Thermoacidophilic Archaebacterium Research Articles

Stability and Rupture of Archaebacterial Cell Membrane: A Model Study

It is known that the thermoacidophilic archaebacterium Sulfolobus acidocaldarius can grow in hot springs at 65-80 degrees C and live in acidic environments (pH 2-3); however, the origin of its unusual thermal stability remains unclear. In this work, using a vesicle as a model, we study the thermal stability and rupture of archaebacterial cell membrane. We perform a simulation investigation of the structure-property relationship of monolayer membrane formed by bolaform lipids and compare it with that of bilayer membrane formed by monopolar lipids. The origin of the unusually thermal stability of archaebacterial cell and the mechanism for its rupture are presented in molecular details.

An authoring system for computer-assisted structured radiology reporting

A type II restriction endonuclease (SuaI) has been isolated from the thermoacidophilic archaebacterium Sulfolobusacidocaldarius. The enzyme is an isoschizomer of BspRI. It does not cut S. acidocaldarius DNA, as the recognition sequence GGCC in this DNA contains modified nucleotide(s). The enzyme is most active at 60–70°C and is highly thermostable.

Cellular polyamines of the acidophilic, thermophilic and thermoacidophilic archaebacteria, Acidilobus, Ferroplasma, Pyrobaculum, Pyrococcus, Staphylothermus, Thermococcus, Thermodiscus and Vulcanisaeta.

Cellular polyamines of newly isolated acidophilic, thermophilic and thermoacidophilic archaebacteria were investigated for the chemotaxonomic significance of polyamine distribution profiles. In addition to spermidine, spermine and agmatine, a quaternary branched penta-amine, N(4)-bis(aminopropyl)spermidine, was found in thermophilic Thermococcus waiotapuensis, Thermococcus aegaeus and Pyrococcus glycovorans belonging to the order Thermococcales. An acidophilic euryarchaeon, Ferroplasma acidiphilum located in the order Thermoplasmatales, contained spermidine and agmatine. Norspermidine, spermidine, norspermine and spermine were found in thermoacidophilic Acidilobus aceticus and thermophilic Thermodiscus maritimus located in the order Desulfurococcales, and in thermophilic Pyrobaculum arsenaticum, Pyrobaculum oguniense, Vulcanisaeta distributa and Vulcanisaeta souniana belonging to the order Thermoproteales; however, the four genera differ on their tetra- and penta-amine levels. Thermophilic Staphylothermus hellenicus belonging to Desulfurococcales contained caldopentamine, caldohexamine and N1-acetylcaldopentamine in addition to norspermidine, spermidine and norspermine. This is the first report on the occurrence of acetylated penta-amine in nature.

Motility proteins and the origin of the nucleus.

Hypotheses on the origin of eukaryotic cells must account for the origin of the microtubular cytoskeletal structures (including the mitotic spindle, undulipodium/cilium (so-called flagellum) and other structures underlain by the 9(2)+2 microtubular axoneme) in addition to the membrane-bounded nucleus. Whereas bacteria with membrane-bounded nucleoids have been described, no precedent for mitotic, cytoskeletal, or axonemal microtubular structures are known in prokaryotes. Molecular phylogenetic analyses indicate that the cells of the earliest-branching lineages of eukaryotes contain the karyomastigont cytoskeletal system. These protist cells divide via an extranuclear spindle and a persistent nuclear membrane. We suggest that this association between the centriole/kinetosome axoneme (undulipodium) and the nucleus existed from the earliest stage of eukaryotic cell evolution. We interpret the karyomastigont to be a legacy of the symbiosis between thermoacidophilic archaebacteria and motile eubacteria from which the first eukaryote evolved. Mutually inconsistent hypotheses for the origin of the nucleus are reviewed and sequenced proteins of cell motility are discussed because of their potential value in resolving this problem. A correlation of fossil evidence with modern cell and microbiological studies leads us to the karyomastigont theory of the origin of the nucleus.

Folding Mechanism of Indole-3-glycerol Phosphate Synthase from Sulfolobus solfataricus: A Test of the Conservation of Folding Mechanisms Hypothesis in (βα) 8 Barrels

As a test of the hypothesis that folding mechanisms are better conserved than sequences in TIM barrels, the equilibrium and kinetic folding mechanisms of indole-3-glycerol phosphate synthase (sIGPS) from the thermoacidophilic archaebacterium Sulfolobus solfataricus were compared to the well-characterized models of the alpha subunit of tryptophan synthase (αTS) from Escherichia coli. A multifaceted approach combining urea denaturation and far-UV circular dichroism, tyrosine fluorescence total intensity, and tyrosine fluorescence anisotropy was employed. Despite a sequence identity of only 13%, a stable intermediate (I) in sIGPS was found to be similar to a stable intermediate in αTS in terms of its thermodynamic properties and secondary structure. Kinetic experiments revealed that the fastest detectable folding event for sIGPS involves a burst-phase (<5 ms) reaction that leads directly to the stable intermediate. The slower of two subsequent phases reflects the formation/disruption of an off-pathway dimeric form of I. The faster phase reflects the conversion of I to the native state and is limited by folding under marginally stable conditions and by isomerization or rearrangement under strongly folding conditions. By contrast, αTS is thought to fold via an off-pathway burst-phase intermediate whose unfolding controls access to a set of four on-pathway intermediates that comprise the stable equilibrium intermediate. At least three proline isomerization reactions are known to limit their interconversions and lead to a parallel channel mechanism. The simple sequential mechanism deduced for sIGPS reflects the dominance of the on-pathway burst-phase intermediate and the absence of prolyl residues that partition the stable intermediate into kinetically distinguishable species. Comparison of the results for sIGPS and αTS demonstrates that the thermodynamic properties and the final steps of the folding reaction are better conserved than the early events. The initial events in folding appear to be more sensitive to the sequence differences between the two TIM barrel proteins.

Molecular modeling of archaebacterial bipolar tetraether lipid membranes

Membranes composed of glycerol dialkylnonitol tetraether (GDNT) lipids from the thermoacidophilic archaebacterium Sulfolobus acidocaldarius have been studied by molecular modeling. GDNT membranes containing eight cyclopentane rings in the molecule are packed much tighter than those without rings. When containing eight cyclopentane rings, the β- d-galactosyl- d-glucose head-group of GDNT runs almost parallel to the membrane surface. However, when containing no rings, the head-group is oriented perpendicular to the membrane surface. Using molecular dynamics calculations, we have also conducted comparative studies of membrane packing between GDNT and various non-archaebacterial membranes. Compared to gel state dipalmitoylphosphatidylcholine (DPPC) and gel state distearoylphosphatidylcholine (DSPC) bilayers, the GDNT membrane with eight cyclopentane rings has a more negative interaction energy, thus a tighter membrane packing, while the GDNT without rings is less tightly packed than gel state DSPC. Based on the calculated interaction energies, the GDNT membranes (with and without rings) are much more tightly packed than DPhPC (an ester-linked diphytanyl PC) and DPhyPC (an ether-linked diphytanyl PC) bilayers. This suggests that the branched methyl group in the phytanyl chain is not the major contributor of the tight packing of GDNT membranes. The biological implication of this study is that the cyclopentane ring could increase GDNT membrane thermal stability. This explains why the number of cyclopentane rings in archaebacterial lipid increases with increasing growth temperature. Perhaps, through the ring-temperature compensation mechanism, the plasma membrane of thermoacidophilic archaebacteria is able to maintain a tight and rigid structure, consequently, a constant proton gradient between the extracelluar (pH 2.5) and intracelluar compartment (pH 6.5), over a wide range of growth temperatures.

Studies of Archaebacterial Bipolar Tetraether Liposomes by Perylene Fluorescence

Membrane packing and dynamics of bipolar tetraether liposomes composed of the polar lipid fraction E (PLFE) from the thermoacidophilic archaebacterium Sulfolobus acidocaldarius have been studied by perylene fluorescence. At a probe-to-PLFE lipid ratio of 1:400, we have detected an unusual fluorescence intensity increase with increasing temperature, while the fluorescence lifetime changed little. As the ratio was decreased, the intensity anomaly was diminished. At 1:3200 and 1:6400, the anomaly disappeared. A remarkable perylene intensity anomaly was also observed in bilayers composed of saturated monopolar diester phosphatidylcholines at their main phase transition temperatures. These results suggest that the intensity anomaly may be due to probe aggregation caused by tight membrane packing. At the same probe-to-lipid ratio (1:400), however, 1,2-diphytanoyl- sn-glycero-3-phosphocholine (DPhPC) and 1,2-diphytanoyl- sn-glycero-3-phosphoglycerol (DPhPG) liposomes did not exhibit any intensity anomaly with increasing temperature. This suggests that DPhPC and DPhPG liposomes are more loosely packed than PLFE liposomes; thus the branched methyl groups are not the contributing factor of the tight membrane packing found in PLFE liposomes. Using a multiexcitation method, we have also determined the average ( R), in-plane ( R ip), and out-of-plane ( R op) rotational rates of perylene in PLFE liposomes at various temperatures (20–65°C). R and R ip, determined at two different probe-to-lipid ratios (1:400 and 1:3200), both undergo an abrupt increase when the temperature is elevated to ∼48°C. These data suggest that PLFE liposomes are rigid and tightly packed at low temperatures, but they begin to possess appreciable “membrane fluidity” at temperatures close to the minimum growth temperature (∼50°C) of thermoacidophilic archaebacteria.

The structure of calditol isolated from the thermoacidophilic archaebacterium Sulfolobus acidocaldarius

We have achieved for the first time the stereoselective chemical synthesis of a polyhydroxylated cyclopentanic compound which proved fully identical to a sample of calditol isolated from the thermoacidophilic archaebacterium Sulfolobus acidocaldarius by Akihiko Sugai et al.

Differential scanning calorimetry study of the thermodynamic stability of some mutants of Sso7d from Sulfolobus solfataricus.

Sso7d from the thermoacidophilic archaebacterium Sulfolobus solfataricus is a small globular protein with a known three-dimensional structure. Inspection of the structure reveals that Phe31 is a member of the aromatic cluster forming the protein hydrophobic core, whereas Trp23 is located on the protein surface and its side chain exposed to the solvent. The thermodynamic consequences of the substitution of these two residues in Sso7d have been investigated by comparing the temperature-induced denaturation of Sso7d with that of three mutants: F31A-Sso7d, F31Y-Sso7d, and W23A-Sso7d. The denaturation processes proved to be reversible for all proteins, and represented well by the two-state N if D transition model in a wide range of pH. All three mutants are less thermally stable than the parent protein; in particular, in the pH range of 5.0-7.0, the F31A substitution leads to a decrease of 24 degreesC in the denaturation temperature, the F31Y substitution to a decrease of 10 degreesC, and the W23A substitution to a decrease of 6 degreesC. A careful thermodynamic analysis of such experimental data is carried out.

Low permeability of liposomal membranes composed of bipolar tetraether lipids from thermoacidophilic archaebacterium Sulfolobus acidocaldarius.

The physical origin of the extremely high thermal stability of tetraether liposomes composed of the polar lipid fraction E (PLFE) from the thermoacidophilic archaebacterium Sulfolobus acidocaldarius has been investigated. The leakage rate of trapped 5, 6-carboxyfluorescein (5(6)CF) and the proton permeability in PLFE liposomes have been measured using fluorescence probe techniques in the temperature range of 25-85 degrees C. The results are compared with those obtained from nonarchaebacterial liposomes. Egg yolk phosphatidylglycerol (eggPG) and PLFE liposomes exhibit similar large negative zeta-potentials (-31 to -34 mV) and low permeability coefficients for 5(6)CF, indicating that membrane surface charge is responsible for the low leakage rate of 5(6)CF in PLFE liposomes. This assertion is confirmed by the observation of an increased leakage rate of 5(6)CF with decreasing membrane surface negative charge via varying the content of egg yolk phosphatidylcholine (eggPC) in eggPC/eggPG binary mixtures. Gel-state dipalmitoylphosphatidylcholine bilayers and PLFE liposomes exhibit similar permeability coefficients for 5(6)CF, suggesting that lipid packing also plays an important role in the low leakage rate of 5(6)CF. PLFE liposomes, especially those approximately 60 nm in diameter, are remarkably thermally stable in regard to proton permeability, which increases by less than 2 x 10(-10) cm/s from 25 to 82 degrees C. The proton permeability comparison of various liposomes reveals that the tight and rigid lipid packing is the major contributor of the extremely low proton permeation in PLFE liposomes; the inositol moiety and the branched methyl groups may also contribute, but to a much lesser extent.

Autotrophic carbon dioxide fixation in Acidianus brierleyi.

The autotrophic CO2 fixation pathway in Acidianus brierleyi, a facultatively anaerobic thermoacidophilic archaebacterium, was investigated by measuring enzymatic activities from autotrophic, mixotrophic, and heterotrophic cultures. Contrary to the published report that the reductive tricarboxylic acid cycle operates in A. brierleyi, the enzymatic activity of ATP:citrate lyase, the key enzyme of the cycle, was not detected. Instead, activities of acetyl-CoA carboxylase and propionyl-CoA carboxylase, key enzymes of the 3-hydroxypropionate cycle, were detected only when A. brierleyi was growing autotrophically. We conclude that a modified 3-hydroxypropionate pathway operates in A. brierleyi.

Uracil phosphoribosyltransferase from the extreme thermoacidophilic archaebacterium Sulfolobus shibatae is an allosteric enzyme, activated by GTP and inhibited by CTP

Uracil phosphoribosyltransferase, which catalyses the formation of UMP and pyrophosphate from uracil and 5-phosphoribosyl α-1-pyrophosphate (PRPP), was partly purified from the extreme thermophilic archaebacterium Sulfolobus shibatae. The enzyme required divalent metal ions for activity and it showed the highest activity at pH 6.4. The specific activity of the enzyme was 50-times higher at 95°C than at 37°C, but the functional half-life was short at 95°C. The activity of uracil phosphoribosyltransferase was strongly activated by GTP, which increased V max of the reaction by approximately 20-fold without much effect on K m for the substrates. The concentration of GTP required for half-maximal activation was about 80 μM. CTP was a strong inhibitor and acted by raising the concentration of GTP needed for half-maximal activation of the enzyme. We conclude that uracil phosphoribosyltransferase from S. shibatae is an allosteric enzyme which is activated by a purine nucleotide and inhibited by a pyrimidine nucleotide as seen for several enzymes in the pyrimidine nucleotide biosynthetic pathway of Escherichia coli, but not observed before for any phosphoribosyltransferase.

Relative configurations of carbapseudopentose moieties of hopanoids of the bacterium Zymomonas mobilis and the cyanobacterium ‘ Anacystis montana’

A bacteriohopanetetrol cyclitol ether with a new configuration of its carbapseudopentose moiety has been isolated from the cyanobacteriu, ‘ Anacystis montana’ and compared to a similar hopanoid previously isolated from Zymomonas mobilis. As shown by two dimensional 1H-NMR spectroscopy using Nuclear Overhauser Effect correlations, both compounds were diastereomers and differed from a third stereomer found in the biphytanyl lipids of the thermoacidophilic archaebacterium Sulfolobus sp.

Purification and characterization of thermostable maltooligosyl trehalose trehalohydrolase from the thermoacidophilic archaebacterium Sulfolobus acidocaldarius.

A thermostable maltooligosyl trehalose trehalohydrolase from the thermoacidophilic archaebacterium Sulfolobus acidocaldarius ATCC 33909 was purified from a cell-free extract to an electrophoretically pure state by successive column chromatographies on Sepabeads FP-DA13, Butyl-Toyopearl 650M, DEAE-Toyopearl 650S, Toyopearl HW-55S and Ultrogel AcA44. The enzyme had a molecular mass of 59,000 by SDS-polyacrylamide gel electrophoresis and a pI of 6.1 by gel isoelectrofocusing. The N-terminal amino acid of the enzyme was methionine. The enzyme showed the highest activity from pH 5.5 to 6.0 and at 75 degrees C, and was stable from pH 5.5 to 9.5 and up to 85 degrees C. The activity was inhibited by Hg2+, Cu2+, Fe2+, Pb2+, and Zn2+. The Km values of the enzyme for maltosyl trehalose, maltotriosyl trehalose, maltotetraosyl trehalose, and maltopentaosyl trehalose were 16.7 mM, 2.7 mM, 3.7 mM, and 4.9 mM, respectively.

Purification and characterization of thermostable maltooligosyl trehalose synthase from the thermoacidophilic archaebacterium Sulfolobus acidocaldarius.

A thermostable maltooligosyl trehalose synthase was purified from a cell-free extract of the thermoacidophilic archaebacterium Sulfolobus acidocaldarius ATCC 33909 to an electrophoretically homogeneous state by successive column chromatography on Sepabeads FP-DA13, Butyl-Toyopearl 650M, DEAE-Toyopearl 650S, Ultrogel AcA44, and Mono Q. The enzyme had a molecular mass of 74,000 by SDS-polyacrylamide gel electrophoresis and a pI of 5.9 by gel isoelectrofocusing. The N-terminal amino acid of the enzyme was methionine. The enzyme showed the highest activity from pH 5.0 to 5.5 and at 75 degrees C, and was stable from pH 4.5 to 9.5 and up to 85 degrees C. The enzyme activity was inhibited by Hg2+ and Cu2+. The Kms of the enzyme for maltotetraose, maltopentaose, maltohexaose, maltoheptaose, and short chain amylose (DP 18) were 41.5 mM, 7.1 mM, 5.7 mM, 1.4 mM, and 0.6 mM, respectively.

Purification and characterization of 3-isopropylmalate dehydrogenase from a thermoacidophilic archaebacterium Sulfolobus sp. strain 7

3-Isopropylmalate dehydrogenase was purified (about 2000-fold) to homogeneity for the first time from an archaebacterium, Sulfolobus sp. strain 7. The enzyme showed an apparent molecular mass of about 110 kDa by gel filtration and a single 36-kDa polypeptide band on SDS-PAGE, suggesting tri- or tetrameric structure. The p I value was 6.9. The N-terminal amino acid sequence was similar to enzymes from other sources. The enzyme activity was greatly stimulated by the presence of Mn 2+, Cd 2+, Mg 2+, or Co 2+. In contrast to 3-isopropylmalate dehydrogenase from other sources, monovalent cations such as K 2+ and Na 2+ were neither essential for activity nor stability of the protein. The enzyme was extraordinarily thermostable.

Purification and characterization of 3-isopropylmalate dehydrogenase from a thermoacidophilic archaebacterium Sulfolobus sp. strain 7.

3-Isopropylmalate dehydrogenase was purified (about 2000-fold) to homogeneity for the first time from an archaebacterium, Sulfolobus sp. strain 7. The enzyme showed an apparent molecular mass of about 110 kDa by gel filtration and a single 36-kDa polypeptide band on SDS-PAGE, suggesting tri- or tetrameric structure. The pI value was 6.9. The N-terminal amino acid sequence was similar to enzymes from other sources. The enzyme activity was greatly stimulated by the presence of Mn2+, Cd2+, Mg2+, or Co2+. In contrast to 3-isopropylmalate dehydrogenase from other sources, monovalent cations such as K+ and Na+ were neither essential for activity nor stability of the protein. The enzyme was extraordinarily thermostable.

Characterization of redox proteins from extreme thermophilic archaebacteria: studies on alcohol dehydrogenase and thioredoxins

Proteins isolated from extreme thermophilic microorganisms for their general stability to the common protein denaturants (heating, pH, organic solvents, urea, SDS, proteases) represent an important development in the potential exploitation of proteins and enzymes for practical purposes. Here we report studies on the thermoactivity and thermostability of an alcohol dehydrogenase purified from the extreme thermoacidophilic archaebacterium Sulfolobus solfataricus, in the absence and in the presence of water-miscible organic solvents, as well as studies on enzyme immobilization and co-enzyme recycling. Three thermostable thioredoxins isolated and purified from Bacillus acidocaldarius, Sulfolobus solfataricus and Pyrococcus furiosus, have been partially characterized.

Sulfolobus acidocaldarius terminal oxidase. A kinetic investigation and its structural interpretation.

The thermoacidophilic archaebacterium Sulfolobus acidocaldarius possesses a very unusual terminal oxidase. We report original kinetic experiments on membranes of this microorganism carried out by stopped flow, using time-resolved optical spectroscopy combined with singular value decomposition analysis. The reduced-oxidized kinetic difference spectrum of the Sulfolobus membranes is characterized by three significant peaks in the visible region at 605, 586, and 560 nm. The 605-nm peak and part of the 586-nm peak (cytochrome aa3-type quinol oxidase) are reduced synchronously by both ascorbate plus N,N,N',N'-tetramethyl-p-phenylendiamine (TMPD) and dithionite, and they are very rapidly oxidized by molecular oxygen. A second pool of cytochromes seems to contribute to the 586-nm peak which is not reduced by ascorbate plus TMPD and reacts very slowly with dithionite. The b-type cytochromes (560 nm peak) are reduced by both reductants and are essentially "non-autoxidizable" at room temperature. Only one CO binding site with spectral features, kinetic properties, and ligand affinity not very dissimilar from those of mammalian cytochrome oxidase can be detected in the ascorbate-reduced membranes. On the contrary, a second CO binding site having unusual properties for aa3 terminal oxidases can be detected in the dithionite-reduced membranes.

Conformation of the Central, Three-helix Junction of the 5 S Ribosomal RNA of Sulfolobus acidocaldarius

The current investigation has focused on the structure of the central, three-helix junction of the 5 S ribosomal RNA from Sulfolobus acidocaldarius, a thermoacidophilic archaebacterium. The 5 S molecule from S. acidocaldarius represents a paradigm for the study of the 5 S junction (and branched RNA structures in general) due to its unusually high degree of predicted secondary structure and stability. In order to study the junction in isolation, a set of three RNA heteroduplex molecules was assembled in which pairs of helices bounding the junction were extended by 70 base-pairs per helix. Since the extended helices comprise more than 95% of the heteroduplex structure, the relative solution conformations of the heteroduplex molecules, in effect, "report" the interhelix (branch) angles bounded by the extended pairs of helices. Examination of these heteroduplex molecule, using a combination of gel electrophoresis and transient electric birefringence measurements, has revealed a tertiary structure for the central branch in which helices I and V are essentially collinear, and in which helix II is relatively free to reorient with respect to the I-V axis.