Affinity chromatography of nicotinamide nucleotide-dependent dehydrogenases on immobilized nucleotide derivatives

A series of chemically-defined adenosine phosphate ligands attached to Sepharose 4B were used as active-site probes in studying the interaction of enzymes with their coenzymes and substrates and to test the suitability of these matrices for `general ligand' affinity chromatography. Nicotinamide nucleotide-dependent dehydrogenases were used as models to test this methodology. Elution from these columns by NAD⁺ and/or AMP gradients (in the presence or the absence of substrates and/or nicotinamide mononucleotide) was consistent with: (1) the compulsory ordered addition of substrates to lactate and malate dehydrogenase; (2) the necessity for the NMN moiety of NAD⁺ to bind to these enzymes before the substrate; and illustrated: (3) that the binding of these two hydrogenases to these columns compared very well with the published three-dimensional models for these enzymes and (4) that separation of mixtures of dehydrogenases depended on the choice of matrix and displacing ion and whether any additions (e.g. substrates) were made to the gradients used. These techniques were used to purify UDP-glucose dehydrogenase from a crude starting material on a phosphate-linked UDP (or ADP) matrix. The binding of this enzyme to these two columns was not consistent with either an ordered or random addition of substrates and suggested a more complex mechanism.     

Competition for Ammonium between Nitrifying and Heterotrophic Bacteria in Continuously Percolated Soil Columns

Although the absence of nitrate formation in grassland soils rich in organic matter has often been reported, low numbers of nitrifying bacteria are still found in these soils. To obtain more insight into these observations, we studied the competition for limiting amounts of ammonium between the chemolithotrophic ammonium-oxidizing species Nitrosomonas europaea and the heterotrophic species Arthrobacter globiformis in the presence of Nitrobacter winogradskyi with soil columns containing calcareous sandy soil. The soil columns were percolated continuously at a dilution rate of 0.007 h^-1, based on liquid volumes, with medium containing 5 mM ammonium and different amounts of glucose ranging from 0 to 12 mM.A. globiformis was the most competitive organism for limiting amounts of ammonium. The numbers of N. europaea and N. winogradskyi cells were lower at higher glucose concentrations, and the potential ammonium-oxidizing activities in the uppermost 3 cm of the soil columns were nonexistent when at least 10 mM glucose was present in the reservoir, although 10⁷ nitrifying cells per g of dry soil were still present. This result demonstrated that there was no correlation between the numbers of nitrifying bacteria and their activities. The numbers and activities of N. winogradskyi cells decreased less than those of N. europaea cells in all layers of the soil columns, probably because of heterotrophic growth of the nitrite-oxidizing bacteria on organic substrates excreted by the heterotrophic bacteria or because of nitrate reduction at reduced oxygen concentrations by the nitrite-oxidizing bacteria. Our conclusion was that the nitrifying bacteria were less competitive than the heterotrophic bacteria for ammonium in soil columns but that they survived as viable inactive cells. Inactive nitrifying bacteria may also be found in the rhizosphere of grassland plants, which is rich in organic carbon. They are possibly reactivated during periods of net mineralization.     

Purification and Characterization of Lysine- and Arginine-Specific Gingivain Proteases from Porphyromonas Gingivalis

Abstract

Four gingivain proteases, active in presence of L-cysteine, were purified from spent culture media of oral pathogen Porphyromonas gingivalis by ion-exchange chromatography on MonoQ and chromatofocusing on MonoP columns. Three of the purified proteases, with molecular masses of 75 kDa, 70 kDa and 55 kDa, respectively, hydrolyzed synthetic chromogenic substrates with arginine in the P1 position. One protease, with a molecular mass of 80 kDa, hydrolyzed substrates with lysine in the P1 position. It is proposed these enzymes be named: arg-gingivain-75, arg-gingivain-70, arg-gingivain-55, and lys-gingivain-80, respectively, based on their molecular mass and specificity for either arginine or lysine in the P1 position.     

Properties of two apyrases from Solanum tuberosum

Two homogeneous isoenzymes of apyrase from Pimpernel and Desirée varieties of Solanum tuberosum were obtained by affinity chromatography on agarose-Cibacron Blue or agarose-ATP-phosphonate columns. Both enzymes split POP bonds of organic and inorganic di- and triphosphates. The ratio of ATPase/ADPase is different for the two apyrases: 10 for Pimpernel and 1 for Desirée. All these activities require bivalent metals. Both isoapyrases have the same MW (49 000) but differ in their pI (8.74 for Pimpernel and 6.69 for Desirée). The optimum pH of hydrolysis of organic di- and triphosphates is 6 (except for Pimpernel ADPase) and 5 for inorganic substrates. Chemical modification of tryptophan, tyrosine, arginine and carboxylic residues decreased all enzymic activities of both enzymes. Protection by substrates and inactivation rates of the individual activities are different for each isoenzyme.     

Interactions between Nematodes and Earthworms: Enhanced Dispersal of Steinernema carpocapsae

Dispersal of the nematode Steinernema carpocapsae (All strain), applied on the top or the bottom of soil columns, was tested in the presence or absence of two earthworm species, Lumbricus terrestris or Aporrectodea trapezoides. Nematode dispersal was estimated after a 2-week period with a bioassay against the greater wax moth, Galleria mellonella. Vertical dispersal of nematodes was increased in the presence of earthworms. When nematodes were placed on the surface of soil columns, significantly more nematodes dispersed to the lower half of the columns when either earthworm species was present than when earthworms were not present. When nematodes were placed on the bottom of soil columns, significantly more nematodes dispersed to the upper half of the columns when L. terrestris was present than when A. trapezoides was present or in the absence of earthworms. Because nematodes were found on the exterior and in the interior of earthworms, nematode dispersal may be enhanced by direct contact with the earthworms.     

Interaction of spinach leaf adenosine diphosphate glucose alpha-1,4-glucan alpha-4-glucosyl transferase and alpha-1,4-glucan, alpha-1,4-glucan-6-glycosyl transferase in synthesis of branched alpha-glucan

Salmonella newington lipopolysaccharide extracted from a cell paste grown up from a single smooth clone was fractionated by chromatography on DEAE-cellulose in the presence of 1% Triton X-100 into seven lipopolysaccharide fractions which differed in their degrees of polymerization of the repeating unit of the O-antigen side chain and in their substitution with ester phosphate. Several of the lipopolysaccharide fractions were hydrolyzed in 1% acetic acid at 100 °C to cleave the linkage between the polysaccharide and lipid A parts of the structure. The polysaccharide fractions from each of the purified lipopolysaccharides could be further fractionated on DEAE-cellulose columns to yield a number of peaks of polysaccharide having monosaccharide ratios quite distinct from those of the parent lipopolysaccharide. The results show a high degree of structural heterogeneity in the original lipopolysaccharide.     

Validation of an isocratic HPLC method to detect 2-fluoro-β-alanine for the analysis of dihydropyrimidine dehydrogenase activity

The efficacy of the chemotherapeutic drug 5′-fluorouracil is reduced by catabolism to 2′-fluoro-β-alanine (FBAL), a three-step reaction in which dihydropyrimidine dehydrogenase (DPD) catalyzes the rate-limiting step. To study in vitro DPD activity, we developed and validated an isocratic, reverse-phase HPLC method to detect and quantify FBAL without using multiple columns or radiolabeled substrates. Pre-column derivatization of FBAL was performed using o-phthalaldehyde in the presence of two sulfur donors, ethanthiol or β-mercaptoethanol, and the resulting products assayed. Calibration curves were linear over a range of 10–200 μg/ml and the method was successfully applied to the examination of DPD activity in cultured cells.     

Pyrosequence analyses of bacterial communities during simulated in situ bioremediation of polycyclic aromatic hydrocarbon-contaminated soil

Barcoded amplicon pyrosequencing was used to generate libraries of partial 16S rRNA genes from two columns designed to simulate in situ bioremediation of polycyclic aromatic hydrocarbons (PAHs) in weathered, contaminated soil. Both columns received a continuous flow of artificial groundwater but one of the columns additionally tested the impact of biostimulation with oxygen and inorganic nutrients on indigenous soil bacterial communities. The penetration of oxygen to previously anoxic regions of the columns resulted in the most significant community changes. PAH-degrading bacteria previously determined by stable-isotope probing (SIP) of the untreated soil generally responded negatively to the treatment conditions, with only members of the Acidovorax and a group of uncharacterized PAH-degrading Gammaproteobacteria maintaining a significant presence in the columns. Additional groups of sequences associated with the Betaproteobacterial family Rhodocyclaceae (including those associated with PAH degradation in other soils), and the Thiobacillus, Thermomonas, and Bradyrhizobium genera were also present in high abundance in the biostimulated column. Similar community responses were previously observed during biostimulated ex situ treatment of the same soil in aerobic, slurry-phase bioreactors. While the low relative abundance of many SIP-determined groups in the column libraries may be a reflection of the slow removal of PAHs in that system, the similar response of known PAH degraders in a higher-rate bioreactor system suggests that alternative PAH-degrading bacteria, unidentified by SIP of the untreated soil, may also be enriched in engineered systems.     

Effects of Grazing by Flagellates on Competition for Ammonium between Nitrifying and Heterotrophic Bacteria in Soil Columns

The enhanced mineralization of immobilized nitrogen by bacteriophagous protozoa has been thought to favor the nitrification process in soils in which nitrifying bacteria must compete with heterotrophic bacteria for the available ammonium. To obtain more insight into this process, the influence of grazing by the flagellate Adriamonas peritocrescens on the competition for ammonium between the chemolithotrophic species Nitrosomonas europaea and the heterotrophic species Arthrobacter globiformis in the presence of Nitrobacter winogradskyi was studied in soil columns, which were continuously percolated with media containing 5 mM ammonium and different amounts of glucose at a dilution rate of 0.007 h^-1 (liquid volumes). A. globiformis won the competition for ammonium. The grazing activities of the flagellates had two prominent effects on the competition between N. europaea and A. globiformis. First, the distribution of ammonium over the profile of the soil columns was more uniform in the presence of flagellates than in their absence. In the absence of flagellates, relatively high amounts of ammonium accumulated in the upper layer (0 to 3 cm), whereas in the underlying layers the ammonium concentrations were low. In the presence of flagellates, however, considerable amounts of ammonium were found in the lower layers, whereas less ammonium accumulated in the upper layer. Second, the potential ammonium-oxidizing activity of N. europaea was stimulated in the presence of flagellates. The numbers of N. europaea at different glucose concentrations in the presence of flagellates were comparable to those in the absence of protozoa. However, in the presence of flagellates, the potential ammonium-oxidizing activities were four to five times greater than those in the absence of protozoa.     

Detection of Thermoactinomyces Species in Selected Agricultural Substrates from Queensland

Selected overheated substrates commercially available for public use in sub-tropical Queensland, Australia were screened for the presence of Thermoactinomyces species using an air sampler. All substrates with the exception of tea tree mulch were found to contain Thermoactinomyces species. Subsequent 16S rDNA oligonucleotide sequencing of the selected eight isolates indicated that some of these species were closely related to previously reported allergenic Thermoactinomyces vulgaris and Laceyella sacchari. In view of this, the isolates were tested to determine their adhesion ability and cytotoxicity to human lung cells (calu-3 cells). The results indicated that all eight isolates were highly adherent and showed cytotoxicity to this cell line. These findings might indicate that the presence of such species in overheated agricultural materials may constitute a public health risk if storage and handling conditions are not optimal and do not meet criteria defined for sub-tropical climates.     

Affinity chromatography of sialoglycoproteins,utilising the interaction of serotonin with N-acetylneuraminic acid and its derivatives

Serotonin, immobilised on Sepharose 4B, has been used to study the affinity chromatography of neuraminic acid and its derivatives. Free N-acetylneuraminic acid and oligosaccharides, polysaccharides, and glycoproteins containing that sugar are specifically bound to the columns. Removal of neuraminic acid from sialoglyco-conjugates, or modification of the neuraminic acid residues by periodate oxidation, abolishes their ability to bind to the ligand. The presence of the N-acetyl group, but not the N-glycolyl group, and the integrity of the side chain (C-7–C-9) of the neuraminic acid are essential for binding to serotonin.     

The identification of oral microbial lectins by cell affinity chromatography

Whole-cell affinity chromatography was used as a novel screening technique for identifying and characterizing oral microbial lectins. First, affinity columns bearing oligosaccharides of defined structure were synthesized as lectin-binding reagents. Fetuin, transferrin (containing terminal NeuAc residues), asialofetuin and asialotransferrin (with terminal Gal residues) were covalently coupled to Sepharose 6MB and incubated with ³H-labeled bacterial suspensions in columns fitted with an 80-μm nylon filter. Bacteria specifically bound were then eluted with the appropriate sugar (NeuAc or Gal). Fusobacterium nucleatum was the most significant binder, with 80% specifically eluted from the asialo-derivatives. Actinomyces viscosus and Actinomyces naeslundii also showed unique specificity for galactose. In contrast, Streptococcus sanguis bound in greatest numbers to fetuin, consistent with the presence of a sialic acid-binding site on these bacteria.     

Immobilized enzymes on chitosan columns: α-Chymotrypsin and acid phosphatase

α-Chymotrypsin and acid phosphatase have been immobilized on chitosan, a polyaminosaccharide, without using any intermediate reagent; the immobilized enzymes are active and their activity is much higher than for chitin-immobilized enzymes. The best pH conditions for operating chitosan columns have been determined and columns have been used to transform substrates in large amounts, with no decrease of activity or enzyme losses. Due to the nonconvalent interaction between chitosan and enzymes, the pure and active enzymes can be eventually recovered from the columns. The effects of metal ions, aldehydes, and salts are reported and discussed. Applications are foreseen in the food and biomedical sciences and industries.     

Immobilised metal-ion affinity chromatography purification of histidine-tagged recombinant proteins: a wash step with a low concentration of EDTA

Immobilised metal-ion affinity chromatography (IMAC) is widely used for the purification of recombinant proteins in which a poly-histidine tag is introduced. However, other proteins may also bind to IMAC columns. We describe the use of a washing buffer with a low concentration of EDTA (0.5 mM) for the removal of proteins without histidine tag from IMAC columns. Four histidine-tagged recombinant proteins/protein complexes were purified to homogeneity from cell culture medium of insect cells by using an EDTA washing buffer. The presence of a low concentration of EDTA in washing buffers during IMAC may have a general application in the purification of histidine-tagged proteins.     

The isolation of coupled mitochondria from Physarum polycephalum and their response to Ca2+

A method for the isolation of coupled mitochondria from the acellular slime mould Physarum polycephalum is described. The mitochondria oxidize respiratory substrates at rates comparable to those of mitochondria from other micro-organisms and show similar responses to respiratory inhibitors. ADP/O values approach similar values to those obtained with mitochondria from higher organisms: 3 with NAD-linked substrates, 2 with succinate, and 1 with ascorbate-TMPD.Mitochondria actively take up low concentrations of Ca²⁺ with stimulation of their respiration. With succinate or pyruvate-malate as substrates respiratory responses are depressed by Ca²⁺ concentrations in excess of 200 μM in the presence or absence of phosphate.Exogenous NADH is unique in supporting the uptake of large amounts of Ca²⁺ in the presence of phosphate and in showing an unusual ‘uncoupled’ response in the absence of phosphate.A sigmoidal relationship occurs between initial velocity of Ca²⁺ uptake and Ca²⁺ concentration with a maximum velocity of approx. 15 nmol/s per mg protein and half maximum velocity occurring at approx. 50 μM Ca²⁺.     

Separation of acid and neutral proteinases of brain.

1. Cerebral proteinases were separated on Sephadex G-100 columns into acid and neutral fractions free from cross-contamination. Acid proteinases were more stable and were purified by additional steps with salt and pH5.0 precipitations, column chromatography on DEAE- or CM-cellulose and free-flow electrophoresis. 2. The separation made it possible to study the properties of the partially purified enzyme fractions. Some of these properties, such as K(m) with selected protein substrates, pH optima and temperature-dependence in the presence and absence of substrates, are described. 3. No requirement for metal ions or added cofactors was demonstrated. Neutral-proteinase activity was more sensitive to inhibition by heavy-metal ions; its activity could be increased by thioglycollate and glutathione, and inhibited by thiol reagents. Neutral and acid proteinases were inhibited by the chymotrypsin inhibitor chloromethyl l-2-phenyl-1-toluene-p-sulphonamidoethyl ketone. 4. In the presence of the appropriate synthetic substrates no cathepsin A activity was found, and only trace quantities of cathepsin B or C activities, which were more than 50-fold less than cathepsin D-like activity.     

Evidence for a single catalytic site on the "beta-D-glucosidase-beta-D-galactosidase" of almond emulsin.

An isoenzyme of glycosidase obtained from almond emulsin, which is both a β-d-glucosidase and a β-d-galactosidase, has now been shown to possess β-D-fucosidase activity. It has been concluded that all three activities reside in a single catalytic site for the following reasons. (i) d-Glucosylamine, d-galactosylamine, and d-fucosylamine (a newly discovered potent inhibitor of this enzyme) each act competitively against all three of the substrates. (ii) Any given inhibitor exhibits the same K_i value when tested in the presence of any of the three substrates, (iii) When the enzyme is incubated with any two of the p-nitrophenyl glycoside substrates, at or above their respective K_m values, the rate of p-nitrophenol formation is not additive, but rather is equal to the value calculated on the basis of the individual K_m values and relative maximum velocities.     

Isolation of a hemorrhagic toxin from the venom of Agkistrodon contortrix laticinctus (broad-banded copperhead) and pathogenesis of the hemorrhage induced by the toxin in mice

• 1.1. A hemorrhagic toxin was isolated from the venom of Agkistrodon contortrix laticinctus (Broad-Banded Copperhead) by Sephacryl S-200 HR column chromatography followed by high performance chromatography on Waters DEAE 5PW and protein Pak 125 columns.
• 2.2. Homogeneity was determined by the presence of a single band in acrylamide gel electrophoresis with silver staining.
• 3.3. ACL hemorrhagic toxin I has a molecular weight of about 29,000, is slightly acidic, and is a metalloprotease with activity towards the substrates N,N-dimethylcasein and bovine fibrinogen. Although the toxin is able to hydrolyze fibrinogen in vitro, it does not possess any defibrinogenating activity in vivo whereas the crude venom does show this activity. It has similar cleavage specificities to other snake venom hemorrhagic toxins.
• 4.4. ACL hemorrhagic toxin I causes hemorrhage of rapid onset, present within 5 min of intramuscular injection into mice, and the pathogenesis is one of hemorrhage per rhexis in which capillary endothelial cells are ruptured.

     

On arabinose as a component of brain hyaluronate Confirmation by chromatographic,enzymatic and chemical ionization-mass spectrometric analyses

The controversy about the presence of the pentose arabinose in brain hyaluronate was reinvestigated using modern analytical technics. The purified bonive brain hyaluronate contained the neutral sugars: arabinose, 0.18%; glucose; 0.05%; and fucose, 0.22%. The confirmation of the presence of arabinose was obtained by paper and thin layer chromatography of the neutral sugars in deionized hyaluronate hydrolysate. Gas-liquid chromatography of the aldononitrile peracetate of the pentose isolated by preparative paper chromatography gave a single distinct peak, corresponding to standard arabinose on three columns packed with three different phases. Chemical ionization data and mass spectrum of the aldononitrile peracetate drivative agreed with those of the authentic arabinonitrile tetracetate. Analysis of the isolated pentose with the help of the enzymes l-arabinose isomerase and l-ribulose kinase, which are specific for their substrates, further established its identity as l-arabinose.     

Specific and non-specific affinities of the extracellular glucosyltransferase complex of Streptococcus mutans 6715

Glucosyltransferases (GTF) from different strains of streptococci exhibited different elution profiles when fractionated on insoluble-dextran affinity columns. The proportions of unadsorbed and adsorbed GTF were not related to their extent of stimulation by exogenous dextran, and GTF preparations exposed to, and freed from, clinical dextran prior to fractionation lost their ability to bind to the dextran columns. Different proportions of bound GTF were released by irrigation of columns with different concentrations of salt and clinical dextran, and the “specific” binding and release of GTF exhibited by a column possessing covalently linked, clinical dextran ligands was duplicated on a control column that did not possess the dextran ligands. These results, and the high affinity of GTF for hydrophobic alkyl (Shaltiel) ligands, demonstrate that ionic and hydrophobic properties of impure GTF aggregates may lead to erroneous characterization of the dextran affinity of some protein fractions. Fractionations on DEAE-Sepharose and on hydroxylapatite showed that the two dextran-dependant GTF activities (GTF-S and GTF-I) were present in the major enzyme fraction (Streptococcus mutans 6715) recovered from a Sephacryl S-200 affinity column. A minor, dextran-independent GTF was not adsorbed onto the Sephacryl column. The presence of SDS (0.005%) and Triton X100 (0.01%) stabilized GTF activity during gel filtration and improved the separation of GTF-S and GTF-I in hydroxylapatite fractionation of the highly aggregated enzyme. A comparable separation of the two enzyme forms on DEAE-Sepharose was achieved only if T10 dextran (10 mg/mL) was included with the detergent mixture in the column irrigant.