Metastable secondary structures in ribosomal RNA: a new method for analyzing the titration behavior of rRNA

The pH titration behavior of E. coli rRNA in the acid range has been analyzed by combining spectrophotometric and potentiometric titration data. The “simplest” model for the system, which considers as possible reactions the protonation of adenine (A), cytosine (C), and guanine (G) residues along with the opening of A·U and G·C base pairs, does not adequately account for the titration properties. It is postulated that extra reactions may occur in addition to those in the “simplest” model, and a new analytical method was developed to deal with this situation. Our approach yields the ultraviolet spectral changes which accompany the extra reactions, from which the nature of these reactions can in principle be deduced. The calculations also give, at each pH, the extents of the extra reactions as well as the extents of those reactions which comprise the “simplest” model. We infer that in acidic RNA solutions of 0.1M ionic strength there occur at least two extra reactions, each of which involves G residues. We propose that in the pH range 6.0 ≥ pH ≥ 3.8 triple-stranded helical sequences, presumably protonated G·C·G, are formed. These regions are replaced at lower pH by acid-stable structures involving G·G and A·A base pairs. In solutions of lower ionic strength (I = 0.01M) no triple strands are formed, but G·G and A·A regions seem to develop even at pH values as high as 6.0. At I = 0.1M, an acid–base titration cycle between pH 7 and 2.8 is not reversible; rRNA shows true hysteresis behavior. We conclude that in ribosomal RNA's, which are generally G-rich, guanine residues may participate in hitherto unpredicted conformations, some of which may be metastable while others are equilibrium structures.     

Influence of iron and pH on the yield and iron,manganese, zinc,and sulfur concentrations of carrots grown on sphagnum peat soil

Summary In two greenhouse experiments, sphagnum peat, adjusted to various pH levels, was used to study the effect of various levels of Fe on the growth of carrots (Daucus carota L., var. sativa D.C.). The Fe was added to the medium as sequesterine 330 chelate. Maximum carrot root and top tissue yields were obtained at soil pH 6.6 and 7.1. At soil pH 5.2 and 7.8 the yields were in the intermediate range. The yields were low at pH 4.3, 4.5 and 8.1 and at pH 8.4 the carrots did not grow. The chlorotic symptoms on carrot leaves, accom-panied by reduced yields, were associated with 39 to 82 ppm Fe and > 332 ppm Mn in the leaf and were likely due to Mn toxicity. Toxic levels of Mn in tissue were found even at soil pH 8.1 and were associated with reduced carrot yields. The leaf tissue concentrations of Fe and Mn decreased as the pH of soil increased; however, at pH 5.2, 7.8, and 8.1 the tissue Mn concentration increased. The added Fe had no effect on the Fe concentration but decreased the Mn and Zn concentration of leaf tissue and increased carrot root yields. There was a significant interaction between added lime and Fe, whereby the decrease in leaf tissue Mn concentration and increases in root yields with added Fe were much greater at pH 4.5 and 5.2 than at pH values of 6.6 and 7.8. The S concentration in the leaf tissue decreased with added Fe and lime. The leaf tissue Zn concentrations of 184 to 490 ppm and S concentrations of 0.32 to 0.63%, as found here, are considered to be high but not in the toxic range.Contribution No. 321, Research Station, Charlottetown, P.E.I. and No. 1534, Research Station, Kentville, N.S.Contribution No. 321, Research Station, Charlottetown, P.E.I. and No. 1534, Research Station, Kentville, N.S.     

Novel salt and alkali tolerant neotropical basidiomycetes for dye decolorisation in simulated textile effluent

The initial alkaline pH and the concentration of sodium chloride in the synthetic liquid medium were a key factor in the capability of twenty-five white-rot fungi strains to decolorise the dye Reactive Blue 19. Six strains decolorised 90% of the dye at pH 8.0, and only Peniophora cinerea decolorized 90% of the dye at pH 9.0. Fourteen strains were capable of decolorising the dye in saline medium (sodium chloride 10 g l⁻¹). P. ostreatus, P. cinerea and T. villosa were able to decolorize the dye both in medium with initial pH 8.0 or in saline medium. These three strains were selected and evaluated for simulated alkali-saline textile effluent decolorisation in different conditions: time of cultivation for effluent addition (0, 5, 7 and 9 days), initial pH (4.5 and 8.0) and agitation (0 and 120 rpm). P. ostreatus and P. cinerea decolorised the alkali-saline textile effluent by 93.0 and 25.4%, when the medium’s initial pH was 8.0 or 4.5, respectively, and the effluent was added in the 7th day of growth. T. villosa decolorized 40% when the effluent was added on the 9th day of cultivation at pH 4.5. Agitation increased the effluent decolorisation by T. villosa, but inhibition was observed for P. cinerea and P. ostreatus. The results showed that each fungus presented a specific behavior in relation to the best culture conditions for decolorisation of alkali-saline effluent containing reactive dyes. The strains of P. ostreatus, P. cinerea and T. villosa were considered as promising alternative for the biodegradation of this effluent, employing the strategy of effluent addition after a certain period of fungal growth.     

Cellulase in red clover exudates

Summary Cellulase was detected in the medium when red clover (Trifolium pratense) seedlings were grown aseptically in flasks. The amount of cellulase found depended on the ionic composition and pH of the medium. Cellulase was found when plants were grown in distilled water. With added salts the amount of cellulase detected was negligible at pH 5.5 or less, but increased with increasing pH; less was released when seedlings were grown throughout in the presence of CaCl₂. The enzyme may be extracytoplasmic, located on the root surface, and released by changes in the salt content and pH of the medium.Enzyme preparations contained at least two components. At pH 3.5 and 20°C one was stable for at least 22 h, whereas the other was destroyed within 0.5 h. The reaction rate of enzyme preparations was almost constant from pH 5 to 7.     

The effects of pH and temperature on orthophosphate removal by immobilized Chlorella vulgaris

Summary When Chlorella vulgaris was immobilized in calcium alginate beads, it removed more than 90% phosphate (10mg P/L) added to artificial wastewater at pH 3 to 9 and from 10 to 30°C. Free cells, however, only removed 40–60% of added phosphate at low pH (3–5) and at 10°C. Immobilized C. vulgaris is shown to have great potentialities for removing phosphate from low pH wastewater and at low temperature.     

Direct fermentation of starch to L-(+)-lactic acid using Lactobacillus amylophilus

Summary Fermentation of L-(+)-lactic acid from soluble starch by Lactobacillus amylophilus was studied. The bacterium produced about 30 g of L-(+)-lactic acid from 50 g of soluble starch when the pH of the culture was ranging from pH 5 to pH 6.8 at 28°C. 53.4 g of L-(+)-lactic acid was produced when 100 g of starch was added in the medium. The fermentation procedures will reduce the cost of complete hydrolysis of starch to glucose prior to fermentation.     

Effect of a soil fulvic acid on stem elongation in peas

Summary Previously observed marked stimulating effects on root initiation produced by a naturally occurring fulvic acid, prompted a further study of the growth reactions of plants exposed for short durations to high concentrations of this acid. Fulvic acid concentrations up to 4000 ppm were found to inhibit stem elongation in dark grown Alaska pea stems in the presence and absence of added IAA by 46% and 33% respectively. Concentrations higher than 4000 ppm produced toxic reactions which increased sharply at pH 4.0 and lower and at pH 7.0 and higher. The fulvic acid appeared to block the uptake of GA₃ in Laxton's Progress No 9 peas when the two substances were applied simultaneously to the leaves, but when these substances were applied separately the fulvic acid had no effect on GA₃-stimulated growth. Contribution No.114 of the Food Research Institute; No.291 Soil Research Institute, Canada Department of Agriculture, Ottawa, Ontario.     

Purification,Crystallization and Some Properties of Extracellular Pullulanase from Aerobacter aerogenes

Extracellular pullulanase was purified and crystallized from the culture fluid of Aerobacter aerogenes. Pullulanase was purified by means of ammonium sulfate fraction, DEAE-cellulose column chromatography and Sephadex column chromatography. Crystalline pullulanase was formed when saturated ammonium sulfate solution was added to the purified enzyme solution. The crystalline enzyme appeared as colorless fine rods. On ultracentrifugation analysis, the enzyme showed a single sharp and symmetrical Schlieren peak. The sedimentation coefficient, s_20,w was 4.39S. Polyacrylamide gel electrophoresis at pH 8.4 gave a main band with two sub-bands and the molecular weight of the main enzyme was estimated to be 66,000 from Polyacrylamide gel electrophoresis and to be 58,000 from sedimentation equilibrium. The optimum pH and temperature for the enzyme action were pH 6.5 and 50°C, respectively.     

Effects of pH on the kinetics of redox reactions in and around the cytochromebf complex in an isolated system

Rate-coefficients describing the electron transfer reactions between P700 and plastocyanin, between cytochromef in cytochromebf complexes and plastocyanin, and between decyl plastoquinol and cytochromebf complexes were determined as a function of pH in the range 4–10 from flash-induced absorbancy changes at four wavelengths. The reactions between P700 and plastocyanin, and between cytochromef and plastocyanin were optimised when there was electrostatic interaction between ionised acidic groups in plastocyanin with a pK_a of 4.3–4.7 and ionised basic constituents in P700 (assumed to be in the PSI-F subunit) and in cytochromef, with a pK_b of 8.9–9.4. The basic groups are thought to be lysine rather than arginine. This mechanism agrees with that inferred from effects of ionic strength changes on rate-coefficients. The relation between the second-order rate-coefficient for decyl plastoquinol oxidation by thebf complex and pH was characterised by a pK_a of 6.1. This is interpreted as showing that the anion radical form of that quinol, which has a pK_a of 6, and which becomes progressively protonated when pH is changed from 7 to 5, is essential to reduce cytochromeb-563 (low potential) during quinol oxidation. Above pH 9, permanent effects were observed on this rate-coefficient, which were absent in the reactions between P700, plastocyanin and cytochromef.     

RELATION BETWEEN THE ACROSOME REACTION AND FERTILIZATION IN THE SEA URCHIN. II. FERTILIZATION IN ACIDIFIED SEA WATER WITH EGG-WATER-TREATED SPERMATOZOA*

Fertilization of sea urchin eggs fails to occur at a pH lower than 6.5. Analytical studies on this problem were made with Hemicentrotus pulcherrimus, Anthocidaris crassispina and Pseudocentrotus depressus. If the spermatozoa have been pretreated with egg water, eggs can be fertilized even at pH 6.5 and 6.0. The acrosome reaction is inhibited at a pH lower than 6.5. Intact spermatozoa fail to adhere to the fixed eggs in acidified sea water, whereas egg-water-treated spermatozoa adhere even at pH 6.5 and 6.0. From these results we infer that the failure of fertilization at pH 6.5–6.0 is caused by non-occurrence of the acrosome reaction, and that fertilization reactions other than the acrosome reaction, such as the binding and fusion of the gametes, are not inhibited in this range of pH. At pH 5.5, the spermatozoa become inert and fertilization is inhibited or suppressed, even though egg-water-treated spermatozoa are employed.     

Enthalpies and Entropies of Cd and Zn Adsorption onto Bacillus licheniformis and Enthalpies and Entropies of Zn Adsorption onto Bacillus subtilis from Isothermal Titration Calorimetry and Surface Complexation Modeling

Determining the thermodynamic driving force of metal-bacteria surface complexation is important for understanding why, from a thermodynamic perspective, these spontaneous reactions occur. We therefore determined the Gibbs energies, enthalpies, and entropies of Cd and Zn complexation onto Bacillus licheniformis and of Zn complexation onto Bacillus subtilis using surface complexation modeling and isothermal titration calorimetry. Our results indicated that Cd and Zn complexation onto Bacillus licheniformis is entropically driven at low pH and enthalpically driven at circumneutral pH. Zn complexation onto Bacillus subtilis is entropically driven, which suggests that Bacillus licheniformis has different donor ligands dominating reactivity around circumneutral pH.     

Formation of radicals during heating lysine and glucose in solution with an intermediate water activity

Abstract

Heating glucose with lysine under alkaline conditions (pH 7.0–10.0) was found to take place with consumption of oxygen together with formation of brown-colored compounds. Highly reactive intermediary radicals were detected when lysine and glucose were heated at intermediate water activity at pH 7.0 and 8.0. The detection was based on initial trapping of highly reactive radicals by ethanol followed by spin trapping of 1-hydroxyethylradicals with α-(4-pyridyl N-oxide)-N-tert-butylnitrone (POBN) and Electron Spin Resonance (ESR) spectroscopy. The generation of reactive intermediary radicals from the Maillard reactions was favored by enhancing alkaline conditions (pH 8.0) and stimulated by presence of the transition metal ion Fe²⁺. The stability of the nitrone spin traps, N-tert-butyl-α-phenylnitrone and POBN was examined in buffered aqueous solutions within the pH range 1–12, and found to be less temperature dependent at acidic pH compared to alkaline conditions. A low rate (k_obs) of hydrolysis of POBN was found at the used experimental conditions of 70°C and pH 7.0 and 8.0, which made this spin trap method suitable for the detection of radicals in the Maillard reaction system.     

Growth and aflatoxin production by Aspergillus parasiticus when in the presence of Streptococcus lactis

Streptococcus lactis was grown with Aspergillus parasiticus in modified APT broth. Three inoculation procedures were used: (a) S. lactis was grown 3 days, then conidia of A. parasiticus were added (SLAP), (b) both organisms were added simultaneously (ST) and (c) A. parasiticus was grown 3 days, then S. lactis was added (APSL). At 3, 6 and 10 days of incubation, contents of flasks were analyzed for growth of each organism, pH of broth and aflatoxin content. S. lactis did not survive past 3 days when grown alone. In ST cultures, S. lactis grew to the same extent as in the control at 3 days; it remained viable at a low level through 10 days. In APSL cultures, S. lactis growth was inhibited at 3 days but the bacterium survived through 7 days (10 days of mold growth) at reduced numbers. At 3 days there were no appreciable differences in growth of A. parasiticus. At 6 days, in ST and SLAP cultures, growth of the mold was inhibited, while in the APSL culture growth increased over that in the control. At 10 days, growth of mold was somewhat increased over the control in all test conditions. The pH of broth in the A. parasiticus control and APSL culture was 6 at 3 days, dropped to 4.5–4.6 at 6 days and rose to 7 by 10 days. In ST and SLAP cultures, the pH was at 4.1 at 3 days and rose to pH 7 by 10 days. Aflatoxin (B₁ plus G₁) content was lowest at 3 days and increased at 6 days. Between 6 and 10 days two patterns were observed. In APSL and SLAP cultures, aflatoxin content decreased, while it increased in the ST culture. These patterns occurred when aflatoxin content was expressed on a total or per gram of dried mycelium basis. At 3 days the amounts of aflatoxin B₁ and G₁ were approximately equal. Between 3–6 days the amount of G₁ increased more rapidly than that of B₁. Between 6 and 10 days in the ST culture, the amount of G₁ increased at a slower rate than that of B₁ while in SLAP and APSL cultures, the amount of G₁ decreased more rapidly than that of B₁. When a different lot of the same medium was used, aflatoxin production was greatly reduced. The pH of broth at all test conditions rose through the incubation period.     

Determination of the transgalactosylation activity of Aspergillus oryzae β-galactosidase: effect of pH, temperature, and galactose and glucose concentrations

The catalytic potential of β-galactosidase is usually determined by its hydrolytic activity over natural or synthetic substrates. However, this method poorly predicts enzyme behavior when transglycosylation instead of hydrolysis is being performed. A system for determining the transgalactosylation activity of β-galactosidase from Aspergillus oryzae was developed, and its activity was determined under conditions for the synthesis of galacto-oligosaccharides and lactulose. Transgalactosylation activity increased with temperature up to 55 °C while the effect of pH was mild in the range from pH 2.5 to 5.5, decreasing at higher values. The effect of glucose and galactose on transgalactosylation activity was also assessed both in the reactions for the synthesis of galacto-oligosaccharides and lactulose and also in the reaction of hydrolysis of o-nitrophenyl β-d-galactopiranoside. Galactose was a competitive inhibitor and its effect was stronger in the reactions of transgalactosylation than in the reaction of hydrolysis. Glucose was a mild activator of β-galactosidase in the reaction of hydrolysis, but its mechanism of action was more complex in the reactions of transgalactosylation, having this positive effect only at low concentrations while acting as an inhibitor at high concentrations. This information is relevant to properly assess the effect of monosaccharides during the reactions of the synthesis of lactose-derived oligosaccharides, such as galacto-oligosaccharides and lactulose.     

Culture method to enhance the productivity of hepatitis B surface antigen (pre S2 + S Ag) with recombinant Saccharomyces cerevisiae

Summary The optimum culture condition for the production of recombinant hepatitis B surface antigen (pre S2 + S Ag) was investigated. The productivity of hepatitis B surface antigen in recombinant Saccharomyces cerevisiae, which contains GAP (glyceraldehyde - 3 - phosphate dehydrogenase) promoter, was increased by 25% when the pH was changed from 5 to 8 during the stationary growth phase and by 46% when phenyl methyl sulfonyl fluoride was added at 0.344mM in the stationary phase.     

Observations on the pathogenicity of Pasteuria penetrans, a parasite of root-knot nematodes

A simple test was used to determine whether or not Pasteuria penetrans spores would attach to 17 species of nematodes. All susceptible individuals had spores attached to their cuticles after 24 h of gentle agitation in suspensions containing 10⁵spores/ml. Spores of P. penetrans from six populations of Meloidogyne only adhered to species of Meloidogyne and they adhered in greatest numbers to the species from which they had been originally isolated. Sonication of spores from infected females increased attachment but the effect was dependent on pH and whether the test was conducted in tap or distilled water. Invasion of tomato roots was reduced by up to 86% when, rather than using healthy juveniles, second-stage juveniles bearing 15 or more spores were added to soil at high densities (1000 or 3000/plant); at low densities (500/plant) invasion was not significantly affected. The rate of development of M. incognita juveniles infected with P. penetrans was slower than that of healthy juveniles. The numbers of second-generation of M. incognita were reduced by 82–93% when juveniles encumbered with 1–15 spores were added to soil instead of those bearing no spores. Pasteuria penetrans populations differed in their aggressiveness and when juveniles encumbered with the same number of spores from two populations were added to soil there were differences in the numbers of females that became infected. The implications of these results for the development of P. penetrans as a biological control agent are discussed.     

Na<Superscript>+</Superscript> and flagella-dependent swimming of alkaliphilic <Emphasis Type="Italic">Bacillus pseudofirmus</Emphasis> OF4: a basis for poor motility at low pH and enhancement in viscous media in an “up-motile” variant

Flagella-based motility of extremely alkaliphilic Bacillus species is completely dependent upon Na⁺. Little motility is observed at pH values < ∼8.0. Here we examine the number of flagella/cell as a function of growth pH in the facultative alkaliphile Bacillus pseudofirmus OF4 and a derivative selected for increased motility on soft agar plates. Flagella were produced by both strains during growth in a pH range from 7.5 to 10.3. The number of flagella/cell and flagellin levels of cells were not strongly dependent on growth pH over this range in either strain although both of these parameters were higher in the up-motile strain. Assays of the swimming speed indicated no motility at pH < 8 with 10 mM Na⁺, but significant motility at pH 7 at much higher Na⁺ concentrations. At pH 8–10, the swimming speed increased with the increase of Na⁺ concentration up to 230 mM, with fastest swimming at pH 10. Motility of the up-motile strain was greatly increased relative to wild-type on soft agar at alkaline pH but not in liquid except when polyvinylpyrrolidone was added to increase viscosity. The up-motile phenotype, with increased flagella/cell may support bundle formation that particularly enhances motility under a subset of conditions with specific challenges.     

Inhibition of yeast by lactic acid bacteria in continuous culture: nutrient depletion and/or acid toxicity?

Lactic acid was added to batch very high gravity (VHG) fermentations and to continuous VHG fermentations equilibrated to steady state with Saccharomyces cerevisiae. A 53% reduction in colony-forming units (CFU) ml^–1 of S. cerevisiae was observed in continuous fermentation at an undissociated lactic acid concentration of 3.44% w/v; and greater than 99.9% reduction was evident at 5.35% w/v lactic acid. The differences in yeast cell number in these fermentations were not due to pH, since batch fermentations over a pH range of 2.5–5.0 did not lead to changes in growth rate. Similar fermentations performed in batch showed that growth inhibition with added lactic acid was nearly identical. This indicates that the apparent high resistance of S. cerevisiae to lactic acid in continuous VHG fermentations is not a function of culture mode. Although the total amount of ethanol decreased from 48.7 g l^–1 to 14.5 g l^–1 when 4.74% w/v undissociated lactic acid was added, the specific ethanol productivity increased ca. 3.2-fold (from 7.42×10^–7 g to 24.0×10^–7 g ethanol CFU^–1 h^–1), which indicated that lactic acid stress improved the ethanol production of each surviving cell. In multistage continuous fermentations, lactic acid was not responsible for the 83% (CFU ml^–1) reduction in viable S. cerevisiae yeasts when Lactobacillus paracasei was introduced to the system at a controlled pH of 6.0. The competition for trace nutrients in those fermentations and not lactic acid produced by L. paracasei likely caused the yeast inhibition.     

Metal-ion-catalyzed hydrolysis of monomethyl and dimethyl esters of 3-(2-imidazoleazo)phthalic acid: Bifunctional catalysis by carboxyl group and the metal ion in the hydrolysis of an alkyl ester

The Cu(II) or Ni(II) ion-catalyzed hydrolysis of methyl 2-carboxy-6-(2-imidazoleazo)benzoate (1) and the corresponding dimethyl ester (2) was studied kinetically at various pH values. For 2, the ester group located at the o position to the azo substiuent was hydrolyzed. From the rate data obtained at various metal concentrations, the values of k_cat and K_f were estimated at each pH value. For the Ni(II)-catalyzed hydrolysis of 1 at pH < 4, k_cat increases as pH is lowered, indicating bifunctional catalysis by the carboxyl group and the metal ion. For most of the reactions investigated under other conditions, the ester hydrolysis was subjected to sole catalysis by the metal ions. Detailed analysis of kinetic data obtained for these reactions indicated that the metal-ion catalysis involves the rate-determining breakdown of the tetrahedral intermediates formed by the addition of a water molecule or hydroxide ion. The bifunctional catalysis by the carboxyl group and Ni(II) ion can be considered as a model for carboxypeptidase A. The kinetic data indicate that the bifunctional catalysis proceeds through the nucleophilic attack of the carboxylate ion at the Ni(II)-coordinated carbonyl group.     

Gating properties of channels formed by colicin Ia in planar lipid bilayer membranes

Summary Colicin Ia forms voltage-dependent channels when incorporated into planar lipid bilayers. A membrane containing many Colicin Ia channels shows a conductance which is turned on when high positive voltages (>+10 mV) are applied to thecis side (side to which the protein is added). The ionic current flowing through the membrane in response to a voltage step shows at first an exponential and then a linear rise with time. The relationship between the steady-state conductance, achieved immediately after the exponential portion, and voltage is S-shaped and is adequately fit by a Boltzmann distribution. The time constant () of the exponential is also dependent on voltage, and the relation between these two parameters is asymmetric aroundV _o (voltage at which half of the channels are open). In both cases the steepness of the voltage dependence, a consequence of the number of effective gating particles (n) present in the channel, is greatly influenced by the pH of the bathing solutions. Thus, increasing the pH leads to a reduction inn, while acidic pH's have the opposite effects. This result is obtained either by changing the pH on both sides of the membrane or on only one side, be itcis orrans. On the other hand, changing pH on only one side by addition of an impermeant buffer fails to induce any change inn. At the single-channel level, pH had an effect both on the unitary conductance, doubling it in going from pH 4.5 to 8.2, as well as on the fraction of time the channels stay open,F _(v). For a given voltage,F _(v) is clearly diminished by increasing the pH. This titration of the voltage sensitivity leads to the conclusion that gating in the Colicin Ia molecule is accomplished by charged amino-acid residues present in the protein molecule. Our results also support the notion that these charged groups are inside the aqueous portion of the channel.