Xylohexaose

The most commonly used method for the measurement of the level of endo-xylanase in commercial enzyme preparations is the 3,5-dinitrosalicylic acid (DNS) reducing sugar method with birchwood xylan as substrate. It is well known that with the DNS method, much higher enzyme activity values are obtained than with the Nelson-Somogyi (NS) reducing sugar method. In this paper, we have compared the DNS and NS reducing sugar assays using a range of xylan-type substrates and accurately compared the molar response factors for xylose and a range of xylo-oligosaccharides. Purified beechwood xylan or wheat arabinoxylan is shown to be a suitable replacement for birchwood xylan which is no longer commercially available, and it is clearly demonstrated that the DNS method grossly overestimates endo-xylanase activity. Unlike the DNS assay, the NS assay gave the equivalent colour response with equimolar amounts of xylose, xylobiose, xylotriose and xylotetraose demonstrating that it accurately measures the quantity of glycosidic bonds cleaved by the endo-xylanase. The authors strongly recommend cessation of the use of the DNS assay for measurement of endo-xylanase due to the fact that the values obtained are grossly overestimated due to secondary reactions in colour development.

Microarrays are powerful tools for high throughput analysis, and hundreds or thousands of molecular interactions can be assessed simultaneously using very small amounts of analytes. Nucleotide microarrays are well established in plant research, but carbohydrate microarrays are much less established, and one reason for this is a lack of suitable glycans with which to populate arrays. Polysaccharide microarrays are relatively easy to produce because of the ease of immobilizing large polymers noncovalently onto a variety of microarray surfaces, but they lack analytical resolution because polysaccharides often contain multiple distinct carbohydrate substructures. Microarrays of defined oligosaccharides potentially overcome this problem but are harder to produce because oligosaccharides usually require coupling prior to immobilization. We have assembled a library of well characterized plant oligosaccharides produced either by partial hydrolysis from polysaccharides or by de novo chemical synthesis. Once coupled to protein, these neoglycoconjugates are versatile reagents that can be printed as microarrays onto a variety of slide types and membranes. We show that these microarrays are suitable for the high throughput characterization of the recognition capabilities of monoclonal antibodies, carbohydrate-binding modules, and other oligosaccharide-binding proteins of biological significance and also that they have potential for the characterization of carbohydrate-active enzymes.

A xylanase gene of glycoside hydrolase family 10, GtXyn10, was cloned from Gloeophyllum trabeum CBS 900.73 and expressed in Pichia pastoris GS115. Purified recombinant GtXyn10 exhibited significant activities to xylan (100.0%), lichenan (11.2%), glucan (15.2%) and p-nitrophenol-β-cellobiose (18.6%), demonstrated the maximum xylanase and glucanase activities at pH 4.5–5.0 and 75°C, retained stability over the pH range of 2.0–7.5 and at 70°C, and was resistant to pepsin and trypsin, most metal ions and SDS. Multiple sequence alignment and modeled-structure analysis identified a unique Gly48 in GtXyn10, and site-directed mutagenesis of Gly48 to Lys improved the temperature optimum up to 80°C. Under simulated mashing conditions, GtXyn10 (80 U) reduced the mash viscosity by 12.8% and improved the filtration rate by 31.3%. All these properties above make GtXyn10 attractive for potential applications in the feed and brewing industries.

Hemicelluloses isolated from holocellulose (MHOC) from Miscanthus were characterized by RP-HPLC-UV, FT-IR, and NMR. The hemicelluloses and recombinant hemicellulases, including endo-β-1,4-xylanases (HoXyn11A and AnXyn10C), β-xylosidases (AnXln3D), and α-L-arabinofuranosidases (AnAxh62A), as well as their interaction mechanisms were investigated by enzymatic hydrolysis. AnXyn10C released shorter end products than HoXyn11A from isolated hemicelluloses (IHEC). AnAxh62A was able to release all single-substituted α-L-arabinofuranosyl residues from IHEC. AnXyn10C and HoXyn11A were able to directly act on MHOC, whereas AnAxh62A and AnXln3D did not. The combination of HoXyn11A and AnAxh62A produced the highest xylo-oligosaccharides (XOS) yield from IHEC, whereas AnXyn10C alone produced the highest XOS yield from MHOC. The combination of HoXyn11A, AnAxh62A, and AnXln3D achieved the highest xylose yield from IHEC, whereas the combination of AnXyn10C, AnAxh62A, and AnXln3D achieved the highest xylose yield from MHOC. This study contributes to the development of efficient enzyme cocktails for the bioconversion of hemicelluloses from Miscanthus into monosaccharides and XOS.

Background: Conversion of plant cell walls to bioethanol and bio-based chemicals requires pretreatment as a necessary step to reduce recalcitrance of cell walls to enzymatic and microbial deconstruction. In this study, the sweet sorghum stems were subjected to various hydrothermal pretreatment processes (110°C to 230°C, 0.5 to 2.0 h), and the focus of this work is to systematically evaluate the degraded products of polysaccharides and lignins in the liquor phase obtained during the pretreatment process. Results: The maximum yield of xylooligosaccharides (52.25%) with a relatively low level of xylose and other degraded products was achieved at a relatively high pretreatment temperature (170°C) for a short reaction time (0.5 h). Higher temperature (>170°C) and/or longer reaction time (>0.5 h at 170°C) resulted in a decreasing yield of xylooligosaccharides, but increased the concentration of arabinose and galactose. The xylooligosaccharides obtained are composed of xylopyranosyl residues, together with lower amounts of 4-O-Me-α-D-GlcpA units. Meanwhile, the concentrations of the degraded products (especially furfural) increased as a function of pretreatment temperature and time. Molecular weights of the water-soluble polysaccharides and lignins indicated that the degradation of the polysaccharides and lignins occurred during the conditions of harsh hydrothermal pretreatment. In addition, the water-soluble polysaccharides (rich in xylan) and water-soluble lignins (rich in β-O-4 linkages) were obtained at 170°C for 1.0 h. Conclusions: The present study demonstrated that the hydrothermal pretreatment condition had a remarkable impact on the compositions and the chemical structures of the degraded products. An extensive understanding of the degraded products from polysaccharides and lignins during the hydrothermal pretreatment will be beneficial to value-added applications of multiple chemicals in the biorefinery for bioethanol industry.

This paper reports on a novel β-xylosidase from the hemicellulolytic fungus Talaromyces amestolkiae. The expression of this enzyme, called BxTW1 could be induced by beechwood xylan and was purified as a glycoprotein from culture supernatants. We characterized the gene encoding this enzyme as an intron-less gene belonging to the Glycoside Hydrolase Gene Family 3 (GH 3). BxTW1 exhibited transxylosylation activity in a regioselective way. This feature would allow synthesizing oligosaccharides or other compounds not available from natural sources, such as alkyl glycosides displaying antimicrobial or surfactant properties. Regioselective transxylosylation, an uncommon combination, makes the synthesis reproducible, which is desirable for its potential industrial application. BxTW1 showed high pH stability and Cu²⁺ tolerance. The enzyme displayed a pI of 7.6, a molecular mass around 200 kDa in its active dimeric form and K_m and V_max values of 0.17 mM and 52.0 U/mg, respectively, using commercial p-nitrophenyl-β-D-xylopyranoside as substrate. The catalytic efficiencies for xylooligosaccharides hydrolysis were remarkably high, making it suitable for different applications in food and bioenergy industries.

Immobilization technology offers many enzymatic advantages and overcomes the limitations of free enzymes. Bi- or multifunctional enzymes for industrial use have elicited much interest in recent years. The present work reported that a novel carbon nanoparticle-based supports was prepared by layer-by-layer self-assemble approach. The constructed bifunctional enzyme (ATXX) was successfully immobilized on the supports by covalent bonds. The prepared carbon-coated chitosan nanoparticles showed high binding capacity of about 289.9 mg g^-1-particles for ATXX. The Michaelis-Menten constants (K_m) and maximal activity (V_mat) of immobilized ATXX were 4.83 mg ml^-1 and 67.42 µmol min^-1 mg^-1-particles (xylanase activity), as well as 6.13 mg ml^-1 and 17.92 µmol min^-1 mg^-1-particles (cellulase activity), respectively. The immobilized ATXX showed improved thermostability and storage stability compared with the free enzyme. The immobilized ATXX retained 82.6% xylanase activity after seven successive reactions. High-performance liquid chromatography (HPLC) analysis revealed that xylobiose (X2) was the main hydrolysis product released from beechwood xylan, birchwood xylan, and oat spelt xylan by immobilized ATXX. Wheat bran and wheat bran insoluble xylan could be directly hydrolyzed by immobilized ATXX, which demonstrated a potential use for xylan bioconversion to xylooligosaccharides by the immobilized ATXX.

Autohydrolysis of cellulosic materials for saccharification generates xylose-oligosaccharides (XOS), due to the partial hydrolysis of xylan. Developing an efficient method for the separation and recovery of XOS from the prehydrolyzates would provide an excellent opportunity for the better utilization of the cellulosic material and for value-added co-product production. In this study, we investigated the use of centrifugal partition chromatography (CPC) for the fractionation of XOS from Miscanthus × giganteus (M × G). During autohydrolysis of miscanthus biomass at 180°C for 20 min, 63% of xylan was converted into XOS and xylose. The ensuing XOS concentrate contained up to 30% of XOS, which were distributed as 15.9% xylobiose (DP2), 5.9% xylotriose, (DP3), 5.6% xylotetraose (DP4), 0.8% xylopentaose (DP5) and 0.6% xylohexaose (DP6). The XOS concentrate was further fractionated by CPC with a solvent system composed of 4:1:4 (v/v/v) butanol:methanol:water. Using CPC techniques, 230 mg (80%) of DP2 to DP6 oligomers were fractionated from 1 g of XOS concentrate. The recoveries of individual XOS were 90.2% DP2, 64.5% DP3, 71.2% DP4, 61.9% DP5 and 68.9% DP6. The purities of DP2 to DP6 fractions were 61.9%, 63.2%, 44.5%, 31.5% and 51.3%, respectively. Presence of DP2 and DP3 in the CPC purified fractions was further validated by mass spectrometry analysis. The study provided information on fast recovery of individual XOS from crude biomass prehydrolyzate.

Two endo-β-1,4-xylanases named XylT1 and XylT2, previously purified from Aspergillus terreus, were structurally investigated by fluorescence quenching and characterized with respect to their binding properties with phenolic compounds. Neutral and charged quenchers had access to both enzymes in neutral and alkaline pHs. The greatest access was noted for the negative quencher, possibly due to positive amino acid residues in the vicinity of tryptophan. These tryptophan environments may partially explain the conformational differences and lower binding constants of phenolic compounds for XylT2 than XylT1. These results show that xylanases present structural and functional differences, despite belonging to similar families. XylT1 and XylT2 were also evaluated for their ability to hydrolyze cellulose pulp in different stages of bleaching. Both enzymes promoted hydrolysis of cellulose pulps, which was confirmed by the release of total reducing sugars, pentoses and chromophoric material. Analysis of released xylooligosaccharides demonstrated a preferential release of xylobiose. None of xylanases released glucose, showing that they do not hydrolyze the cellulose present in the pulp, making both enzymes excellent choices for bio-bleaching applications.

Advances in industrial biotechnology offer potential opportunities for economic utilization of agro-industrial residues such as sugarcane bagasse, which is the major by-product of the sugarcane industry. Due to its abundant availability and despite the complex chemical composition, it can be considered an ideal substrate for microbial processes for the production of value-added products. In the present study we evaluated the enzymatic production of xylooligosaccharides (XOS) and antioxidant compounds from sugarcane bagasse using XynZ from Clostridium thermocellum, a naturally chimeric enzyme comprising activities of xylanase and feruloyl esterase along with a carbohydrate binding module (CBM6). In order to reveal the biotechnological potential of XynZ, the XOS released after enzymatic hydrolysis using different substrates were characterized by capillary electrophoresis and quantified by high performance anion exchange chromatography. In parallel, the antioxidant capacity related to the release of phenolic compounds was also determined. The results indicated noteworthy differences regarding the amount of XOS and antioxidant phenolic compounds produced, as well as the XOS profile, functions of the pre-treatment method employed. The ability of XynZ to simultaneously produce xylooligosaccharides, natural probiotics, phenolic compounds and antioxidant molecules from natural substrates such as sugarcane bagasse demonstrated the biotechnological potential of this enzyme. Production of value-added products from agro-industrial residues is of great interest not only for advancement in the biofuel field, but also for pharmaceutical and food industries.

In this paper we describe the effect of enzyme treatments on the production of polymeric xylan, oligosaccharides and hemicellulose lean pulp by alkaline extraction of bleached hardwood kraft pulp. Enzyme treatments were carried out before one or in between two subsequent alkaline extractions by purified Trichoderma reesei xylanase and endoglucanase II (Cel 5a) as well as by a commercial monocomponent endoglucanase (FibreCareR). Without enzyme pre-treatment 61% and 7% of the pulp xylan was extracted in high purity in the first and second alkaline stage, respectively. Higher molecular mass xylan was obtained in the second than in the first alkaline extraction. Xylanase treatment before alkaline extraction hydrolyzed up to 12% of xylan to xylooligosaccharides. According to our results, preparation of polymeric xylan, and/or oligosaccharides as well as hemicellulose lean pulp with cellulose content of 93–94%, is possible by enzyme-aided alkaline extraction process.

Xylan is a major component of the plant cell wall and the most abundant noncellulosic component in the secondary cell walls that constitute the largest part of plant biomass. Dicot glucuronoxylan consists of a linear backbone of β(1,4)-linked xylose residues substituted with α(1,2)-linked glucuronic acid (GlcA). Although several genes have been implicated in xylan synthesis through mutant analyses, the biochemical mechanisms responsible for synthesizing xylan are largely unknown. Here, we show evidence for biochemical activity of GUX1 (for GlcA substitution of xylan 1), a member of Glycosyltransferase Family 8 in Arabidopsis (Arabidopsis thaliana) that is responsible for adding the glucuronosyl substitutions onto the xylan backbone. GUX1 has characteristics typical of Golgi-localized glycosyltransferases and a K_m for UDP-GlcA of 165 µM. GUX1 strongly favors xylohexaose as an acceptor over shorter xylooligosaccharides, and with xylohexaose as an acceptor, GlcA is almost exclusively added to the fifth xylose residue from the nonreducing end. We also show that several related proteins, GUX2 to GUX5 and Plant Glycogenin-like Starch Initiation Protein6, are Golgi localized and that only two of these proteins, GUX2 and GUX4, have activity as xylan α-glucuronosyltransferases.

The importance of capillary zone electrophoresis (CZE) has been increasing in use for: structural analysis of plant cell walls, characterization of enzymes that degrade polysaccharides, and profiling of oligosaccharides to characterize cell wall mutants. CZE with laser-induced fluorescence detection provides high separation efficiencies, high speed analysis, with extremely small sample requirements. Here, we describe the instrumentation we use and the methods for attaching fluorescent labels to oligosaccharides so that they can be detected.

Background: Enzyme dynamics has recently been shown to be crucial for structure-function relationship. Among various structure dynamics analysis platforms, HDX (hydrogen deuterium exchange) mass spectrometry stands out as an efficient and high-throughput way to analyze protein dynamics upon ligand binding. Despite the potential, limited research has employed the HDX mass spec platform to probe regional structure dynamics of enzymes. In particular, the technique has never been used for analyzing cell wall degrading enzymes. We hereby used xylanase as a model to explore the potential of HDX mass spectrometry for studying cell wall degrading enzymes. Results: HDX mass spectrometry revealed significant intrinsic dynamics for the xylanase enzyme. Different regions of the enzymes are differentially stabilized in the apo enzyme. The comparison of substrate-binding enzymes revealed that xylohexaose can significantly stabilize the enzyme. Several regions including those near the reaction centres were significantly stabilized during the xylohexaose binding. As compared to xylohexaose, xylan induced relatively less protection in the enzyme, which may be due to the insolubility of the substrate. The structure relevance of the enzyme dynamics was discussed with reference to the three dimensional structure of the enzyme. HDX mass spectrometry revealed strong dynamics-function relevance and such relevance can be explored for the future enzyme improvement. Conclusion: Ligand-binding can lead to the significant stabilization at both regional and global level for enzymes like xylanase. HDX mass spectrometry is a powerful high-throughput platform to identify the key regions protected during the ligand binding and to explore the molecular mechanisms of the enzyme function. The HDX mass spectrometry analysis of cell wall degrading enzymes has provided a novel platform to guide the rational design of enzymes.

Endo-xylanases play a key role in the depolymerization of xylan and recently, they have attracted much attention owing to their potential applications on biofuels and paper industries. In this work, we have investigated the molecular basis for the action mode of xylanases 10B at high temperatures using biochemical, biophysical and crystallographic methods. The crystal structure of xylanase 10B from hyperthermophilic bacterium Thermotoga petrophila RKU-1 (TpXyl10B) has been solved in the native state and in complex with xylobiose. The complex crystal structure showed a classical binding mode shared among other xylanases, which encompasses the −1 and −2 subsites. Interestingly, TpXyl10B displayed a temperature-dependent action mode producing xylobiose and xylotriose at 20°C, and exclusively xylobiose at 90°C as assessed by capillary zone electrophoresis. Moreover, circular dichroism spectroscopy suggested a coupling effect of temperature-induced structural changes with this particular enzymatic behavior. Molecular dynamics simulations supported the CD analysis suggesting that an open conformational state adopted by the catalytic loop (Trp297-Lys326) provokes significant modifications in the product release area (+1,+2 and +3 subsites), which drives the enzymatic activity to the specific release of xylobiose at high temperatures.

Recent studies have demonstrated that xylo-oligosaccharides (XOS), which are classified as emerging prebiotics, selectively enhance the growth of bifidobacteria in general and of Bifidobacterium animalis subsp. lactis strains in particular. To elucidate the metabolism of XOS in the well-documented and widely used probiotic strain B. animalis subsp. lactis BB-12, a combined proteomic and transcriptomic approach was applied, involving DNA microarrays, real-time quantitative PCR (qPCR), and two-dimensional difference gel electrophoresis (2D-DIGE) analyses of samples obtained from cultures grown on either XOS or glucose. The analyses show that 9 of the 10 genes that encode proteins predicted to play a role in XOS catabolism (i.e., XOS-degrading and -metabolizing enzymes, transport proteins, and a regulatory protein) were induced by XOS at the transcriptional level, and the proteins encoded by three of these (β-D-xylosidase, sugar-binding protein, and xylose isomerase) showed higher abundance on XOS. Based on the obtained results, a model for the catabolism of XOS in BB-12 is suggested, according to which the strain utilizes an ABC (ATP-binding cassette) transport system (probably for oligosaccharides) to bind XOS on the cell surface and transport them into the cell. XOS are then degraded intracellularly through the action of xylanases and xylosidases to D-xylose, which is subsequently metabolized by the D-fructose-6-P shunt. The findings obtained in this study may have implications for the design of a synbiotic application containing BB-12 and the XOS used in the present study.

The cellulosome of Clostridium thermocellum is a highly organized multi-enzyme complex of cellulases and hemicellulases involved in the hydrolysis of plant cell-wall polysaccharides. The bifunctional multi-modular xylanase Xyn10B is one of the hemicellulase components of the C. thermocellum cellulosome. The enzyme contains an internal glycoside hydrolase family 10 catalytic domain (GH10) and a C-terminal family 1 carbohydrate esterase domain (CE1). The N-terminal moiety of Xyn10B (residues 32-551), comprising a carbohydrate-binding module (CBM22-1) and the GH10 E337A mutant, was crystallized in complex with xylohexaose. The crystals belong to the trigonal space group P3₂21 and contain a dimer in the asymmetric unit. The crystals diffracted to beyond 2.0 Å resolution.

The mode of action of xylanase A from a phytopathogenic bacterium, Erwinia chrysanthemi, classified in glycoside hydrolase family 5, was investigated on xylooligosaccharides and polysaccharides using TLC, MALDI-TOF MS and enzyme treatment with exoglycosidases. The hydrolytic action of xylanase A was found to be absolutely dependent on the presence of 4-O-methyl-D-glucuronosyl (MeGlcA) side residues in both oligosaccharides and polysaccharides. Neutral linear β-1,4-xylooligosaccharides and esterified aldouronic acids were resistant towards enzymatic action. Aldouronic acids of the structure MeGlcA³Xyl₃ (aldotetraouronic acid), MeGlcA³Xyl₄ (aldopentaouronic acid) and MeGlcA³Xyl₅ (aldohexaouronic acid) were cleaved with the enzyme to give xylose from the reducing end and products shorter by one xylopyranosyl residue: MeGlcA²Xyl₂, MeGlcA²Xyl₃ and MeGlcA²Xyl₄. As a rule, the enzyme attacked the second glycosidic linkage following the MeGlcA branch towards the reducing end. Depending on the distribution of MeGlcA residues on the glucuronoxylan main chain, the enzyme generated series of shorter and longer aldouronic acids of backbone polymerization degree 3–14, in which the MeGlcA is linked exclusively to the second xylopyranosyl residue from the reducing end. Upon incubation with β-xylosidase, all acidic hydrolysis products of acidic oligosaccharides and hardwood glucuronoxylans were converted to aldotriouronic acid, MeGlcA²Xyl₂. In agreement with this mode of action, xylose and unsubstituted oligosaccharides were essentially absent in the hydrolysates. The E. chrysanthemi xylanase A thus appears to be an excellent biocatalyst for the production of large acidic oligosaccharides from glucuronoxylans as well as an invaluable tool for determination of the distribution of MeGlcA residues along the main chain of this major plant hemicellulose.

Glycosynthases are mutant glycosidases in which the acidic nucleophile is replaced by a small inert residue. In the presence of glycosyl fluorides of the opposite anomeric configuration (to that of their natural substrates), these enzymes can catalyze glycosidic bond formation with various acceptors. In this study we demonstrate that XynB2E335G, a nucleophile-deficient mutant of a glycoside hydrolase family 52 β-xylosidase from G. stearothermophilus, can function as an efficient glycosynthase, using α-D-xylopyranosyl fluoride as a donor and various aryl sugars as acceptors. The mutant enzyme can also catalyze the self-condensation reaction of α-D-xylopyranosyl fluoride, providing mainly α-D-xylobiosyl fluoride. The self-condensation kinetics exhibited apparent classical Michaelis–Menten behavior, with kinetic constants of 1.3 s^-1 and 2.2 mm for K_cat and K_M(acceptor), respectively, and a K_cat/K_M(acceptor) value of 0.59 s^-1 mm^-1. When the β-xylosidase E335G mutant was combined with a glycoside hydrolase family 10 glycosynthase, high-molecular-weight xylooligomers were readily obtained from the affordable α-D-xylopyranosyl fluoride as the sole substrate.

Ferulic acid (4-hydroxy-3-methoxycinnamic acid), predominantly in ester form in arabinoxylan chains, is the main phenolic acid present in barley and malt. Only about 1% of the total ferulic acid in barley is present in the free form. A number of previous works concerned the contents of free and esterified ferulic acid in a broad range of popular beers, but there is little information about the possible composition of feruloylated oligosaccharides in beers. The aim of this preliminary work was to purify the feruloylated oligosaccharides from lager beers (by the means of preparative chromatography) followed by composition elucidation using TLC, HPLC with RI or UV detection and ¹H-NMR. Indeed, the qualitative analyses of isolated fractions from beer revealed that the fractions contained ferulic acid in the ester form (as proven after mild alkaline hydrolysis). It was also shown that molecular masses of oligosaccharides present in the purified beer fractions were similar to the masses of arabinose and xylooligosaccharides in the range of xylose to xylohexaose. Although a number of purified beer samples contained oligosaccharides of higher molecular masses, these were not further characterized. Taking under consideration the presented results, it can be concluded that beer can be a good source of feruloylated oligosaccharides, significant in the context of human health benefits.