Isolation and characterization of rhamnogalacturonan oligomers, liberated during degradation of pectic hairy regions by rhamnogalacturonase

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.

Expression and action pattern of Botryotinia fuckeliana (Botrytis cinerea) rhamnogalacturonan hydrolase in Pichia pastoris

The cDNA sequence coding for the complete rhamnogalacturonan hydrolase (RGase) of Botryotinia fuckeliana (Botrytis cinerea) was introduced into Pichia pastoris and expressed under the control of the alcohol oxidase promoter. The RGase was secreted into the medium of the yeast driven by the alpha-factor secretion peptide and could be purified using the C-terminal His6-tag fusion. RGase activity was measured using a traditional reducing end assay with linseed rhamnogalacturonan (RG) as the substrate, or with an assay using a fluorescent RG oligomer as the substrate and detection and identification of hydrolysis products by capillary zone electrophoresis (CZE). Both methods showed the recombinant enzyme to have a specific activity of about ten units per milligram of protein. Since the CZE method allows identification of the hydrolysis products, it was used to show that the RGase lacks a multiple attack mechanism and needs at least five GalA-Rha repeating disaccharides to be active. This finding is contrary to the action pattern of the native RGase of Aspergillus aculeatus which has the same substrate length requirement, but exhibits multiple attack, leading to products containing only two and three Rha-GalA repeat units without the appearance of intermediate sized fragments. No plant cell wall degrading enzymes were detected in the culture medium of un-transformed P. pastoris, thus the recombinant enzyme, devoid of extraneous activities, can be applied for fine structural studies on cell walls.

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.

Hydration of pectic polysaccharides

The hydration and swelling of pectic polysaccharides was examined at different pHs and ionic strengths as a function of osmotic stress. For weakly charged pectic polysaccharides at low concentrations of a monovalent salt (20 mM), the main driving force for swelling originates from a polyelectrolyte effect due to the translational entropy of ions within the film. Swelling is reduced at higher salt concentrations and lower pHs. Polyelectrolyte collapse and minimal swelling is observed for more highly charged pectic polysaccharides. Replacement of the Na(+) counterion with Ca(2+) results in minimal swelling and the formation of network structures even for the weakly charged pectic polysaccharides.

Characterization of arabinose and ferulic acid rich pectic polysaccharides and hemicelluloses from sugar beet pulp

Pectic polysaccharides were extracted from sugar beet pulp to yield fractions representing homogalacturonans, rhamnogalacturonans, arabinans and relatively small amounts of glucomannans and xyloglucans. The homogalacturonans had an apparent molecular weight of 21 kDa and contained relatively high amounts of methyl esters and relatively low amounts of acetyl groups as compared with the ramified 'hairy' regions. Three populations which originated from the ramified 'hairy' regions of pectin were distinguished. Two of these were rhamnogalacturonans with high apparent molecular weights of 1300 and 120 kDa, respectively. These populations had a high Ara and ferulic acid content. Despite the high neutral sugar content, these rhamnogalacturonans strongly bound to a DEAE column. The third population which originated from the ramified 'hairy' regions was a neutral population, which did not interact with the DEAE column and had a low apparent molecular weight and a high Ara and ferulic acid content. The arabinan side-chains of the rhamnogalacturonans were heavily branched in all populations. Enzymatic degradation of the xyloglucans showed similarities with apple xyloglucans with respect to the substitution with Fuc and Gal.

Extracellular polysaccharide of Erwinia chrysanthemi A350 and ribotyping of Erwinia chrysanthemi spp

Erwinia chrysanthemi spp. are gram-negative bacterial phytopathogens causing soft rots in a number of plants. The structure of the extracellular polysaccharide (EPS) produced by the E. chrysanthemi strain A350, which is a lacZ- mutant of the wild type strain 3937, pathogenic to Saintpaulia, has been determined using a combination of chemical and physical techniques including methylation analysis, low-pressure gel-filtration and anion-exchange chromatography, high-pH anion-exchange chromatography, partial acid hydrolysis, mass spectrometry and 1- and 2D NMR spectroscopy. In contrast to the structures of the EPS reported for other strains of E. chrysanthemi, the EPS from strain A350 contains D-GalA, together with L-Rhap and D-Galp in a 1:4:1 ratio. Evidence is presented for the following hexasaccharide repeat unit: [structure: see text] All the Erwinia chrysanthemi spp. studied to date have been analyzed by ribotyping and collated into families, which are consistent with the related structures of their EPS.

Glucuronic acid directly linked to galacturonic acid in the rhamnogalacturonan backbone of beet pectins

Sugar-beet pulp was de-esterified and submitted to 72 h hydrolysis by 0.1 M HCl at 80 degrees C. Oligomers containing a single glucuronic acid (GlcA) moiety in addition to n(>/= 2) repeats of the dimer -->4)-alpha-D-GalpA-(1-->2)-alpha-L-Rhap-(1--> were isolated from the hydrolysate by ion-exchange and gel-permeation. Glycosyl linkage composition analysis and 1H NMR studies indicated that the GlcA was attached to O-3 of a galacturonic acid (GalA) residue, as shown for the two pentamers beta-D-GlcpA-(1-->3)-alpha-D-GalpA-(1-->2)-alpha-L-Rhap-(1-->4)-alpha-D-GalpA-(1-->2)-L-Rhap and alpha-D-GalpA-(1-->2)-alpha-L-Rhap-(1-->4)-[beta-D-GlcpA-(1-->3)]-alpha-D-GalpA-(1-->2)-L-Rhap. Substitution by GlcA was estimated as occurring on one GalA residue out of 72 in the rhamnogalacturonan fraction of the backbone of beet pectins.

Mode of action of RG-hydrolase and RG-lyase toward rhamnogalacturonan oligomers. Characterization of degradation products using RG-rhamnohydrolase and RG-galacturonohydrolase

The mode of action of RG-hydrolase and RG-lyase toward purified linear rhamnogalacturonan (RG) oligomers has been studied. Major tools in the characterization of the degradation products were the exo-acting RG-rhamnohydrolase and RG-galacturonohydrolase. They were used to prepare a series of standards of RG oligomers for HPAEC. 1H NMR spectroscopy confirmed the structure assignment made using HPAEC for a selection of isolated degradation products. Identification of degradation products from purified RG oligomers was then performed by comparing retention times of HPAEC peaks with those of standards. RG-hydrolase was able to cleave RG oligomers which contained five Rha units or more, i.e. DP 9 with a Rha unit at both nonreducing and reducing end. Its preferential cleavage site was at four units from the first nonreducing Rha. RG-lyase was active toward oligomers that contained at least six GalA units, i.e. DP 12 with a GalA at the nonreducing and a Rha at the reducing end. The preferential cleavage site was for the smaller oligomers four residues, and for the largest oligomer six residues from the reducing Rha. From the observed cleavage patterns it can be speculated that in hairy regions, the RG stretches have to be at least 13 residues long for RG-hydrolase and 16 residues long for RG-lyase in order to produce one tetramer.

Scarcity or complete lack of single rhamnose residues interspersed within the homogalacturonan regions of citrus pectin

Commercial citrus pectin containing galacturonic acid and rhamnose in a ratio of approximately 40:1 was saponified and then exhaustively digested with endopolygalacturonase (EPG). The products were separated by ultrafiltration into low-molecular-weight (LMW) and high-molecular-weight (HMW) fractions. The LMW fraction accounted for 80% of the starting material, but for only 10% of the total rhamnose. The molar ratio of galacturonic acid to rhamnose of the LMW fraction was 236, suggesting that very few small Rha-containing oligomers were generated by the EPG digestion. No distinct Rha-containing oligomers were found by various chromatographic analyses of the LMW fraction. The HMW fraction, which only accounted for 10% by weight of the starting pectin, contained more than 85% of the rhamnose. The ratio of GalA to Rha in the HMW fraction was 1.7:1 and partial acid hydrolysis of this fraction produced a series of oligomers consisting of GalA-Rha repeating units, suggesting that it contained rhamnogalacturonan, which has a backbone composed of GalA-Rha disaccharide repeating units. The HMW fraction also contained large amounts of arabinose and galactose, which probably originated from side chains linked to some of the rhamnose residues. We propose that commercial citrus pectin is composed of two regions: the predominant region consists of chains of uninterrupted 1,4-linked alpha-D-GalA residues with between 60-70% of the residues methyl esterified; and the other region consists of rhamnogalacturonan with a backbone composed of GalA-Rha disaccharide repeating units and neutral sugar side chains.

Characterization of recombinant rhamnogalacturonan alpha-L-rhamnopyranosyl-(1,4)-alpha-D-galactopyranosyluronide lyase from Aspergillus aculeatus. An enzyme that fragments rhamnogalacturonan I regions of pectin

The four major oligomeric reaction products from saponified modified hairy regions (MHR-S) from apple, produced by recombinant rhamnogalacturonan (RG) alpha-L-rhamnopyranosyl-(1, 4)-alpha-D-galactopyranosyluronide lyase (rRG-lyase) from Aspergillus aculeatus, were isolated and characterized by 1H-nuclear magnetic resonance spectroscopy. They contain an alternating RG backbone with a degree of polymerization of 4, 6, 8, and 10 and with an alpha-Delta-(4,5)-unsaturated D-galactopyranosyluronic acid at the nonreducing end and an L-rhamnopyranose at the reducing end. L-Rhamnopyranose units are substituted at C-4 with beta-galactose. The maximum reaction rate of rRG-lyase toward MHR-S at pH 6.0 and 31 degreesC was 28 units mg-1. rRG-lyase and RG-hydrolase cleave the same alternating RG I subunit in MHR. Both of these enzymes fragment MHR by a multiple attack mechanism. The catalytic efficiency of rRG-lyase for MHR increases with decreasing degree of acetylation. Removal of arabinose side chains improves the action of rRG-lyase toward MHR-S. In contrast, removal of galactose side chains decreased the catalytic efficiency of rRG-lyase. Native RG-lyase was purified from A. aculeatus, characterized, and found to be similar to the rRG-lyase expressed in Aspergillus oryzae.

Rhamnogalacturonan alpha-d-galactopyranosyluronohydrolase. An enzyme that specifically removes the terminal nonreducing galacturonosyl residue in rhamnogalacturonan regions of pectin

A new enzyme, rhamnogalacturonan (RG) alpha-d-galactopyranosyluronohydrolase (RG-galacturonohydrolase), able to release a galacturonic acid residue from the nonreducing end of RG chains but not from homogalacturonan, was purified from an Aspergillus aculeatus enzyme preparation. RG-galacturonohydrolase acted with inversion of anomeric configuration, initially releasing beta-d-galactopyranosyluronic acid. The enzyme cleaved smaller RG substrates with the highest catalytic efficiency. A Michaelis constant of 85 &mgr;m and a maximum reaction rate of 160 units mg-1 was found toward a linear RG fragment with a degree of polymerization of 6. RG-galacturonohydrolase had a molecular mass of 66 kD, an isoelectric point of 5.12, a pH optimum of 4.0, and a temperature optimum of 50 degreesC. The enzyme was most stable between pH 3.0 and 6.0 (for 24 h at 40 degreesC) and up to 60 degreesC (for 3 h).

Stereochemical course of hydrolysis catalysed by alpha-L-rhamnosyl and alpha-D-galacturonosyl hydrolases from Aspergillus aculeatus

The stereochemical course of hydrolysis catalysed by four Aspergillus aculeatus enzymes acting on alpha-L-rhamnosyl and alpha-D-galacturonosyl linkages in the hairy regions of pectins has been determined using 1H-NMR. Exogalacturonase acts with inversion of anomeric configuration (e-->a), shown by the initial release of beta-D-GalpA from the non-reducing end of polygalacturonic acid. Similarly, rhamnogalacturonan (RG) hydrolase also acts with inversion of anomeric configuration (e-->a) during hydrolysis of alpha-D-GalpA-(1-->2)-alpha-L-Rhap linkages in RG, initially releasing oligosaccharides with beta-D-GalpA at the reducing end. This result is consistent with the recently solved crystal structure of this enzyme, as well as its classification based on amino acid sequence similarity into glycosyl hydrolase family 28. alpha-L-Rhamnosidase and RG-rhamnohydrolase also act with inversion of configuration (a-->e), initially releasing beta-L-Rhap from p-nitrophenyl alpha-L-rhamnopyranoside and RG oligosaccharides, respectively. Thus, all four enzymes examined are inverting hydrolases which probably catalyse hydrolysis via single displacement mechanisms.

Isolation and structural characterisation of rhamnogalacturonan oligomers generated by controlled acid hydrolysis of sugar-beet pulp

Controlled acid hydrolysis was applied to a deesterified beet pulp and the resulting soluble fraction was fractionated on a Biorad AG 1X8 column eluted by ammonium acetate pH 6 from 0.05 to 2 M. Eight retained fractions were obtained, containing almost exclusively GalA and Rha. Three types of oligomers could be identified: homogalacturonans, of which mono-,di- and tri-GalA were isolated as individual components, and two series of rhamnogalacturonan (RG) oligomers. One RG oligomer, isolated after ion-exchange chromatography, was identified as alpha-D-GalAp-(1-->2)-alpha-L-Rhap-(1-->4)-alpha-D-GalA p-(1-->2)-L-Rhap. The major peak contained oligomers of dp 6 to more than 20, of which dp 6 to 16 could be isolated on Bio-Gel P-6 + P-4. NMR of the oligomers of dp 6 to 10 showed the following structure: alpha-D-GalAp-(1[-->2)-alpha-L-Rhap-(1-->4)-alpha-D-GalA p-(1]n-->2)-L-Rhap. A second, quantitatively minor, series of RG oligomers eluted at higher ionic strength. These oligomers, which could be hydrolysed by RG-hydrolase and RG-lyase, were based on the alternating RG structure. Their non-reducing end was GalA, susceptible to hydrolysis by RG-galacturonohydrolase, and their reducing end might have more than one consecutive GalA.

Cloning and characterization of two rhamnogalacturonan hydrolase genes from Aspergillus niger

A rhamnogalacturonan hydrolase gene of Aspergillus aculeatus was used as a probe for the cloning of two rhamnogalacturonan hydrolase genes of Aspergillus niger. The corresponding proteins, rhamnogalacturonan hydrolases A and B, are 78 and 72% identical, respectively, with the A. aculeatus enzyme. In A. niger cultures which were shifted from growth on sucrose to growth on apple pectin as a carbon source, the expression of the rhamnogalacturonan hydrolase A gene (rhgA) was transiently induced after 3 h of growth on apple pectin. The rhamnogalacturonan hydrolase B gene was not induced by apple pectin, but the rhgB gene was derepressed after 18 h of growth on either apple pectin or sucrose. Gene fusions of the A. niger rhgA and rhgB coding regions with the strong and inducible Aspergillus awamori exlA promoter were used to obtain high-producing A. awamori transformants which were then used for the purification of the two A. niger rhamnogalacturonan hydrolases. High-performance anion-exchange chromatography of oligomeric degradation products showed that optimal degradation of an isolated highly branched pectin fraction by A. niger rhamnogalacturonan hydrolases A and B occurred at pH 3.6 and 4.1, respectively. The specific activities of rhamnogalacturonan hydrolases A and B were then 0.9 and 0.4 U/mg, respectively, which is significantly lower than the specific activity of A. aculeatus rhamnogalacturonan hydrolase (2.5 U/mg at an optimal pH of 4.5). Compared to the A enzymes, the A. niger B enzyme appears to have a different substrate specificity, since additional oligomers are formed.

Some preliminary results on the action of rhamnogalacturonase on rhamnogalacturonan oligosaccharides from beet pulp

Sugar-beet pulp was saponified and then hydrolysed with 0.1 M HCl at 80 degrees C for 72 h, and a rhamnogalacturonan fraction was isolated by ion-exchange chromatography on AG 1X8 resin. Four individual oligomers, and a mixture of oligomers with higher degrees of polymerization, were obtained by chromatography on BioGel P-4. They all presented the alpha-D-GalAp-(1[-->2)-alpha-L-Rhap-(1-->4)-alpha-D-GalAp -(1]n-->2)-L-Rhap structure (with n > or = 2) The five fractions were submitted to hydrolysis with rhamnogalacturonase. The enzyme was active on oligomers with degrees of polymerization > or = 10, and gave as main products alpha-L-Rhap-(1-->4)-alpha-D-GalAp-(1-->2)-alpha-L-Rhap++ +(1-->4)-D-GalAp and alpha-D-GalAp-(1--2)-alpha-L-Rhap-(1-->4)-alpha-D-GalAp++ +-(1-->2)-alpha-L-Rhap- 1-->4)-D-GalAp.

Molecular cloning and characterization of a rhamnogalacturonan acetylesterase from Aspergillus aculeatus. Synergism between rhamnogalacturonan degrading enzymes

A rhamnogalacturonan acetylesterase (RGAE) was purified to homogeneity from the filamentous fungus Aspergillus aculeatus, and the NH2-terminal amino acid sequence was determined. Full-length cDNAs encoding the enzyme were isolated from an A. aculeatus cDNA library using a polymerase chain reaction-generated product as a probe. The 936-base pair rha1 cDNA encodes a 250-residue precursor protein of 26,350 Da, including a 17-amino acid signal peptide. The rha1 cDNA was overexpressed in Aspergillus oryzae, a filamentous fungus that does not possess RGAE activity, and the recombinant enzyme was purified and characterized. Mass spectrometry of the native and recombinant RGAE revealed that the enzymes are heterogeneously glycosylated. In addition, the observed differences in their molecular masses, lectin binding patterns, and monosaccharide compositions indicate that the glycan moieties on the two enzymes are structurally different. The RGAE was shown to act in synergy with rhamnogalacturonase A as well as rhamnogalacturonase B from A. aculeatus in the degradation of apple pectin rhamnogalacturonan. RNA gel blot analyses indicate that the expression of rhamnogalacturonan degrading enzymes by A. acculeatus is regulated at the level of transcription and is subjected to carbon catabolite repression by glucose.

Different populations of pectic hairy regions occur in apple cell walls

Alcohol insoluble solids from apple were extracted in sequence by buffer at 20 degrees C and at 70 degrees C, EDTA/oxalate, and mild alkali, yielding four populations of pectins. These pectins and the insoluble residue were characterized by their sugar composition, degree of esterification (methyl ester and O-acetyl groups), molecular weight distribution, and degradability by the combination of endopolygalacturonase (PG) and pectin esterase (PE) and by rhamnogalacturonase (RGase) after chemical saponification. After PG/PE treatment, the remaining high molecular weight material representing the pectic hairy regions was isolated and characterized. Clear differences were found in the sugar composition of the fractions obtained, while only small variations were observed in the sugar linkage composition. The pectic hairy regions were further degraded by RGase and the digests separated into high molecular weight and oligomeric degradation products. These "RGase oligomers" consisted of between 4 and 9 sugar units with a backbone of alternating rhamnose and galacturonic acid residues, partly substituted with galactose linked to C-4 of the rhamnose moiety. Both the absolute amount of RGase oligosaccharides released as well as the degree of galactose-substitution of the oligomers increased when severer extraction conditions were used. Relatively more RGase oligomers were released from the low molecular weight hairy regions as compared to the high molecular weight fraction. Typical high molecular weight fragments isolated from the RGase digests of various hairy regions included residual segments of the rhamnogalacturonan backbone rich in arabinose and a polymer presumably enriched in xylogalacturonan segments.

Cloning, sequence and expression of the gene coding for rhamnogalacturonase of Aspergillus aculeatus; a novel pectinolytic enzyme

Rhamnogalacturonase was purified from culture filtrate of Aspergillus aculeatus after growth in medium with sugar-beet pulp as carbon source. Purified protein was used to raise antibodies in mice and with the antiserum obtained a gene coding for rhamnogalacturonase (rhgA) was isolated from a lambda cDNA expression library. The cloned rhgA gene has an open-reading frame of 1320 base pairs encoding a protein of 440 amino acids with a predicted molecular mass of 45 962 Da. The protein contains a potential signal peptidase cleavage site behind Gly-18 and three potential sites for N-glycosylation. Limited homology with A. niger polygalacturonase amino acid sequences is found. A genomic clone of rhgA was isolated from a recombinant phage lambda genomic library. Comparison of the genomic and cDNA sequences revealed that the coding region of the gene is interrupted by three introns. Furthermore, amino acid sequences of four different peptides, derived from purified A. aculeatus rhamnogalacturonase, were also found in the deduced amino acid sequence of rhgA. A. aculeatus strains overexpressing rhamnogalacturonase were obtained by cotransformation using either the A. niger pyrA gene or the A. aculeatus pyrA gene as selection marker. For expression of rhamnogalacturonase in A. awamori the A. awamori pyrA gene was used as selection marker. Degradation patterns of modified hairy regions, determined by HPLC, show the recombinant rhamnogalacturonase to be active, and the enzyme was found to have a positive effect in the apple hot-mash liquefaction process.