Biomedical subjects

A G Voragen

Publications and source records attributed to A G Voragen.

At least 19 recordsLinked to original sources

PubMed2001

The Pseudomonas cellulosa glycoside hydrolase family 51 arabinofuranosidase exhibits wide substrate specificity.

To investigate the mechanism by which Pseudomonas cellulosa releases arabinose from polysaccharides and oligosaccharides, a gene library of P. cellulosa genomic DNA was screened for 4-methylumbelliferyl-alpha-L-arabinofuranosidase (MUAase) activity. A single MUAase gene (abf51A) was isolated, which encoded a non-modular glycoside hydrolase family (GH) 51 arabinofuranosidase (Abf51A) of 57000 Da. The substrate specificity of the Abf51A showed that it preferentially removed alpha1,2- and alpha1,3-linked arabinofuranose side chains from either arabinan or arabinoxylan, and hydrolysed alpha1,5-linked arabino-oligosaccharides, although at a much lower rate. The activity of Abf51A against arabinoxylan was similar to a GH62 arabinofuranosidase encoded by a P. cellulosa gene. Glu-194 and Glu-321 of Abf51A are conserved in GH51 enzymes, and it has been suggested that these amino acids comprise the key catalytic acid/base and nucleophile residues, respectively. To evaluate this hypothesis the biochemical properties of E194A and E321A mutants of Abf51A were evaluated. The data were consistent with the view that Glu-194 and Glu-321 comprise the key catalytic residues of Abf51A. These data, in conjunction with the results presented in the accompanying paper [Beylot, Emami, McKie, Gilbert and Pell (2001) Biochem. J. 358, 599-605], indicate that P. cellulosa expresses a membrane-bound GH51 arabinofuranosidase that plays a pivotal role in releasing arabinose from a range of polysaccharides and oligosaccharides.

Amino Acid Sequence↗

PubMed2001

Study of the mode of action of endopolygalacturonase from Fusarium moniliforme.

One endopolygalacturonase from Fusarium moniliforme was purified from the culture broth of a transformed strain of Saccharomyces cerevisiae. Its kinetic parameters and mode of action were studied on galacturonic acid oligomers and homogalacturonan. The dimer was not a substrate for the enzyme. The enzyme was shown to follow Michaelis-Menten behaviour towards the other substrates tested. Affinity and maximum rate of hydrolysis increased with increasing chain length, up to the hexamer or heptamer, for which V(max) was in the same range as with homogalacturonan. The enzyme was demonstrated to have a multi-chain attack mode of action and its active site included five subsites ranging from -3 to +2. The final products of hydrolysis of homogalacturonan were the monomer and the dimer of galacturonic acid.

Binding Sites↗

PubMed2001

Structural analyses of two arabinose containing oligosaccharides derived from olive fruit xyloglucan: XXSG and XLSG.

Xyloglucan oligosaccharides were prepared by endo-(1-->4)-beta-D-glucanase digestion of alkali-extractable xyloglucan from olive fruit and purified by a combination of gel-permeation (Bio-Gel P-2) chromatography and high-performance anion-exchange chromatography. The two most abundant oligosaccharides were converted to the corresponding oligoglycosyl alditols by borohydride reduction and structurally characterised by NMR spectroscopy and post-source decay (PSD) fragment analysis of matrix-assisted laserinduced desorption/ionisation time-of-flight (MALDI-TOF) mass spectra. The results revealed that olive fruit xyloglucan is mainly built from two novel oligosaccharides: XXSG and XLSG. The structure of the oligosaccharides confirmed the presence of a specific xyloglucan in olive fruit with alpha-L-Araf-(1-->2)-alpha-D-Xylp sidechains as was suggested previously. The presence of such sidechains is a common feature of xyloglucans with an XXGG core produced by solanaceous plants but has not been demonstrated for other dicotyledonous plants, which have in general an XXXG core. Direct treatment of cell wall material from olive fruit with pectin degrading enzymes in combination with endo-(1-->4)-beta-D-glucanase revealed that some of the arabinose residues of the oligosaccharides XXSG and XLSG are substituted with either 1 or 2 O-acetyl groups.

Arabinose↗

PubMed2001

A new family of rhamnogalacturonan lyases contains an enzyme that binds to cellulose.

Pseudomonas cellulosa is an aerobic bacterium that synthesizes an extensive array of modular cellulases and hemicellulases, which have a modular architecture consisting of catalytic domains and distinct non-catalytic carbohydrate-binding modules (CBMs). To investigate whether the main-chain-cleaving pectinases from this bacterium also have a modular structure, a library of P. cellulosa genomic DNA, constructed in lambdaZAPII, was screened for pectinase-encoding sequences. A recombinant phage that attacked arabinan, galactan and rhamnogalacturonan was isolated. The encoded enzyme, designated Rgl11A, had a modular structure comprising an N-terminal domain that exhibited homology to Bacillus and Streptomyces proteins of unknown function, a middle domain that exhibited sequence identity to fibronectin-3 domains, and a C-terminal domain that was homologous to family 2a CBMs. Expression of the three modules of the Pseudomonas protein in Escherichia coli showed that its C-terminal module was a functional cellulose-binding domain, and the N-terminal module consisted of a catalytic domain that hydrolysed rhamnogalacturonan-containing substrates. The activity of Rgl11A against apple- and potato-derived rhamnogalacturonan substrates indicated that the enzyme had a strong preference for rhamnogalacturonans that contained galactose side chains, and which were not esterified. The enzyme had an absolute requirement for calcium, a high optimum pH, and catalysis was associated with an increase in absorbance at 235 nm, indicating that glycosidic bond cleavage was mediated via a beta-elimination mechanism. These data indicate that Rgl11A is a rhamnogalacturonan lyase and, together with the homologous Bacillus and Streptomyces proteins, comprise a new family of polysaccharide lyases. The presence of a family 2a CBM in Rgl11A, and in a P. cellulosa pectate lyase described in the accompanying paper [Brown, Mallen, Charnock, Davies and Black (2001) Biochem. J. 355, 155-165] suggests that the capacity to bind cellulose plays an important role in the activity of main-chain-cleaving Pseudomonas pectinases, in addition to cellulases and hemicellulases.

Amino Acid Sequence↗

PubMed2001

Modulation of the degree and pattern of methyl-esterification of pectic homogalacturonan in plant cell walls. Implications for pectin methyl esterase action, matrix properties, and cell adhesion.

Homogalacturonan (HG) is a multifunctional pectic polysaccharide of the primary cell wall matrix of all land plants. HG is thought to be deposited in cell walls in a highly methyl-esterified form but can be subsequently de-esterified by wall-based pectin methyl esterases (PMEs) that have the capacity to remove methyl ester groups from HG. Plant PMEs typically occur in multigene families/isoforms, but the precise details of the functions of PMEs are far from clear. Most are thought to act in a processive or blockwise fashion resulting in domains of contiguous de-esterified galacturonic acid residues. Such de-esterified blocks of HG can be cross-linked by calcium resulting in gel formation and can contribute to intercellular adhesion. We demonstrate that, in addition to blockwise de-esterification, HG with a non-blockwise distribution of methyl esters is also an abundant feature of HG in primary plant cell walls. A partially methyl-esterified epitope of HG that is generated in greatest abundance by non-blockwise de-esterification is spatially regulated within the cell wall matrix and occurs at points of cell separation at intercellular spaces in parenchymatous tissues of pea and other angiosperms. Analysis of the properties of calcium-mediated gels formed from pectins containing HG domains with differing degrees and patterns of methyl-esterification indicated that HG with a non-blockwise pattern of methyl ester group distribution is likely to contribute distinct mechanical and porosity properties to the cell wall matrix. These findings have important implications for our understanding of both the action of pectin methyl esterases on matrix properties and mechanisms of intercellular adhesion and its loss in plants.

Antibodies, Monoclonal↗

PubMed2001

The occurrence of internal (1 --> 5)-linked arabinofuranose and arabinopyranose residues in arabinogalactan side chains from soybean pectic substances.

CDTA-extractable soybean pectic substances were subjected to enzymatic digestion with arabinogalactan degrading enzymes yielding a resistant polymeric pectic backbone and arabino-, galacto-, and arabinogalacto-oligomers. The complex digest was fractionated using size-exclusion chromatography. Monosaccharide composition analysis, HPAEC fractionation and MALDI-TOF MS analysis of the resulting fractions showed that each contained a mixture of oligosaccharides of essentially the same degree of polymerisation, composed of only arabinose and galactose. MALDI-TOF MS analysis was used for molecular mass screening of oligosaccharides in underivatised HPAEC fractions. The monosaccharide sequence and the branching pattern of oligosaccharides (degree of polymerisation from 4 to 8) were determined using linkage analysis and ES-CID tandem MS analysis of the per-O-methylated oligosaccharides in each of the HPAEC fractions. These analyses indicated the presence of common linear (1 --> 4)-linked galacto-oligosaccharides, and both linear and branched arabino-oligosaccharides. In addition, the results unambiguously showed the presence of oligosaccharides containing (1 --> 4)-linked galactose residues bearing an arabinopyranose residue as the non-reducing terminal residue, and a mixture of linear oligosaccharides constructed of (1 --> 4)-linked galactose residues interspersed with an internal (1 --> 5)-linked arabinofuranose residue. The consequences of these two new structural features of pectic arabinogalactan side chains are discussed.

Arabinose↗

PubMed2001

Nonesterified galacturonic acid sequence homology of pectins.

The methyl ester distribution of pectins was studied with a recently developed enzymatic method. Endopolygalacturonase of Kluyveromyces fragilis was used to degrade pectin and the composition of the degradation products was determined with high-performance anion-exchange chromatography at pH 5. Three characteristics indicative for the distribution of nonesterified galacturonic acid residues were obtained: the percentage of nonesterified galacturonic acid residues liberated of the total number of nonesterified galacturonic acid in the undigested polymer, the proportion of nonesterified mono-, di-, and trigalacturonic acid released, and the ratio of the sum of the peak areas of methyl ester containing oligomers divided by the sum of the peak areas of the nonesterified oligomers detected. From these characteristics and the degree of methyl esterification, the mean sequence similarity of the methyl ester distributions was calculated. Computational techniques commonly employed in the determination of the sequence similarity of DNA and proteins were used to discriminate the various types of distributions found and to construct a distance tree. In general, three types of methyl ester distributions could be discerned in pectin: random, high, and blockwise esterified. This report is the first to describe a parametric approach for the comparison of the substituent distribution in polymers. The importance of this novel approach in the study of the methyl ester distribution and the functional properties of pectin is discussed.

Carbohydrate Conformation↗

PubMed2001

Study of the methyl ester distribution in pectin with endo-polygalacturonase and high-performance size-exclusion chromatography.

A method was developed that enables the study of the methyl ester distribution in the polymers of pectin on a molecular level. Endo-polygalacturonase was used to extensively degrade three 70% methyl esterified pectins. The molecular weight distribution of the non- and enzymatically degraded pectins was determined with high-performance size-exclusion chromatography. Next, the molecular weight distribution was converted into a degree of polymerization distribution of galacturonan fragments. Monte Carlo methods were employed for the reconstruction of the parental polymers from their enzymatic degradation products. The results for the random methyl esterified pectin revealed that the enzyme-degradable sites were indeed randomly distributed, which confirmed the correctness of the procedure developed. The two other pectins studied differed greatly in the amount of non-, low-, and high-esterified regions present in the reconstructed pectic molecules of a given molecular mass. That the approach developed is able to reveal such detailed information makes it unique. The information on the fragmental composition of pectic polymers obtained is an important addition to the study of the methyl ester distribution and the functional properties of pectin.

Chromatography, High Pressure Liquid↗

PubMed2001

The CDTA-soluble pectic substances from soybean meal are composed of rhamnogalacturonan and xylogalacturonan but not homogalacturonan.

Structural characteristics of pectic substances extracted from soybean meal cell walls (water unextractable solids) with a chelating agent-containing buffer (0.05M 1,2-diaminocyclohexane-N,N,N',N'-tetraacetic acid (CDTA) and 0.05M NH(4)-oxalate in 0.05M NaOAc buffer) were studied. The arabinogalactans present as side chains to the rhamnogalacturonan backbone were largely removed by enzymatic hydrolysis using endo-galactanase, exo-galactanase, endo-arabinanase, and arabinofuranosidase B. The remaining pectic backbone appeared to be resistant to enzymatic degradation by pectolytic enzymes. After partial acid hydrolysis of the isolated pectic backbone, one oligomeric and two polymeric populations were obtained by size-exclusion chromatography. Monosaccharide and linkage analyses, enzymatic degradation, and NMR spectroscopy of these populations showed that the pectic substances in the original extract contain both rhamnogalacturonan and xylogalacturonan regions, while homogalacturonan is absent.

Acids↗

PubMed2001

Effects of structural modifications on some physical characteristics of exopolysaccharides from Lactococcus lactis.

The relationship between the primary structure and the chain stiffness of exopolysaccharides (EPSs) and modified EPSs produced by two strains of Lactococcus lactis subsp. cremoris was investigated. The molar mass and radius of gyration of these exopolysaccharides were analyzed by multiangle static light scattering after size-exclusion chromatography. From these results and the chemical structure of the repeating units of the investigated EPSs, the Kuhn lengths could be calculated. We found that the initial Kuhn lengths of the two native EPSs are similar. Modification of the EPSs by removing parts of the side groups resulted in a decrease in both the absolute value and the normalized value of the Kuhn length. It is therefore concluded that partial removal of the side groups of these polysaccharides could make them less efficient as thickeners if no specific interaction with other components occurs.

Carbohydrate Conformation↗

PubMed2001

Solubilization of rhamnogalacturonan I galactosyltransfrases from membranes of a flax cell suspension.

Galactosyltransferases (GalTs), capable of transferring a galactosyl residue from UDP-galactose (UDP-Gal) to polysaccharide acceptor, were solubilized from flax (Linum usitatissimum L.) membranes using 0.5% CHAPS. The observed requirement for a rhamnogalacturonan I (RG-I) exogenous substrate to stimulate the solubilized GalT activity provided the first evidence for the presence of RG-I GalT activities in flax cells. An assay to measure specifically the products of this RG-I GalT activity was designed, based on size-exclusion chromatography. Labelled products were characterized as an RG-I polymer by using purified RG-I hydrolase or lyase. At pH 8 and in the presence of 5 mM CaCl2, beta-D-galactosyl residues were specifically transferred onto RG-I branches of short beta-(1 --> 4)-D-galactan side chains. These side chains were liable to hydrolysis by beta-galactosidase and endo-beta-(1 --> 4)-D-galactanase. The RG-I GalT had a temperature optimum of 30 degrees C. an apparent Km for UDP-Gal and exogenous RG-I substrate of 460 +/- 40 microM and 1.1 +/- 0.1 mg ml(-1) respectively, and a Vmax of 3.0 +/- 0.5 pkat mg(-1) protein.

Cell Membrane↗

PubMed2001

Effect of enzyme treatment during mechanical extraction of olive oil on phenolic compounds and polysaccharides.

The effect of the use of cell-wall-degrading-enzyme preparations during the mechanical extraction process of virgin olive oil on the phenolic compounds and polysaccharides was investigated. The use of the enzyme preparations increased the concentration of phenolic compounds in the paste, oil, and byproducts. Especially, the contents of secoiridiod derivatives such as the dialdehydic form of elenolic acid linked to 3,4-dihydroxyphenylethanol (3,4-DHPEA-EDA) and an isomer of oleuropein aglycon (3,4-DHPEA-EA), which have high antioxidant activities, increased significantly in the olive oil. Furthermore, the use of an N(2) flush during processing strongly increased the phenolic concentration. Analyses of the pectic polymers present in the paste showed that the use of pectinolytic enzyme preparations increased the yield of the buffer soluble pectins and the proportion of molecules with a lower molecular mass. Also, the content of uronic acids in the buffer soluble extract increased considerably due to the use of the enzyme preparations. Analysis of the polymeric carbohydrates in the vegetation waters showed the presence of mainly pectic polymers. The addition of commercial enzyme preparations increased the uronic acid content of the polysaccharides in the vegetation water substantially compared to the blank. This study showed that the addition of cell-wall-degrading enzymes did improve the olive oil quality; however, mechanisms remained unclear.

Cell Wall↗

PubMed2001

Peroxidase-mediated cross-linking of a tyrosine-containing peptide with ferulic acid.

The tyrosine-containing peptide Gly-Tyr-Gly (GYG) was oxidatively cross-linked by horseradish peroxidase in the presence of hydrogen peroxide. As products, covalently coupled di- to pentamers of the peptide were identified by LC-MS. Oxidative cross-linking of ferulic acid with horseradish peroxidase and hydrogen peroxide resulted in the formation of dehydrodimers. Kinetic studies of conversion rates of either the peptide or ferulic acid revealed conditions that allow formation of heteroadducts of GYG and ferulic acid. To a GYG-containing incubation mixture was added ferulic acid in small aliquots, therewith keeping the molar ratio of the substrates favorable for hetero-cross-linking. This resulted in a predominant product consisting of two ferulic acid molecules dehydrogenatively linked to a single peptide and, furthermore, two ferulic acids linked to peptide oligomers, ranging from dimers to pentamers. Also, mono- and dimers of the peptide were linked to one molecule of ferulic acid. A mechanism explaining the formation of all these products is proposed.

Coumaric Acids↗

PubMed2001

Enzymatic extractability of soybean meal proteins and carbohydrates: heat and humidity effects.

To study the incomplete enzymatic extractability of proteins and carbohydrates of thermally treated soybean meals, one unheated and three heat-treated soybean meals were produced. To obtain truly enzyme-resistant material, the meals were extracted by a repeated hydrolysis procedure using excessive concentrations of different combinations of commercial protease and carbohydrase preparations. The water extractability of protein from the different meals varied considerably (13-67%). For all soybean meals, enzymatic treatment extracted most of the original protein (89-94%). Carbohydrase preparations did not improve protein extraction. High-humidity heat treatment led to a more effective enzymatic extraction, which seemed to correlate with the extent of protein denaturation. Results with purified proteins indicated that the soybean meal matrix affects the enzymatic extraction of protein from the meals. Interactions between protein and other components (e.g., cellulose) may explain the incomplete enzymatic extractability of protein from the meals.

Carbohydrate Metabolism↗

PubMed2001

Relative abundance and inhibitory distribution of protease inhibitors in potato juice from cv. Elkana.

Protease inhibitors from potato juice of cv. Elkana were purified and quantified. The protease inhibitors represent ca. 50% of the total soluble proteins in potato juice. The protease inhibitors were classified into seven different families: potato inhibitor I (PI-1), potato inhibitor II (PI-2), potato cysteine protease inhibitor (PCPI), potato aspartate protease inhibitor (PAPI), potato Kunitz-type protease inhibitor (PKPI), potato carboxypeptidase inhibitor (PCI), and "other serine protease inhibitors". The most abundant families were the PI-2 and PCPI families, representing 22 and 12% of all proteins in potato juice, respectively. Potato protease inhibitors show a broad spectrum of enzyme inhibition. All the families (except PCI) inhibited trypsin and/or chymotrypsin. PI-2 isoforms exhibit 82 and 50% of the total trypsin and chymotrypsin inhibiting activity, respectively. A strong variation within the latter activities was shown within one family and between protease inhibitor families.

Chymotrypsin↗

PubMed2001

Emulsion properties of casein and whey protein hydrolysates and the relation with other hydrolysate characteristics.

Casein and whey protein were hydrolyzed using 11 different commercially available enzyme preparations. Emulsion-forming ability and emulsion stability of the digests were measured as well as biochemical properties with the objective to study the relations between hydrolysate characteristics and emulsion properties. All whey protein hydrolysates formed emulsions with bimodal droplet size distributions, signifying poor emulsion-forming ability. Emulsion-forming ability of some casein hydrolysates was comparable to that of intact casein. Emulsion instability was caused by creaming and coalescence. Creaming occurred mainly in whey hydrolysate emulsions and in casein hydrolysate emulsions containing large emulsion droplets. Coalescence was dominant in casein emulsions with a broad particle size distribution. Emulsion instability due to coalescence was related to apparent molecular weight distribution of hydrolysates; a relative high amount of peptides larger than 2 kDa positively influences emulsion stability.

Caseins↗

PubMed2001

Effects of pH and heat treatments on the structure and solubility of potato proteins in different preparations.

The soluble potato proteins are mainly composed of patatin and protease inhibitors. Using DSC and both far-UV and near-UV CD spectroscopy, it was shown that potato proteins unfold between 55 and 75 degrees C. Increasing the ionic strength from 15 to 200 mM generally caused an increase in denaturation temperature. It was concluded that either the dimeric protein patatin unfolds in its monomeric state or its monomers are loosely associated and unfold independently. Thermal unfolding of the protease inhibitors was correlated with a decrease in protease inhibitor activities and resulted in an ionic strength dependent loss of protein solubility. Potato proteins were soluble at neutral and strongly acidic pH values. The tertiary structure of patatin was irreversibly altered by precipitation at pH 5. At mildly acidic pH the overall potato protein solubility was dependent on ionic strength and the presence of unfolded patatin.

Calorimetry, Differential Scanning↗

PubMed2001

The influence of olfactory concept on the probability of detecting sub- and peri-threshold components in a mixture of odorants.

The headspace of apple juice was analysed to obtain an ecologically relevant stimulus model mixture of apple volatiles. Two sets of volatiles were made up: a set of eight supra-threshold volatiles (MIX) and a set of three sub-threshold volatiles. These sets were used to test the hypothesis that sub-threshold components can change the quality of a familiar smelling mixture of odorants when added to this mixture. In order to test this hypothesis, three successive dilutions of the sub-threshold volatiles were prepared in such a way that the strongest was at the threshold concentration and the two lower concentrations were below the threshold. The detection probabilities of the sub-threshold components in a blank stimulus were compared with the detectabilities in MIX. The sub- and peri-threshold volatiles were detected no better in MIX than in a blank. On the contrary, sub- and peri-threshold volatiles were better detected alone than when added to MIX. However, when the group of subjects was split into two sub-groups, employing either a rough or a detailed concept definition of the target stimulus, respectively, the subjects with highly refined concepts were better able to detect the presence of sub-threshold volatiles in MIX than those with poorly refined stimulus concepts. The effect of stimulus concept definition occurred independently of the proportions of correct detections of sub-threshold volatiles in a blank.

Adolescent↗