Conformational Transitions of Subunit ? in ATP Synthase from Thermophilic Bacillus PS3

Subunit ɛ of bacterial and chloroplast F_OF₁-ATP synthase is responsible for inhibition of ATPase activity. In Bacillus PS3 enzyme, subunit ɛ can adopt two conformations. In the “extended”, inhibitory conformation, its two C-terminal α-helices are stretched along subunit γ. In the “contracted”, noninhibitory conformation, these helices form a hairpin. The transition of subunit ɛ from an extended to a contracted state was studied in ATP synthase incorporated in Bacillus PS3 membranes at 59°C. Fluorescence energy resonance transfer between fluorophores introduced in the C-terminus of subunit ɛ and in the N-terminus of subunit γ was used to follow the conformational transition in real time. It was found that ATP induced the conformational transition from the extended to the contracted state (half-maximum transition extent at 140 μM ATP). ADP could neither prevent nor reverse the ATP-induced conformational change, but it did slow it down. Acid residues in the DELSEED region of subunit β were found to stabilize the extended conformation of ɛ. Binding of ATP directly to ɛ was not essential for the ATP-induced conformational change. The ATP concentration necessary for the half-maximal transition (140 μM) suggests that subunit ɛ probably adopts the extended state and strongly inhibits ATP hydrolysis only when the intracellular ATP level drops significantly below the normal value.     

Photoaffmity cross-linking of F1ATPase from the thermophilic bacterium PS 3 by 3'-arylazido-β-alanyl-8-azido ATP

To study the localization of the nucleotide binding sites of coupling factor 1 (TF₁) from the thermophilic bacterium PS3 we used the bifunctional (cross-linking) 3'-arylazido-β-alanyl-8-azido ATP (DiN₃ATP) for photoaffinity labeling. DiN₃ATP is hydrolyzed by TF₁ in the absence of ultraviolet light. Irradiation (UV light) of TF₁ in the presence of DiN₃ATP results in a nucleotide-specific reduction of ATPase activity and in a nucleotide-specific formation of different cross-linked proteins (dimers, trimers, oligomers) formed by the major subunits α and/or β. The results suggest that nucleotide binding sites (one, two, possibly all) are located at the interfaces between these subunits.     

Oxidation of arsenite by two β-proteobacteria isolated from soil

Two heterotrophic As(III)-oxidizing bacteria, SPB-24 and SPB-31 were isolated from garden soil. Based on 16S rRNA gene sequence analysis, strain SPB-24 was closely related to genus Bordetella, and strain SPB-31 was most closely related to genus Achromobacter. Both strains exhibited high As(III) (15 mM for SPB-24 and 40 mM for SPB-31) and As(V) (>300 mM for both strains) resistance. Both strains oxidized 5 mM As(III) in minimal medium with oxidation rate of 554 and 558 μM h⁻¹ for SPB-24 and SPB-31, respectively. Washed cells of both strains oxidized As(III) over broad pH and temperature range with optimum pH 6 and temperature 42°C for both strains. The As(III) oxidation kinetic by washed cells showed K _m and V _max values of 41.7 μM and 1,166 μM h⁻¹ for SPB-24, 52 μM and 1,186 μM h⁻¹ for SPB-31. In the presence of minimal amount of carbon source, the strains showed high As(III) oxidation rate and high specific arsenite oxidase activity. The ability of strains to resist high concentration of arsenic and oxidize As(III) with highest rates reported so far makes them potential candidates for bioremediation of arsenic-contaminated environment.     

Sequential hydrolysis of the γ- and β-phosphate groups of ATP by the ATP diphosphohydrolase from pig pancreas

The ATP dipbosphohydrolase (EC 3.6.1.5) from pig pancreas hydrolyzes triphospho- and diphosphonucleosides. The reaction products of ATP hydrolysis are ADP, AMP and orthophosphate, but AMP accumulates at a faster rate than ADP. A time-course study showed a simultaneous breakdown of ATP and ADP with initial rates for ATP and ADP hydrolysis of 2.1 and 3.8μmol/min per mg protein, respectively. However, the rates reached similar values toward the end of the incubation period. According to double reciprocal plots and Dixon plots, the K_m values for ATP and ADP are similar, V_max for ADP hydrolysis is twice the V_max for ATP hydrolysis and both nucleotides are competitive inhibitors of the other with their K_i values similar to their K_m. These results are consistent with a sequential hydrolysis of the two diphosphoester bonds of ATP: ATP first binds to the enzyme, its γ-phosphate group is hydrolyzed and released, resulting in an enzyme-ADP complex which either breaks down to free enzyme and ADP or is further processed via hydrolysis of the β-phosphate group, releasing free enzyme, AMP and P_i. The experimental data showed that the processing step is favored.     

Unisite Hydrolysis of [γ32P]ATP by Soluble Mitochondrial F1ATPase and Its Release by Excess ADP and ATP. Effect of Trifluoperazine

Some of the characteristics of unisite hydrolysis of [³²P]ATP as well as the changes that occur on the transition to multisite catalysis were further studied. It was found that a fraction of [³²P]ATP bound at the catalytic sites of F₁ under unisite conditions undergoes both hydrolysis and release induced by medium nucleotides upon addition of millimolar concentrations of ADP or ATP. The fraction of [³²P]ATP that undergoes release is similar to the fraction that undergoes hydrolytic cleavage, indicating that the rates of the release and hydrolytic reactions of bound [³²P]ATP are in the same range. As part of studies on the mechanisms through which trifluoperazine inhibits ATP hydrolysis, its effect on unisite hydrolysis of [³²P]ATP was also studied. Trifluoperazine diminishes the rate of unisite hydrolysis by 30–40%. The inhibition is accompanied by a nearly tenfold increase in the ratio of [³²P]ATP/³²Pi bound at the catalytic site and a 50% diminution in the rate of ³²Pi release from the enzyme into the media. Trifluoperazine also induces heterogeneity of the three catalytic sites of F₁ in the sense that in a fraction of F₁ molecules, the high-affinity catalytic site has a turnover rate lower than the other two. Trifluoperazine does not modify the release of previously bound [³²P]ATP induced by medium nucleotides. The latter indicates that hindrances in the release of Pi do not necesarily accompany alterations in the release of ATP even though both species lie in the same site.     

Relaxation by β3-adrenoceptor agonists of the isolated human internal anal sphincter

AimsIn this study, responses of β₃-adrenoceptor agonists were examined on human isolated internal anal sphincter (IAS) in order to explore their relaxant effects on hypertonicity of IAS.Main methodsThe relaxant efficacy (E_max) and potency (? logIC₅₀) of BRL37344 and SR58611A, β₃-adrenoceptor agonists, were examined in contracted IAS muscle strips. The presence of β₃-adrenoceptors, and changes in intracellular calcium and cyclic nucleotide levels in IAS muscle were tested by Western blotting, epifluorescence microscopy and enzyme immunoassay, respectively.Key findingsBRL37344 and SR58611A relaxed contracted IAS muscle (E_max = 27 ± 3% and 35 ± 3%; -logIC₅₀ = 6.26 ± 0.24 and 4.87 ± 0.13; respectively). These relaxant responses were blocked by SR59230A, a selective β₃-antagonist but not by β₁/β₂-selective antagonists, neuronal inhibitor or inhibition of nitric oxide synthase. The E_max of β₃-agonists was similar to that of β₂-selective agonists but smaller than that of isoprenaline (nonselective agonist) or β₁-selective agonists. BRL37344 (100 μM) increased cAMP (1.5-fold) without cGMP change, and depressed intracellular calcium signal. β₃-Adrenoceptor expression was smaller than that of β₁- and β₂-adrenoceptors.SignificanceThis is the first study demonstrating the presence of β₃-adrenoceptor in human IAS muscle and β₃-mediated relaxation of augmented sphincter tone. However, direct β₃-relaxation appears smaller than that obtained for nonselective agonists which may limit their potential use in the treatment of anorectal hypertonicity disorders.     

Photoaffinity cross-linking of oligomycin-sensitive ATPase from beef heart mitochondria by 3′-arylazido-8-azido ATP

Photoaffinity cross-linking of the oligomycin-sensitive ATPase from beef heart mitochondria by 3′-arylazido-8-azido ATP results in a nucleotide specific formation of a cross-link between α and/or β subunits. Moreover a nucleotide independent decrease of the heterogeneous 29–31 kd protein band is observed. This decrease can be reduced by addition of 2,4-dinitrophenol or 2-azido-4-nitrophenol.     

Molecular Characterization of a Highly-Active Thermophilic β-Glucosidase from Neosartorya fischeri P1 and Its Application in the Hydrolysis of Soybean Isoflavone Glycosides

Isoflavone occurs abundantly in leguminous seeds in the form of glycoside and aglycone. However, isoflavone glycoside has anti-nutritional effect and only the free type is beneficial to human health. In the present study we identified a β-glucosidase from thermophilic Neosartorya fischeri P1, termed NfBGL1, capable of efficiently converting isoflavone glycosides into free isoflavones. The gene, belonging to glycoside hydrolase family 3, was successfully overexpressed in Pichia pastoris at high cell density in a 3.7-l fermentor. Purified recombinant NfBGL1 had higher specific activity (2189±1.7 U/mg) and temperature optimum (80°C) than other fungal counterparts when using p-nitrophenyl β-d-glucopyranoside as the substrate. It retained stable at temperatures up to 70°C and over a broad pH range of 3.0−10.0. NfBGL1 had broad substrate specificity including glucosidase, cellobiase, xylanase and glucanase activities, and displayed preference for hydrolysis of β-1,2 glycosidic bond rather than β-1,3, β-1,4, β-1,6 bonds. The enzyme showed high bioconversion ability for major soybean isoflavone glycosides (daidin, gensitin and glycitin) into free forms. These properties make NfBGL1 potential for the wide use in the food, feed, pharmacy and biofuel industries.     

Amino acid sequences of allophycocyanin α- and β-subunits isolated from Anabaena cylindrica: Presence of an unknown derivative of aspartic acid in the β-subunit

Allophycocyanin (APC) α- and β-subunits were isolated from Anabaena cylindrica and their amino acid sequences were determined. The α- and β-subunits consisted of 160 and 161 amino acid residues, respectively, and lacked tryptophan. The β-subunit contained an unknown derivative of aspartic acid. The sequences were compared with those of other allophycocyanins.     

Association of α-subunits with nucleotide-modified β-subunits induces asymmetry in the catalytic sites of the F1-ATPase α3β3

The photoaffinity spin-labeled ATP analog, 2-N₃-SL-adenosine triphosphate (ATP), was used to covalently modify isolated β-subunits from F₁-ATPase of the thermophilic bacterium PS3. Approximately 1.2 mol of the nucleotide analog bound to the isolated subunit in the dark. Irradiation leads to covalent incorporation of the nucleotide into the binding site. ESR spectra of the complex show a signal that is typical for protein-immobilized radicals. Addition of isolated α-subunits to the modified β-subunits results in ESR spectra with two new signals indicative of two distinctly different environments of the spin-label, e.g., two distinctly different conformations of the catalytic sites. The relative ratio of the signals is approx 2∶1 in favor of the more closed conformation. The data show for the first time that when nucleotides are bound to isolated β-subunits, binding of α-subunits induces asymmetry in the catalytic sites even in the absence of the γ-subunit. This work was supported by a grant from the Deutsche Forschungsgemeinschaft to PDV.     

Hydrolysis of starches by the action of an α-amylase from Bacillus subtilis

A moderately thermophilic Bacillus subtilis strain, isolated from fresh sheep’s milk, produced extracellular thermostable α-amylase. Maximum amylase production was obtained at 40 °C in a medium containing low starch concentrations. The enzyme displayed maximal activity at 135 °C and pH 6.5 and its thermostability was enhanced in the presence of either calcium or starch. This thermostable α-amylase was used for the hydrolysis of various starches. An ammonium sulphate crude enzyme preparation as well as the cell-free supernatant efficiently degraded the starches tested. The use of the clear supernatant as enzyme source is highly advantageous mainly because it decreases the cost of the hydrolysis. Upon increase of reaction temperature to 70 °C, all substrates exhibited higher hydrolysis rates. Potato starch hydrolysis resulted in a higher yield of reducing sugars in comparison to the other starches at all temperatures tested. Soluble and rice starch took, respectively, the second and third position regarding reducing sugars liberation, while the α-amylase studied showed slightly lower affinity for corn starch and oat starch.     

An Ancient Repeat Sequence in the ATP Synthase β-Subunit Gene of Forcipulate Sea Stars

A novel repeat sequence with a conserved secondary structure is described from two nonadjacent introns of the ATP synthase β-subunit gene in sea stars of the order Forcipulatida (Echinodermata: Asteroidea). The repeat is present in both introns of all forcipulate sea stars examined, which suggests that it is an ancient feature of this gene (with an approximate age of 200 Mya). Both stem and loop regions show high levels of sequence constraint when compared to flanking nonrepetitive intronic regions. The repeat was also detected in (1) the family Pterasteridae, order Velatida and (2) the family Korethrasteridae, order Velatida. The repeat was not detected in (1) the family Echinasteridae, order Spinulosida, (2) the family Astropectinidae, order Paxillosida, (3) the family Solasteridae, order Velatida, or (4) the family Goniasteridae, order Valvatida. The repeat lacks similarity to published sequences in unrestricted GenBank searches, and there are no significant open reading frames in the repeat or in the flanking intron sequences. Comparison via parametric bootstrapping to a published phylogeny based on 4.2 kb of nuclear and mitochondrial sequence for a subset of these species allowed the null hypothesis of a congruent phylogeny to be rejected for each repeat, when compared separately to the published phylogeny. In contrast, the flanking nonrepetitive sequences in each intron yielded separate phylogenies that were each congruent with the published phylogeny. In four species, the repeat in one or both introns has apparently experienced gene conversion. The two introns also show a correlated pattern of nucleotide substitutions, even after excluding the putative cases of gene conversion. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Hydrolysis of 3′,4′-dichloropropionanilide by an aryl acylamidase from Taraxacum officinale

An aryl acylamidase (aryl-acylamine amidohydrolase, E.C. 3.5. 1.a) which hydrolyses the herbicide propanil (3′,4′-dichloropropionanilide), was isolated from dandelion roots and partially purified and characterized. Specificity tests on the enzyme revealed that it could hydrolyse various chlorine ring-substituted propionanilides and 3,4-dichloroanilide alkyl compounds. The partially purified enzyme was inhibited by several sulfhydryl reagents and metal ions. The pH optimum was broad, between 7·4 and 7·8. The apparent activation energy, determined from an Arrhenius plot, was 9·0 kcal/mol (37 700 J/mol) for the hydrolysis of 3′,4′-dichloropropionanilide. The apparent K_m was 1·7 × 10⁻⁴ M with propanil as substrate.     

Hydrolysis of natural and synthetic substrates by α-l-fucosidase, β-d-glucuronidase and β-n-acetylhexosaminidase purified from molluscs

• 1.1. Several mollusc glycosidases have been studied for their activities towards natural substrates. α-l-Fucosidases from Chamelea gallina, Tapes rhomboideus and Mytilus edulis hydrolyze oligosaccharides (di, tri and pentasaccharides) with α1 → 2, α1 → 3 and α1 → 4 bonds, fucose-containing glycopeptides from bovine thyroglobulin and the porcine submandibular mucin (devoid of sialic acid); α-l-fucosidase from Littorina littorea hydrolyzes fucose-containing glycopeptides from bovine thyroglobulin.
• 2.2. β-d-Glucuronidase from L. littorea hydrolyzes hyaluronic acid, chondroitin 4-sulfate and heparin with a very low activity; however, it is much more active on oligosaccharides (from the above-mentioned macromolecules) containing non-reducing terminal glucuronyl residues.
• 3.3. β-N-Acetylhexosaminidase from Helicella ericetorum acts mainly with an endo-hydrolase activity on β1 → 4N-acetylhexosamine linkages of ovalbumin, ovomucoid, chitin, hyaluronic acid and chondroitin
• 4.4-sulfate; it has also a secondary exo-hydrolase activity on these substrates.

     

Effect of Lysophosphatidylcholine on ATP and ρ-Nitrophenyl Phosphate Hydrolysis by the Plasma Membrane H+-ATPase from Soybean Hypocotyls

The stimulatory effect of lysophosphatidylcholine (lyso-PC) on ATP and ρ-nitrophenyl phosphate (PNPP) hydrolysis by the plasma membrane H+-ATPase from soybean (Glycine max (L.) Merr.) hypocotyls was studied. Results showed that lyso-PC stimulated the hydrolysis of ATP; ATP hydrolysis was enhanced dramatically when lyso-PC was within 0-0.03%, and increased slightly when lyso-PC was higher than 0.03%. At the concentration of 0.03%, lyso-PC stimulated ATP hydrolysis by 80.5%. Kinetics analysis showed that V max increased from 0.46μmol Pi·mg-1 protein·min-1 to 0.87 μmol Pi·mg-1 protein·min-1 while Km increased from 0.88 mmol/L to 1.15 mmol/L under lyso-PC treatment. The optimum pH of ATP hydrolysis was shifted from 6.5 to 7.0. Moreover, it was found lyso-PC enhanced the inhibition of ATP hydrolysis by hydroxylamine. In the presence of 200 mmol/L hydroxylamine, ATP hydrolysis was inhibited by 74.4%, while it was inhibited by 84.4% when treated with lyso-PC. However, PNPP hydrolysis and the inhibitory effect of vanadate were not affected by lyso-PC. The above results indicated that the kinase domain might be an action site or regulatory region of the C-terminal autoinhibitory domain in the plant plasma membrane H+-ATPase.     

Functional characterization of the PS II–LHC II supercomplex isolated by a direct method from spinach thylakoid membranes

Recently, a novel procedure to isolate a highly pure and active Photosystem II preparation directly from thylakoid membranes, referred to as PS II–LHC II supercomplex, was reported [Eshaghi et al. (1999) FEBS Lett 446: 23–26]. In addition to the reaction center core proteins, the supercomplex contains all the extrinsic proteins of the oxygen evolving complex and a set of chlorophyll a/b binding proteins. In this paper, the functional properties of this isolated supercomplex are further characterized by using EPR spectroscopy, thermoluminescence, fluorescence relaxation kinetics and flash induced oxygen yield measurements. The PS II–LHC II supercomplex contains, in addition to Q_A and Q_B, a small pool of plastoquinone (PQ). Although the isolated complex is no longer membrane bound, it has preserved functional characteristics of a well defined PS II preparation with the exception of some modification of Q_B sites. This revised version was published online in June 2006 with corrections to the Cover Date.     

Characterization of α-maltotetraohydrolase produced by Pseudomonas sp. MS300 isolated from the deepest site of the Mariana Trench

We have isolated a Pseudomonas-like amylase producer, the strain MS300, which displayed a large halo on starch medium, from the deepest site of the Mariana Trench. The strain MS300 produced two major and two minor α-maltotetraohydrolases (G4-amylase). The two major G4-amylases share the same molecular weight of 55 000 but had different pI values, 5.0 and 4.7, respectively. The optimum temperature for activity of both major G4-amylases is 40°C, and the optimum pH is 6.8 for one and 8.9 for the other. MS300 produced more amylase under high hydrostatic pressure than under atmospheric pressure. Strain MS300 may be active in the deep sea at a depth of 10 897 m. Received: December 11, 1997 / Accepted: April 16, 1998     

The isolation and amino acid sequence of the β- and γ-subunits of the lectin from the seeds of Dioclea Grandiflora

Although the two smaller β- and γ- subunits of the lectin from Dioclea grandiflora were clearly resolved by sodium dodecyl sulphate (SDS) gel electrophoresis, the concensus of other techniques including ultracentrifugation, isoelectric focusing in 8 M urea, size-exclusion chromatography in dissociating solvents and amino acid and sequence analysis indicated that they were similar in molecular size and that they had arisen either by a single enzymic cleavage at Asn¹¹⁸-Ser¹¹⁹ in the middle of the 237 residue-long mature α-subunit or by multiple cleavages occurring during post-translational processing of intermediates. The existence of minor forms of the β- and γ- subunits resulting from a cleavage at Asn¹²⁴-Ser¹²⁵ of the α-subunit was also recognized. The results indicated that the apparent difference in molecular size of the β- and γ-subunits deduced from SDS-gel electrophoresis could be explained by the anomalous behaviour of both subunits in this separation technique. The structural features of the D. grandiflora lectin are compared with those of concanavalin A obtained from seeds of the botanically related Canavalia ensiformis.     

Characterization of inducible cold-active β-glucosidases from the psychrotolerant bacterium Shewanella sp. G5 isolated from a sub-Antarctic ecosystem

The psychrotolerant bacterium Shewanella sp. G5 was used to study differential protein expression on glucose and cellobiose as carbon sources in cold-adapted conditions. This strain was able to growth at 4 °C, but reached the maximal specific growth rate at 37 °C, exhibiting similar growing rates values with glucose (μ: 0.4 h⁻¹) and cellobiose (μ: 0.48 h⁻¹). However, it grew at 15 °C approximately in 30 h, with specific growing rates of 0.25 and 0.19 h⁻¹ for cellobiose and glucose, respectively. Thus, this temperature was used to provide conditions related to the environment where the organism was originally isolated, the intestinal content of Munida subrrugosa in the Beagle Channel, Fire Land, Argentina. Cellobiose was reported as a carbon source more frequently available in marine environments close to shore, and its degradation requires the enzyme β-glucosidase. Therefore, this enzymatic activity was used as a marker of cellobiose catabolism. Zymogram analysis showed the presence of cold-adapted β-glucosidase activity bands in the cell wall as well as in the cytoplasm cell fractions. Two-dimensional gel electrophoresis of the whole protein pattern of Shewanella sp. G5 revealed 59 and 55 different spots induced by cellobiose and glucose, respectively. Identification of the quantitatively more relevant proteins suggested that different master regulation schemes are involved in response to glucose and cellobiose carbon sources. Both, physiological and proteomic analyses could show that Shewanella sp. G5 re-organizes its metabolism in response to low temperature (15 °C) with significant differences in the presence of these two carbon sources.     

A thermostable β-glucosidase isolated from a bacterial species of the genus Thermus

Summary An extremely thermophilic aerobic bacterium which produced -glucosidase was isolated from soil collected at the Yudanaka hot spring in Japan. It was identified as belonging to the genus Thermus. Production of -glucosidase by this bacterium was stimulated by the addition of cellobiose or laminaribiose to the medium. The optimum pH and temperature of the enzyme were 4.5–6.5 and 85° C respectively. The enzyme was stable in the pH range of 4.5–7.0 at 70° C for 2 h and the half-life at 75° C was 5 days. The K _m value of the enzyme for p-nitrophenyl--d-glucopyranoside, determined at 70° C in 0.1 M sodium phosphate buffer (pH 6.5), was 0.28 mM while the K _m was 2.0 mM for cellobiose. The enzyme effectively hydrolysed cellobiose at 70° C and the conversion yields of cellobiose to glucose were 95%, 93% and 90% at substrate concentrations of 5%, 10% and 15%, respectively.