Hyperthermophilic Archaebacterium Pyrococcus Furiosus Research Articles

Secretory production of designed multipeptides displayed on a thermostable bacterial thioredoxin scaffold in Pichia pastoris

Internal grafting of designed peptides to scaffold proteins is a valuable strategy for a variety of applications including recombinant peptide antigen construction. A peptide epitope from human papillomavirus (HPV) minor capsid protein L2 displayed on thioredoxin (Trx) has been validated preclinically as a broadly protective and low-cost alternative HPV vaccine. Focusing on thioredoxin from the hyperthermophilic archaebacterium Pyrococcus furiosus (PfTrx) as a scaffold, we have constructed a modified Pichia pastoris expression vector and used a PfTrx fusion derivative containing three tandemly repeated copies of a 19 amino acids peptide epitope from HPV-L2 for expression optimization and biochemical-immunological characterization of the Pichia-produced PfTrx-L2 antigen. We show that PfTrx-L2 is produced at high levels (up to 100 mg from a 100 ml starting culture using a multi-cycle induction protocol) and secreted into the culture medium as a highly enriched (>70% pure), non-glycosylated polypeptide that can be purified to homogeneity in a single step. Oxidation and aggregation state, thermal stability and immunogenicity of the endotoxin-free PfTrx-L2 antigen produced in P. pastoris were tested and found to be identical to those of the same antigen produced in Escherichia coli. Secretory production of endotoxin-free PfTrx-peptides in P. pastoris represents a cost- and time-effective alternative to E. coli production. Specifically designed for peptide antigens, the PfTrx-expression vector and conditions described herein are easily transferable to a variety of applications centred on the use of structurally constrained bioactive peptides as immune as well as target-specific binder reagents.

Destabilization of the Homotetrameric Assembly of 3-Deoxy-d-Arabino-Heptulosonate-7-Phosphate Synthase from the Hyperthermophile Pyrococcus furiosus Enhances Enzymatic Activity

Many proteins adopt homomeric quaternary structures to support their biological function, including the first enzyme of the shikimate pathway that is ultimately responsible for the biosynthesis of the aromatic amino acids in plants and microorganisms. This enzyme, 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase (DAH7PS), adopts a variety of different quaternary structures depending on the organism in which it is found. The DAH7PS from the hyperthermophilic archaebacterium Pyrococcus furiosus was previously shown to be tetrameric in its crystalline form, and this quaternary association is confirmed in an improved structure in a different crystal system. This tetramer is also present in solution as revealed by small-angle X-ray scattering and analytical ultracentrifugation. This homotetrameric form has two distinct interfaces, both of which bury over 10% each of the surface area of a single monomer. Substitution of Ile for Asp in the hydrophobic region of one interface gives a protein with a remarkable 4-fold higher maximum catalytic rate than the wild-type enzyme. Analytical ultracentrifugation at pH7.5 reveals that the tetrameric form is destabilized; although the protein crystallizes as a tetramer, equilibrium exists between tetrameric and dimeric forms with a dissociation constant of 22μM. Thus, under the conditions of kinetic assay, the enzyme is primarily dimeric, revealing that the dimeric form is a fully functional catalyst. However, in comparison to the wild-type protein, the thermal stability of the dimeric protein is significantly compromised. Thus, an unusual compromise of enzymatic activity versus stability is observed for this DAH7PS from an organism that favors a hyperthermophilic environment.

Protein Repair Methyltransferase from the Hyperthermophilic Archaeon Pyrococcus furiosus: UNUSUAL METHYL-ACCEPTING AFFINITY FORd-ASPARTYL AND N-SUCCINYL-CONTAINING PEPTIDES

Protein l-isoaspartate-(d-aspartate) O-methyltransferases (EC ), present in a wide variety of prokaryotic and eukaryotic organisms, can initiate the conversion of abnormal l-isoaspartyl residues that arise spontaneously with age to normal l-aspartyl residues. In addition, the mammalian enzyme can recognize spontaneously racemized d-aspartyl residues for conversion to l-aspartyl residues, although no such activity has been seen to date for enzymes from lower animals or prokaryotes. In this work, we characterize the enzyme from the hyperthermophilic archaebacterium Pyrococcus furiosus. Remarkably, this methyltransferase catalyzes both l-isoaspartyl and d-aspartyl methylation reactions in synthetic peptides with affinities that can be significantly higher than those of the human enzyme, previously the most catalytically efficient species known. Analysis of the common features of l-isoaspartyl and d-aspartyl residues suggested that the basic substrate recognition element for this enzyme may be mimicked by an N-terminal succinyl peptide. We tested this hypothesis with a number of synthetic peptides using both the P. furiosus and the human enzyme. We found that peptides devoid of aspartyl residues but containing the N-succinyl group were in fact methyl esterified by both enzymes. The recent structure determined for the l-isoaspartyl methyltransferase from P. furiosus complexed with an l-isoaspartyl peptide supports this mode of methyl-acceptor recognition. The combination of the thermophilicity and the high affinity binding of methyl-accepting substrates makes the P. furiosus enzyme useful both as a reagent for detecting isomerized and racemized residues in damaged proteins and for possible human therapeutic use in repairing damaged proteins in extracellular environments where the cytosolic enzyme is not normally found.

Short duplication in a cDNA clone of the rbcL gene from Picea abies.

The plastidic rbcL gene encodes the LSU of Rubisco (EC 4.1.1.39), the enzyme that catalyzes CO, fixation during photosynthesis (Hallick and Bottomley, 1983). In higher plants the enzyme structure is commonly given as a hexadecameric structure composed of eight LSUs and eight small subunits. Nucleotide sequence data from the rbcL gene have been used extensively in studies of plant phylogeny and molecular evolution (Morden and Golden, 1991; Pasternak and Glick, 1992). To investigate the expression of the rbcL gene in damaged and undamaged Norway spruce trees (Picea abies), we have isolated a rbcL cDNA clone via reverse transcriptasePCR (Table I). Using the proofreading ability of the DNA polymerase from the hyperthermophilic archaebacterium Pyrococcus furiosus (Pfu DNA polymerase) we have minimized the number of mutations obtained from amplifications performed with Taq DNA polymerase (Lundberg et al., 1991). The primer sequences were determined by sequence alignment of coniferous rbcL genes using the EMBL data library. The clone was sequenced by the dideoxynucleotide chain termination method using deletion subclones and additional primers. Sequence analysis of the cDNA clone revealed an ORF encoding a 475-amino acid polypeptide, highly homologous to the deduced protein sequences from the two conifers Pinus thunbergii and Pseudotsuga menziesii (Hipkins et al., 1990; Mukai et al., 1991). Furthermore, nucleic acid sequence comparison with the rbcL genes of these two species revealed no possible RNA editing site. In addition to the whole coding region (1425 bp) the sequence contains 28 bp of the 5’ leader including the possible ribosome binding site, 38 bp of the 3’ trailer, and the two PCR primer sites. Moreover, a short, 19-bp duplication was found at the 3’ end of the ORF, which seems to be a specific feature of the genus Picea. This duplication causes a frameshift that creates a new stop codon. It was also found in the North American species Picea pungens (Doerksen et al., 19911, but not in other coniferous or angiosperm species.

Alpha-amylase from the hyperthermophilic archaebacterium Pyrococcus furiosus. Cloning and sequencing of the gene and expression in Escherichia coli.

A gene encoding a highly thermostable alpha-amylase from the hyperthermophilic archaebacterium Pyrococcus furiosus was cloned and expressed in Escherichia coli. The nucleotide sequence of the gene predicts a 649-amino acid protein with a calculated molecular mass of 76.3 kDa, which corresponds well with the value obtained from purified enzyme using denaturing polyacrylamide gel electrophoresis. The NH2 terminus of the deduced amino acid sequence corresponds precisely to that obtained from the purified enzyme, excluding the NH2-terminal methionine. The amylase expressed in E. coli exhibits temperature-dependent activation characteristic of of the original enzyme from P. furiosus, but has a higher apparent molecular weight which is attributed to the improper formation of the native quaternary structure. No homology was found with previously characterized promotor or termination sequences. The deduced amino acid sequence displayed strong homology to the alpha-amylase A of Dictyoglomus thermophilum, an obligately anaerobic, extremely thermophilic bacterium. Evolutionary implications of this homology are discussed.

The purification and characterization of an extremely thermostable alpha-amylase from the hyperthermophilic archaebacterium Pyrococcus furiosus.

The alpha-amylase from Pyrococcus furiosus, a hyperthermophilic archaebacterium, has been purified to homogeneity. The enzyme is a homodimer with a subunit molecular mass of 66 kDa. The isoelectric point is 4.3. The enzyme displays optimal activity, with substantial thermal stability, at 100 degrees C, with the onset of activity at approximately 40 degrees C. Unlike mesophilic alpha-amylases there is no dependence on Ca2+ for activity or thermostability. The enzyme displays a broad range of substrate specificity, with the capacity to hydrolyze carbohydrates as simple as maltotriose. No subtrate binding occurs below the temperature threshold of activity, and a decrease in Km accompanies an increase in temperature. Except for a decrease in Asp and an increase in Glu, the amino acid composition does not confirm previously defined trends in thermal adaption. Fourth derivative UV spectroscopy and intrinsic fluorescence measurements detected no temperature-dependent structural reorganization. Hydrogen exchange results indicate that the molecule is rigid, with only a slight increase in conformational flexibility at elevated temperature. Scanning microcalorimetry detected no considerable change in the heat capacity function, at the pH of optimal activity, within the temperature range in which activity is induced. The heat absorption peak due to denaturation, under these conditions, occurred within the temperature range of 90-120 degrees C. When the pH was increased, a change in the shape of the heat absorption peak was observed, which when analyzed thermodynamically shows that the process of heat denaturation is complex, and includes at least three stages, indicating that the protein structure consists of three domains. At temperatures below 90 degrees C no excess heat absorption or change in the CD spectra were observed which could be associated with the cooperative conformational transition of the protein. According to the thermodynamic characteristics of the heat denaturation, the cold denaturation of this protein can be expected only at -3 degrees C. Therefore, the observed inactivation of this enzyme is not caused by the cooperative change of its tertiary structure. It can be associated only with the gradual changes of protein domain interaction.

Reduction of sulphur from polysulphidic model compounds by the hyperthermophilic archaebacterium Pyrococcus furiosus

Several polysulphidic model compounds were studied for their reducibility by a hyperthermophilic archaebacterium, Pyrococcus furiosus. Model compounds that may represent forms of organic sulphur in coal were selected for study including model compounds with bulky alkyl and aryl groups surrounding the sulphur atoms and polymeric polysulphides. P. furiosus reduced these organic polysulphides to hydrogen sulphide with varying efficiency. The use of complex model compounds may be more realistic than simple model compounds for evaluating the potential for microbial removal of organic sulphur from coal.

Aldehyde ferredoxin oxidoreductase from the hyperthermophilic archaebacterium Pyrococcus furiosus contains a tungsten oxo-thiolate center

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAldehyde ferredoxin oxidoreductase from the hyperthermophilic archaebacterium Pyrococcus furiosus contains a tungsten oxo-thiolate centerGraham N. George, Roger C. Prince, Swarnalatha Mukund, and Michael W. W. AdamsCite this: J. Am. Chem. Soc. 1992, 114, 9, 3521–3523Publication Date (Print):April 1, 1992Publication History Published online1 May 2002Published inissue 1 April 1992https://doi.org/10.1021/ja00035a055RIGHTS & PERMISSIONSArticle Views254Altmetric-Citations49LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (390 KB) Get e-Alerts Get e-Alerts

Extremely thermostable glutamate dehydrogenase from the hyperthermophilic archaebacterium Pyrococcus furiosus

The hyperthermophilic archaebacterium Pyrococcus furiosus contains high levels of NAD(P)-dependent glutamate dehydrogenase activity. The enzyme could be involved in the first step of nitrogen metabolism, catalyzing the conversion of 2-oxoglutarate and ammonia to glutamate. The enzyme, purified to homogeneity, is a hexamer of 290 kDa (subunit mass 48 kDa). Isoelectric-focusing analysis of the purified enzyme showed a pI of 4.5. The enzyme shows strict specificity for 2-oxoglutarate and L-glutamate but utilizes both NADH and NADPH as cofactors. The purified enzyme reveals an outstanding thermal stability (the half-life for thermal inactivation at 100 degrees C was 12 h), totally independent of enzyme concentration. P. furiosus glutamate dehydrogenase represents 20% of the total protein; this elevated concentration raises questions about the roles of this enzyme in the metabolism of P. furiosus.

Determinants of protein hyperthermostability: purification and amino acid sequence of rubredoxin from the hyperthermophilic archaebacterium Pyrococcus furiosus and secondary structure of the zinc adduct by NMR

The purification, amino acid sequence, and two-dimensional 1H NMR results are reported for the rubredoxin (Rd) from the hyperthermophilic archaebacterium Pyrococcus furiosus, an organism that grows optimally at 100 degrees C. The molecular mass (5397 Da), iron content (1.2 +/- 0.2 g-atom of Fe/mol), UV-vis spectrophotometric properties, and amino acid sequence (60% sequence identity with Clostridium pasteurianum Rd) are found to be typical of this class of redox protein. However, P. furiosus Rd is remarkably thermostable, being unaffected after incubation for 24 h at 95 degrees C. One- and two-dimensional 1H nuclear magnetic resonance spectra of the oxidized [Fe(III)Rd] and reduced [Fe(II)Rd] forms of P. furiosus Rd exhibited substantial paramagnetic line broadening, and this precluded detailed 3D structural studies. The apoprotein was not readily amenable to NMR studies due to apparent protein oxidation involving the free cysteine sulfhydryls. However, high-quality NMR spectra were obtained for the Zn-substituted protein, Zn(Rd), enabling detailed NMR signal assignment for all backbone amide and alpha and most side-chain protons. Secondary structural elements were determined from qualitative analysis of 2D Overhauser effect spectra. Residues A1-K6, Y10-E14, and F48-E51 form a three-strand antiparallel beta-sheet, which comprises ca. 30% of the primary sequence. Residues C5-Y10 and C38-A43 form types I and II amide-sulfur tight turns common to iron-sulfur proteins. These structural elements are similar to those observed by X-ray crystallography for native Rd from the mesophile C. pasteurianum. However, the beta-sheet domain in P. furiosus Rd is larger than that in C. pasteurianum Rd and appears to begin at the N-terminal residue. From analysis of the secondary structure, potentially stabilizing electrostatic interactions involving the charged groups of residues Ala(1), Glu(14), and Glu(52) are proposed. These interactions, which are not present in rubredoxins from mesophilic organisms, may prevent the beta-sheet from "unzipping" at elevated temperatures.

Potentiometric and electron nuclear double resonance properties of the two spin forms of the [4Fe-4S]+ cluster in the novel ferredoxin from the hyperthermophilic archaebacterium Pyrococcus furiosus.

Pyrococcus furiosus ferredoxin contains a single [4Fe-4S] that exists in both S = 1/2 (20%) and S = 3/2 (80%) ground states in the reduced protein. We report here on the temperature-dependent potentiometric properties of the two spin forms, their stability, and on the structural features that differentiate them. The midpoint potential (Em) of the cluster in either spin state was determined at -365 mV (30 degrees C, pH 8.0). By rapidly freezing samples for EPR analyses, it was shown that the Em values of both spin states appear to change by -1.7 mV/degrees C over the range 20 degrees-80 degrees C, and by -6 mV/degrees C between 80 and 89 degrees C. The Em values and the relative amounts of the S = 1/2 and S = 3/2 forms of the cluster were unaffected by pH (6.8-10.5), even at 85 degrees C, and were unchanged by the presence of NaCl (1.0 M), sodium dodecyl sulfate (10%, w/v) or ethylene glycol (50%, v/v), even at 80 degrees C. The S = 1/2 form of the [4Fe-4S]+ cluster was found to exhibit a strongly coupled 1H ENDOR resonance (A = 22 MHz) that was exchangeable with the solvent. Such a large coupling has not been observed in any other iron-sulfur protein. Since a unique feature of this 4Fe-ferredoxin is that only 3 cysteinyl residues appear to be coordinated to the [4Fe-4S] cluster, the ENDOR data are consistent with an H2O molecule being a ligand to the unique Fe site. The S = 3/2 form of the [4Fe-4S]+ cluster exhibited a similar, strongly coupled 1H ENDOR resonance, but in this spin state it was not exchangeable with the solvent. This suggests that the [4Fe-4S]+ cluster exhibiting the S = 3/2, but not the S = 1/2 ground state, is "shielded" from the solvent, presumably by neighboring amino acid residues. In view of the pH dependence of the midpoint potential of the two spin states, the fourth ligand to the cluster and the source of the strongly coupled 1H ENDOR resonance is probably an OH- rather than H2O molecule.

Coal sulphur transformations monitored by hyperthermophilic archaebacteria

The hyperthermophilic archaebacterium Pyrococcus furiosus can reduce polysulphidic compounds as well as elemental sulphur bound in coal. The presence of elemental sulphur in coals is thought to be a result of low temperature oxidation, or weathering, of coal pyrite. Results of controlled coal weathering experiments, in which the transformation of sulphur moieties was monitored using P. furiosus as well as standard chemical analyses, suggest that there may be changes in the organic sulphur content of coal during treatment. Observed transformations make coal sulphur more amenable to reduction by P. furiosus and, perhaps, other sulphur-reducing bacteria. Along these lines, the potential basis for combined biological and chemical treatment of coal to remove organic sulphur should be given serious consideration in developing coal cleaning technology.

Extremely thermostable amylolytic enzyme from the archaebacterium Pyrococcus furiosus

One of the most thermostable and thermoactive enzymes ever described has been characterized from a hyperthermophilic archaebacterium Pyrococcus furiosus. The enzyme system of this bacterium was capable of hydrolyzing starch forming a mixture of various oligosaccharides. Unlike the amylases from aerobic bacteria this enzyme does not require metal ions for activity or stability. The enzyme is catalytically active over a very broad temperature range, namely between 40°C and 140°C. The half life of this peculiar enzyme during autoclaving at 120°C is 2 h.

Extremely thermostable amylolytic enzyme from the archaebacterium Pyrococcus furiosus

One of the most thermostable and thermoactive enzymes ever described has been characterized from a hyperthermophilic archaebacterium Pyrococcus furiosus. The enzyme system of this bacterium was capable of hydrolyzing starch forming a mixture of various oligosaccharides. Unlike the amylases from aerobic bacteria this enzyme does not require metal ions for activity or stability. The enzyme is catalytically active over a very broad temperature range, namely between 40°C and 140°C. The half life of this peculiar enzyme during autoclaving at 120°C is 2 h.

Characterization of a tungsten-iron-sulfur protein exhibiting novel spectroscopic and redox properties from the hyperthermophilic archaebacterium Pyrococcus furiosus.

The archaebacterium, Pyrococcus furiosus, is a strict anaerobe that grows optimally at 100 degrees C by a fermentative-type metabolism in which H2 and CO2 are the only detectable products. Tungsten is known to stimulate the growth of this organism. A red-colored tungsten-containing protein (abbreviated RTP) that is redox-active and extremely thermostable has been purified. RTP is a monomer of Mr = 85,000 and contains approximately 6 iron, 1 tungsten, and 4 acid-labile sulfide atoms/molecule. Titrations using visible spectroscopy were consistent with the oxidation and reduction of the protein each requiring two electrons/molecule, suggesting that these metals and the sulfide are arranged in two redox active centers. P. furiosus ferredoxin served as an electron acceptor for the protein. Dithionite-reduced RTP exhibited a remarkable and complex EPR spectrum at 6 K with g values ranging from 1.3 to 10.0. This was shown to arise from the spin-coupling interaction of two paramagnetic centers. One (center A) has a S = 3/2 spin system (effective g values: gx = 3.33, gy = 4.75, and gz = 1.92, where D = 4.3 cm-1 and lambda = 0.135), whereas the EPR properties of the other (center B) could not be deduced. Nevertheless, theoretical analyses show how the redox properties of both centers may be determined using EPR spectroscopy. Their midpoint potentials (Em) at 20 degrees C and pH 8.0 are -410 mV (center A) and -500 mV (center B) with an effective potential for the spin coupled system (Em, A + B) of -505 mV. The Em values are dependent on temperature (delta Em/delta T = -2 mV/degrees C between 20 and 70 degrees C) and pH with pK alpha values of 8.0 (A) and approximately 8.5 (B). The Em values at 100 degrees C, the growth temperature, were estimated at -590, -650, and -660 mV for centers A, B, and A + B, respectively. These data indicate that RTP catalyzes a dehydrogenase-type reaction of extremely low potential, which involves the transfer of two protons and of two electrons, to and from two adjacent and interacting but nonidentical metal centers.

A novel and remarkably thermostable ferredoxin from the hyperthermophilic archaebacterium Pyrococcus furiosus

The archaebacterium Pyrococcus furiosus is a strict anaerobe that grows optimally at 100 degrees C by a fermentative-type metabolism in which H2 and CO2 are the only detectable products. A ferredoxin, which functions as the electron donor to the hydrogenase of this organism was purified under anaerobic reducing conditions. It had a molecular weight of approximately 12,000 and contained 8 iron atoms and 8 cysteine residues/mol but lacked histidine or arginine residues. Reduction and oxidation of the ferredoxin each required 2 electrons/mol, which is consistent with the presence of two [4Fe-4S] clusters. The reduced protein gave rise to a broad rhombic electronic paramagnetic resonance spectrum, with gz = 2.10, gy = 1.86, gx = 1.80, and a midpoint potential of -345 mV (at pH 8). However, this spectrum represented a minor species, since it quantitated to only approximately 0.3 spins/mol. P. furiosus ferredoxin is therefore distinct from other ferredoxins in that the bulk of its iron is not present as iron-sulfur clusters with an S = 1/2 ground state. The apoferredoxin was reconstituted with iron and sulfide to give a protein that was indistinguishable from the native ferredoxin by its iron content and electron paramagnetic resonance properties, which showed that the novel iron-sulfur clusters were not artifacts of purification. The reduced ferredoxin also functioned as an electron donor for H2 evolution catalyzed by the hydrogenase of the mesophilic eubacterium Clostridium pasteurianum. P. furiosus ferredoxin was resistant to denaturation by sodium dodecyl sulfate (20%, wt/vol) and was remarkably thermostable. Its UV-visible absorption spectrum and electron carrier activity to P. furiosus hydrogenase were unaffected by a 12-h incubation of 95 degrees C.