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PubMed2005

The first crystal structure of a family 31 carbohydrate-binding module with affinity to beta-1,3-xylan.

Here, we present the crystal structure of the family 31 carbohydrate-binding module (CBM) of beta-1,3-xylanase from Alcaligenes sp. strain XY-234 (AlcCBM31) determined at a resolution of 1.25A. The AlcCBM31 shows affinity with only beta-1,3-xylan. The AlcCBM31 molecule makes a beta-sandwich structure composed of eight beta-strands with a typical immunoglobulin fold and contains two intra-molecular disulfide bonds. The folding topology of AlcCBM31 differs from that of the large majority of other CBMs, in which eight beta-strands comprise a beta-sandwich structure with a typical jelly-roll fold. AlcCBM31 shows structural similarity with CBM structures of family 34 and family 9, which also adopt structures based on immunoglobulin folds.

Alcaligenes↗

PubMed1991

Induction of cellulose- and xylan-degrading enzyme systems in Aspergillus terreus by homo- and heterodisaccharides composed of glucose and xylose.

Synthetic heterodisaccharides composed of glucose and xylose were tested as inducers of cellulose- and xylan-degrading enzymes in Aspergillus terreus, and the inducing abilities were compared with those of sophorose and xylobiose or their positional isomers. Measurement of secreted and cell-associated enzyme activities revealed that the heterodisaccharides induced the synthesis of the cellulolytic and xylanolytic enzymes, 2-O-beta-D-glucopyranosyl D-xylose (Glcbeta 1-2Xyl) being the most powerful inducer. Sophorose and 2-O-beta-D-xylopyranosyl D-Xylose (Xylbeta 1-2Xyl), or their positional isomers, selectively induced the synthesis of cellulases and beta-xylanases, respectively. An analysis of the extracellular enzymes (which were separated by isoelectric focusing followed by detection using chromogenic and fluorogenic substrates) showed that Glcbeta 1-2Xyl initiated the synthesis of specific endo-1,4-beta-glucanases and specific endo-1,4-beta-xylanases identical to those produced separately in response to sophorose or Xylbeta 1-2Xyl. Glcbeta 1-2Xyl also induced specific endo-1,4-beta-glucanases that hydrolysed 4-methylumbelliferyl beta-lactoside at the agluconic bond. The results strengthen the concept of separate regulatory control of the synthesis of cullulases and beta-xylanases. The results also suggest that mixed disaccharides, composed of glucose and xylose moieties, which may occur in nature, could play an important role in regulating the synthesis of wood-degrading enzymes.

Aspergillus↗

PubMed2001

Degradation of xylan to D-xylose by recombinant Saccharomyces cerevisiae coexpressing the Aspergillus niger beta-xylosidase (xlnD) and the Trichoderma reesei xylanase II (xyn2) genes.

The beta-xylosidase-encoding xlnD gene of Aspergillus niger 90196 was amplified by the PCR technique from first-strand cDNA synthesized on mRNA isolated from the fungus. The nucleotide sequence of the cDNA fragment was verified to contain a 2,412-bp open reading frame that encodes a 804-amino-acid propeptide. The 778-amino-acid mature protein, with a putative molecular mass of 85.1 kDa, was fused in frame with the Saccharomyces cerevisiae mating factor alpha1 signal peptide (MFalpha1(s)) to ensure correct posttranslational processing in yeast. The fusion protein was designated Xlo2. The recombinant beta-xylosidase showed optimum activity at 60 degrees C and pH 3.2 and optimum stability at 50 degrees C. The K(i(app)) value for D-xylose and xylobiose for the recombinant beta-xylosidase was determined to be 8.33 and 6.41 mM, respectively. The XLO2 fusion gene and the XYN2 beta-xylanase gene from Trichoderma reesei, located on URA3-based multicopy shuttle vectors, were successfully expressed and coexpressed in the yeast Saccharomyces cerevisiae under the control of the alcohol dehydrogenase II gene (ADH2) promoter and terminator. These recombinant S. cerevisiae strains produced 1,577 nkat/ml of beta-xylanase activity when expressing only the beta-xylanase and 860 nkat/ml when coexpressing the beta-xylanase with the beta-xylosidase. The maximum beta-xylosidase activity was 5.3 nkat/ml when expressed on its own and 3.5 nkat/ml when coexpressed with the beta-xylanase. Coproduction of the beta-xylanase and beta-xylosidase enabled S. cerevisiae to degrade birchwood xylan to D-xylose.

Aspergillus niger↗

PubMed1990

The genes for three xylan-degrading activities from Bacteroides ovatus are clustered in a 3.8-kilobase region.

Genes coding for three xylan-degrading activities, xylanase, xylosidase, and arabinosidase, were simultaneously cloned from the colonic anaerobic organism Bacteriodes ovatus. The genes for the three enzymes were located on a 3.8-kilobase EcoRI genomic insert and were cloned by using plasmid pUC18. All three activities were expressed in Escherichia coli JM83, and all were cell associated. Expression of the xylanase gene was independent from expression of the xylosidase and arabinosidase genes, whereas expression of the latter two genes appeared to be coordinated. Restriction endonuclease analysis of the arabinosidase and xylosidase genes and partial purification of these enzyme activities from E. coli suggested that these activities were catalyzed by a bifunctional protein or two proteins of very similar molecular weight. All three enzyme activities were regulated in B. ovatus in response to the carbon source used for growth. This is the first report of the cloning and expression of B. ovatus genes.

Bacteroides↗

PubMed1999

XynX, a possible exo-xylanase of Aeromonas caviae ME-1 that produces exclusively xylobiose and xylotetraose from xylan.

A gene, xynX, encoding a novel xylanase, was cloned from Aeromonas caviae ME-1. This gene encoded an enzyme that was constituted of 334 amino acid residues (38,580 Da) and was similar in sequence to Family 10 (Family F) beta-1,4 endo-xylanases. XynX produced only xylobiose and xylotetraose from birch wood xylan, and xylotriose, xylopentaose, and higher oligosaccharides were not detected in the TLC analysis. We designated it as X2/X4-forming xylanase. This enzyme does not have transglycosylation activity. These data suggested that this enzyme is a possible exo-xylanase. According to homology modeling, the enzyme has a ring-shaped (alpha/beta)8 barrel (TIM barrel) structure, typical of Family 10 endo-xylanases, with the extraordinary feature of a longer bottom-loop structure.

Aeromonas↗

PubMedDate not supplied

Effect of sulfated xylans during the interaction of [125I]-thrombin with antithrombin III or heparin cofactor II of human plasma.

[125I]-Labeled thrombin was incubated with human plasma and its interactions with the two plasma protease inhibitors antithrombin III (AT-III) or heparin cofactor II (HC-II) were investigated in the presence of oat spelts xylan sulfate (OSXS), sodium pentosan polysulfate (SP-54), and the results were compared with heparin and dermatan sulfate. Addition of OSXS or SP-54 enhanced the complexation of thrombin with HC-II or with both AT-III and HC-II depending upon the concentration and the duration of the interactions of the sulfated compounds with plasma. During the 30 s interaction, OSXS and SP-54 enhanced both AT-III-thrombin and HC-II-thrombin interaction while heparin was more selective and enhanced only the AT-III-thrombin interaction. However after a 2 min interaction, heparin showed an increase in the HC-II-thrombin interaction at higher concentrations. The complexations of AT-III-thrombin and HC-II-thrombin were reversed in the presence of 200 micrograms/ml of SP-54 during a 30 s interaction or in presence of 100 micrograms/ml of OSXS during a 2 min interaction. The Western blotting method of detecting thrombin showed that during the 10 s interaction, heparin enhanced the thrombin-AT-III complex formation while OSXS enhanced the thrombin-HC-II complex formation.

Antithrombin III↗

PubMed2004

Extracellular cross-linking of xylan and xyloglucan in maize cell-suspension cultures: the role of oxidative phenolic coupling.

Cell-suspension cultures of maize ( Zea mays L.) released soluble extracellular polysaccharides (SEPs) into their medium. Some or all of the SEPs had feruloyl ester groups. Pulse-labelling with [(3)H]arabinose was used to monitor changes in the SEPs' M(r) (estimated by gel-permeation chromatography) with time after synthesis. Newly released (3)H-SEPs were 1.3-1.6 MDa, but between 2 days and 3 days after radiolabelling (in one experiment) or between 5 days and 6 days (in another), the (3)H-SEPs abruptly increased to approximately 17 MDa, indicating extensive cross-linking. The cross-linking involved both [(3)H]xylan and [(3)H]xyloglucan components of the SEPs. The cross-links could be cleaved by alkali, returning the SEPs to their original M(r). In 0.1 M NaOH at 37 degrees C, 58% cleavage was effected within 24 h. The requirement for such prolonged alkali treatment indicates that ester-bonded (e.g. diferuloyl) groups were not solely responsible for the cross-linking. Bonds cleaved only by relatively severe alkali could include benzyl ether linkages formed between sugar residues and oxidised phenolics that had quinone methide structures. The ability of alkali to cleave the cross-links was independent of the age of the (3)H-SEP molecules. Cross-linking of (3)H-SEPs in vivo was delayed (up to approx. 7 days after radiolabelling) by exogenous sinapic acid, chlorogenic acid or rutin-agents predicted to compete with the oxidative coupling of feruloyl-polysaccharides. The cross-linking was promoted by exogenous ferulic acid or l-tyrosine, possibly because these compounds acted as precursors for polysaccharide feruloylation, thus providing additional partner substrates for the oxidative coupling of previously formed (3)H-SEPs. The ability of certain phenolics to prevent the cross-linking of (3)H-SEPs supports the idea that the cross-linking involved phenolic oxidation.

Cell Culture Techniques↗

PubMed2006

Optimization of the xylan degradation activity of monolithic enzymatic membranes as a function of their composition using design of experiments.

The aim of this work was the development and optimization of enzymatic monolithic membranes with high catalytic activity for the degradation of xylan into xylooligosaccharides. The chemometric tool design of experiments has been utilized here for the first time for the optimization of the enzymatic activity of the monolithic membranes based on their constituents. The effect of three process variables, including the amount of various monomer contents and the porogenic solvents ratio, has been studied on the enzymatic activity of the resulted membranes. The experimental design chosen was a central face centred with six central points in order to obtain an orthogonal model, with the precision of the results being independent of the range of values considered for each parameter. The software Modde(c) 6.0 from Umetrics(c) was used to build and analyze the results of the experimental design using partial least squares regression. The optimization of the suggested model provided the best membrane composition to achieve maximum enzymatic activity, which can be related to the amount of enzyme immobilized on the monolithic membrane. The predictive capacity of the model was evaluated performing additional experiments.

Biodegradation, Environmental↗

PubMed2006

Gene cloning and expression in Escherichia coli of a bi-functional beta-D-xylosidase/alpha-L-arabinosidase from Sulfolobus solfataricus involved in xylan degradation.

An open reading frame encoding a putative bi-functional beta-D-xylosidase/alpha-L-arabinosidase (Sso3032) was identified on the genome sequence of Sulfolobus solfataricus P2, the predicted gene product showing high amino-acid sequence similarity to bacterial and eukaryal individual beta-D-xylosidases and alpha-L-arabinosidases as well as bi-functional enzymes such as the protein from Thermoanaerobacter ethanolicus and barley. The sequence was PCR amplified from genomic DNA of S. solfataricus P2 and heterologous gene expression obtained in Escherichia coli, under optimal conditions for overproduction. Specific assays performed at 75 degrees C revealed the presence in the transformed E. coli cell extracts of this archaeal activity involved in sugar hydrolysis and specific for both substrates. The recombinant protein was purified by thermal precipitation of the host proteins and ethanol fractionation and other properties, such as high thermal activity and thermostability could be determined. The protein showed a homo-tetrameric structure with a subunit of molecular mass of 82.0 kDa which was in perfect agreement with that deduced from the cloned gene. Northern blot analysis of the xarS gene indicates that it is specifically induced by xylan and repressed by monosaccharides like D-glucose and L-arabinose.

Arabinose↗

PubMed1996

4-O-methyl-beta-L-idopyranosyluronic acid linked to xylan from kraft pulp: isolation procedure and characterisation by NMR spectroscopy.

The tetrasaccharide 2"-O-(4-O-methyl-beta-L-idopyranosyluronic acid)xylotriose was isolated from enzymatically hydrolysed, unbleached, birch kraft pulp by anion-exchange chromatography in two steps. The primary structure of the tetrasaccharide was determined by 1H and 13C NMR spectroscopy, using homonuclear and heteronuclear two-dimensional techniques. NOE data and 3JH,H coupling constants show that the 4-O-methyl-beta-L-idopyranosyluronic acid in the tetrasaccharide is predominantly in the 1C4 chair conformation. The pKa value (3.17) for 4-O-methyliduronic acid attached beta-(1-->2) to xylose was determined from the pH-dependent chemical shift of H-5. The amount of 4-O-methyliduronic acid (0.1-0.5 mol%) in surface xylan of unbleached birch and pine kraft pulps was determined by extensive xylanase treatment and further analysis by NMR spectroscopy and high-performance anion-exchange chromatography.

Carbohydrate Conformation↗

PubMed1984

Glycosidic bond rearrangements in isomeric xylobioses by yeast xylan-degrading enzymes.

The cells of Cryptococcus albidus induced for xylan-degrading enzymes are capable of transforming 1,2-beta-xylobiose and 1,3-beta-xylobiose into 1,4-beta-xylobiose, the natural inducer. The conversion involves transglycosylation and hydrolysis catalyzed by beta-xylosidase and beta-xylanase. A probable intermediate of the conversion of 1,2-beta-xylobiose was isolated and identified as a trisaccharide, 4-O-beta-xylopyranosyl-2-O-beta-xylopyranosyl-D-xylopyran ose. The trisaccharide is cleaved by purified endo-1,4-beta-xylanase of C. albidus mainly at the 1,2-beta-linkage yielding xylose and 1,4-beta-xylobiose.

Carbohydrate Conformation↗

PubMed1995

Nucleotide sequences of xylan-inducible xylanase and xylosidase/arabinosidase genes from Bacteroides ovatus V975.

The nucleotide sequences of the xylI and xsa genes of Bacteroides ovatus V975, encoding xylanase and xylosidase activities, were determined. Both genes are part of a xylan-inducible operon, the sequenced region of which also contains a partial open reading frame upstream of the xylanase gene. Deduced amino acid sequence similarly analyses indicate that the xylanase belongs to the Family F series of glycosyl hydrolases.

Amino Acid Sequence↗

PubMed1998

Structure of neutral branched xylooligosaccharides produced by xylanase from in situ reduced hardwood xylan.

Two neutral oligosaccharides from in situ reduced hardwood xylan were isolated and completely characterized by methylation analysis and 2D NMR spectroscopy (COSY, HOHAHA, HMQC, HMQC-TOCSY, NOESY, and HMBC techniques). The oligosaccharides are the xylotetrasaccharide, 4-O-methyl-alpha-D-glucopyranosyl-(1-->2)-D-xylotriose and the xylopentasaccharide 4-O-methyl-alpha-D-glucopyranosyl-(1-->2)-D-xylotetraose. From reactivities observed with these compounds, the mode of action of beta-xylanase is described.

Carbohydrate Sequence↗

PubMed1999

(2-O-alpha-D-galactopyranosyl-4-O-methyl-alpha-D-glucurono)-D-xylan from Eucalyptus globulus Labill.

An unusual heteroxylan composed of galactosyl, 4-O-methyl-glucuronosyl and xylosyl residues with molar ratio 1:3:30 was isolated from the wood of Eucalyptus globulus Labill. The results of linkage analysis, supported by data of 1H, 2D 1H-1H COSY and 13C NMR spectroscopy, revealed that the polysaccharide is a (2-O-alpha-D-galactopyranosyl-4-O-methyl-alpha-D- glucurono)-D-xylan with a (1-->4)-linked beta-D-xylopyranosyl backbone branched at O-2 by short side chains composed of terminal 4-O-methyl-alpha-D-glucuronic acid and of 4-O-methyl-alpha-D-glucuronic acid substituted at O-2 with alpha-D-galactose.

Carbohydrate Conformation↗

PubMed1998

Acetyl xylan esterase II from Penicillium purpurogenum is similar to an esterase from Trichoderma reesei but lacks a cellulose binding domain.

Penicillium purpurogenum produces at least two acetyl xylan esterases (AXE I and II). The AXE II cDNA, genomic DNA and mature protein sequences were determined and show that the axe 2 gene contains two introns, that the primary translation product has a signal peptide of 27 residues, and that the mature protein has 207 residues. The sequence is similar to the catalytic domain of AXE I from Trichoderma reesei (67% residue identity) and putative active site residues are conserved, but the Penicillium enzyme lacks the linker and cellulose binding domain, thus explaining why it does not bind cellulose in contrast to the Trichoderma enzyme. These results point to a possible common ancestor gene for the active site domain, while the linker and the binding domain may have been added to the Trichoderma esterase by gene fusion.

Acetylesterase↗

PubMed1997

O-feruloylated, O-acetylated oligosaccharides as side-chains of grass xylans.

Partial acid hydrolysis of cell wall material from Festuca arundinacea cell cultures yielded a novel O-feruloylated trisaccharide (3). Treatment of 3 with Driselase, which contains beta- but not alpha-D-xylosidase, released xylose plus the known compound, beta-D-xylopyranosyl-(1-->2)-(5-O-feruloyl)-L-arabinose. Since 3 contained one NaIO4-resistant xylose residue, it was concluded to be beta-D-xylopyranosyl-(1-->3)-beta-D-xylopyranosyl-(1--> 2)-(5-O-feruloyl)-L-arabinose. Partial acid hydrolysis of Festuca cell walls also yielded several higher-M(r) feruloylated oligosaccharides, including a feruloylated pentasaccharide, 4 (sugar composition: Ara + Xyl2 + two non-pentose residues) and a feruloylated heptasaccharide, 5 (Ara + Xyl3 + three non-pentose residues). Compounds 4 and 5 were endogenously O-acetylated but 3 was not. Similar or identical compounds were found in hydrolysates of 20 additional species of the Gramineae. These products represent a series of complex side-chains which, in vivo, are attached via Araf residues to the parent xylan. Their possible biological roles are discussed.

Acetylation↗

PubMed1992

High resolution 13C-n.m.r. spectroscopy of 'mixed linkage' xylans.

Three xylan fractions, obtained by stepwise precipitation with ethanol, were analysed by 75-MHz 13C-n.m.r. spectroscopy. Diad frequencies, determined from the C-2 resonances, show that the (1----3)-linkages are interspersed throughout the chain rather than grouped contiguously. This type of distribution is in agreement with a random coil conformation and with the constancy of the optical rotation in solvents of different ionic strength and chaotropic power. These diad frequencies were compared with the theoretical values calculated for a random distribution from the ratio of (1----4)-:(1----3)-linkages in the 1H-n.m.r. spectra, and from the methylation analysis for one of the fractions.

Carbohydrate Conformation↗

PubMed1999

A single domain thermophilic xylanase can bind insoluble xylan: evidence for surface aromatic clusters.

A clone expressing xylanase activity in Escherichia coli has been selected from a genomic plasmid library of the thermophilic Bacillus strain D3. Subcloning from the 9-kb insert located the xylanase activity to a 2.7-kb HindII/BamHI fragment. The DNA sequence of this clone revealed an ORF of 367 codons encoding a single domain type-F or family 10 enzyme, which was designated as XynA. Purification of the enzyme following over-expression in E. coli produced an enzyme of 42 kDa with a temperature optimum of 75 degrees C which can efficiently bind and hydrolyse insoluble xylan. The pH optimum of the enzyme is 6.5, but it is active over a broad pH range. A homology model of the xylanase has been constructed which reveals a series of surface aromatic residues which form hydrophobic clusters. This unusual structural feature is strikingly similar to the situation observed in the structure determined for the type-G xylanase from the Bacillus D3 strain and may constitute a common evolutionary mechanism imposed on different structural frameworks by which these xylanases may bind potential substrates and exhibit thermostability.

Amino Acid Sequence↗