermococcus onnurineus NA1

A genomic analysis of the hyperthermophilic archaeon Thermoccoccus onnurineus NA1 (TNA1) revealed the presence of a deblocking aminopeptidase (DAP) gene with high similarity to the genes of DAPs from Pyrococcus furiosus (86%) and Pyrococcus horikoshii (83% identity). The optimum aminopeptidase activity of the recombinant enzyme was observed at pH 7.5 and in the range of 90 degrees C to 100 degrees C. The specific aminopeptidase and deblocking activities of the enzyme toward Leu-pNA and Ac-Leu-pNA were 18- and 3-fold higher than those of a P. horikoshii DAP (DAP2), respectively. The enzyme activity was significantly increased by Co(2+) ions. The presence of Co(2+) ions induced the activation of the enzyme with heating and changed the large oligomer to a dimer. The enzyme activated by Co(2+) ions appeared to eventually be inactivated by autodegradation, which was confirmed by mass spectrometry.     

Properties of an alcohol dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernix K1

A NAD+-dependent medium-chain alcohol dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernix K1 was expressed in Escherichia coli and purified. The recombinant enzyme was a homotetramer of molecular mass 1.6 x 10(2) kDa. The optimum pH for the oxidative reaction was around 10.5 and that for the reductive reaction was around 8.0. The enzyme had a broad substrate specificity including aliphatic and aromatic alcohols, aliphatic and aromatic ketones, and benzylaldehyde. This enzyme produced (S)-alcohols from the corresponding ketones. The enzyme was thermophilic and the catalytic activity increased up to 95 degrees C. It maintained 24% of the original catalytic activity after incubation for 30 min at 98 degrees C, indicating that this enzyme is highly thermostable.     

Kinetic study of thermostable L-threonine dehydrogenase from an archaeon Pyrococcus horikoshii

In the genome data base of the hyperthermophilic archaeon Pyrococcus horikoshii, an open reading frame with sequence homology to a gene encoding alcohol dehydrogenase was found. It was demonstrated that the encoded enzyme was a thermostable L-threonine dehydrogenase which can oxidize the hydroxy alkyl residue of L-threonine associated with the reduction of NAD+ or NADP+. This enzyme is a member of the zinc-containing L-threonine dehydrogenase family. One enzyme molecule contained one zinc atom, and this metal was considered to contribute to the hyperthermostablility of the enzyme. The reaction of the enzyme proceeded via a sequential mechanism. The Michaelis constants (Km) for L-threonine and NAD+ were 0.013 and 0.010 mM, respectively, and the maximum reaction rate (Vmax) was 1.75 mmol NADH formed/min/mg-protein at 65 degrees C. The Km values for both L-threonine and NADP+ were larger than those for L-threonine and NAD+ with a similar Vmax value. These results indicate that the enzyme has lower affinity to NADP+ than to NAD+, and the binding affinity for L-threonine depends on the coenzymes.     

Biophysical analysis of heat-induced structural maturation of glutamate dehydrogenase from a hyperthermophilic archaeon

Tertiary structure of the recombinant glutamate dehydrogenase from Thermococcus kodakaraensis KOD1 (Tk-rGDH) converts into an intact form induced by the heat treatment. This phenomenon, heat-induced structural maturation, means that high temperature plays an important role in the proper folding and oligomerization of Tk-rGDH. In this work, we analyzed the heat-induced structural maturation of Tk-rGDH by differential scanning microcalorimetry (DSC), circular dichroism (CD), and activity measurements. In DSC measurements, the peak of adsorption of non-heated Tk-rGDH (nh-Tk-rGDH) was two times smaller than that of Tk-rGDH heated at 70 degrees C for 30 min (h-Tk-rGDH). The transition temperature (T(m)) of h-Tk-rGDH was 115 degrees C, which was about 3 degrees C higher than that of nh-Tk-rGDH. In the presence of 0.5 M NaCl, the nh-Tk-rGDH showed two peaks at 107 degrees C and 114 degrees C, while the h-Tk-rGDH showed a single peak at 115.7 degrees C. The heat-induced conformational change process was monitored by changes in CD intensity at 222 nm, and the result showed that heat-induced structural maturation is irreversible. The heat treatment at 70 degrees C showed the highest enhancement in activity, which was 15% larger than that of heat-treated Tk-rGDH at 40 degrees C. The results indicate that heat-induced structural maturation involves an irreversible process, transforming the non-heated form to the stable and active form.     

Indolepyruvate ferredoxin oxidoreductase: An oxygen-sensitive iron-sulfur enzyme from the hyperthermophilic archaeon Thermococcus profundus

Thermococcus profundus is a strictly anaerobic sulfur-dependent archaeon that grows optimally at 80°C by peptide fermentation. Indolepyruvate ferredoxin oxidoreductase (IOR), an enzyme involved in the peptide fermentation pathway, was purified to homogeneity from the archaeon under strictly anaerobic conditions. The maximal activity was?obtained above the boiling temperature of water (105°C), with a half-life of 62min at 100°C and 20min at 105°C. IOR was oxygen-sensitive with a half-life of 7h at 25°C under aerobic conditions. The specific activity of T.?profundus IOR was found to be dependent on the number of [4Fe-4S] clusters in the enzyme.     

A sterilisation Time–Temperature Integrator based on amylase from the hyperthermophilic organism Pyrococcus furiosus

A candidate Time–Temperature Integrator (TTI) which is potentially suitable for use in validation of sterilisation processes was identified and tested. The TTI was based on the highly thermostable amylase produced from the extracellular medium of a Pyrococcus furiosus fermentation: this organism grows at temperatures in the region of 100 °C. Kinetic properties for the amylase following inactivation by heat showed it to be suitable for use as a sterilisation TTI. Isothermal kinetic data at 121 °C and non-isothermal kinetic data over the range 121 to 131 °C were determined. A decimal reduction time (D_T-value) at 121 °C of 24 min was calculated from isothermal tests and a range from 18.1 to 23.9 min from non-isothermal tests. A z-value of 10 °C was estimated from non-isothermal tests. Thus, sterilisation values (F₀) estimated from this TTI would be similar to F₀-values representative of the destruction of Clostridium botulinum spores. Industrial measurements under non-isothermal conditions were conducted in metal cans processed in an FMC reel and spiral cooker–cooler and a bar simulator, and also in plastic pouches processed in a Lagarde steam-air retort.Industrial relevanceMany food processes, such as canning, are based upon thermal sterilisation of the food material. The development of a reliable Time–Temperature Integrator for such a process would be industrially valuable by providing a simple way of validating such processes. This study demonstrates the feasibility of one such TTI.     

Purification and characterization of the oxygen-thermostable hydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum camini

Aeropyrum camini that was isolated from a deep-sea hydrothermal vent chimney, possessed two hydrogenases (161 and 85 kDa) in its soluble fraction. The 85-kDa hydrogenase was purified to homogeneity using several chromatography columns. The specific activities of the purified hydrogenase were: 14.8 μmol methyl viologen^ox/mg/min for hydrogen oxidation, and 14.6 μmol methyl viologen^red/mg/min for proton reduction. The oxygen stabilities of hydrogenases that were purified from A. camini and the hydrogen thermophilic bacterium Persephonella hydrogeniphila, were compared. The hydrogenase purified from P. hydrogeniphila completely lost its activity following a 96-h exposure to atmosphere; however, the A. camini hydrogenase maintained 75% of its initial activity, even after a 168 h of atmospheric exposure. A. camini hydrogenase showed a half-life of 48 h at 90 °C, while P. hydrogeniphila hydrogenase showed complete denaturation after a 30 min incubation at the same temperature. Nine residues of the N-terminal amino acid sequence of A. camini hydrogenases (MARLLMIPGT) correspond to the protein sequence encoded by the hypothetical soluble hydrogenase subunit gene (APE2423) from A. pernix strain K1. A. camini hydrogenase has a high thermostability and is very tolerant to oxygen; therefore, it may be used for actual H₂ production.     

Growth of the hyperthermophilic marine archaeon Aeropyrum pernix in a defined medium

The nutritional requirements of Aeropyrum pernix were studied to investigate the growth of a hyperthermophilic marine archaeon in a defined medium. Various nutrients including sugars, amino acids, and nucleoside bases were tested to determine their effects on cell growth. It was found that adenine and six amino acids (Arg, Ile, Len, Lys, Met, Val) are essential for the growth of A. pernix. An artificial seawater-based medium, containing 11 amino acids, adenine, vitamins, KH2PO4, Na2S2O3 and trace minerals, enabled the growth of A. pernix at a cell density and specific growth rate similar to those obtained with complex media.     

Effects of exogenous compatible solutes on growth of the hyperthermophilic archaeon Sulfolobus solfataricus

Six known compatible solutes as well as twenty L-amino acids were individually added to a glucose minimal medium and their effects on the growth of Sulfolobus solfataricus (DSM 1617) were examined. Among the compatible solutes tested, putrescine, trehalose, and l-glutamate enhanced the growth of S. solfataricus. On the other hand, glycine betaine, choline, and L-proline showed little or no influence on cell growth. When cells were grown in the glucose medium supplemented with trehalose or L-glutamate, S. solfataricus preferentially utilized the compatible solute over glucose. The growth-enhancement effect of L-glutamate was also observed to be dependent on the glucose concentration in the medium: growth enhancement was higher when the concentration of glucose was low and gradually decreased with increasing glucose concentration. Interestingly, the effects of amino acids on cell growth differed markedly depending on the chemical nature of the amino acid added. While acidic amino acids-L-glutamate and L-aspartate-enhanced the growth rate, almost no growth was observed in the presence of glycine, L-leucine, L-valine, L-phenylalanine, L-threonine, L-methionine, or L-cysteine. Among all the low-molecular-weight solutes tested in this study, the growth-stimulation effect was most profound in the presence of L-glutamate. When S. solfataricus cells were grown in a glucose (1.0 g/l) medium supplemented with 3.0 g/l L-glutamate, the maximal cell density and growth rate were about 3.2- and 2.3-fold higher than those obtained without L-glutamate.