A Comparison of Polysaccharide Substrates and Reducing Sugar Methods for the Measurement of endo-1,4-β-Xylanase
McCleary, B. V. & McGeough, P. (2015). Appl. Biochem. Biotechnol., 177(5), 1152-1163.
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.
Versatile high resolution oligosaccharide microarrays for plant glycobiology and cell wall research.
Pedersen, H. L., Fangel, J. U., McCleary, B., Ruzanski, C., Rydahl, M. G., Ralet, M. C., Farkas, V., Von Schantz, L., Marcus, S. E., Andersen, M.C. F., Field, R., Ohlin, M., Knox, J. P., Clausen, M. H. & Willats, W. G. T. (2012). Journal of Biological Chemistry, 287(47), 39429-39438.
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.
Modulation of cellulosome composition in Clostridium cellulolyticum: Adaptation to the polysaccharide environment revealed by proteomic and carbohydrate‐active enzyme analyses.
Blouzard, J. C., Coutinho, P. M., Fierobe, H. P., Henrissat, B., Lignon, S., Tardif, C., Pages, S. & de Philip, P. (2010). Proteomics, 10(3), 541-554.
Clostridium cellulolyticum is a model mesophilic anaerobic bacterium that efficiently degrades plant cell walls. The recent genome release offers the opportunity to analyse its complete degradation system. A total of 148 putative carbohydrate-active enzymes were identified, and their modular structures and activities were predicted. Among them, 62 dockerin-containing proteins bear catalytic modules from numerous carbohydrate-active enzymes' families and whose diversity reflects the chemical and structural complexity of the plant carbohydrate. The composition of the cellulosomes produced by C. cellulolyticum upon growth on different substrates (cellulose, xylan, and wheat straw) was investigated by LC MS/MS. The majority of the proteins encoded by the cip-cel operon, essential for cellulose degradation, were detected in all cellulosome preparations. In the presence of wheat straw, the natural and most complex of the substrates studied, additional proteins predicted to be involved in hemicellulose degradation were produced. A 32-kb gene cluster encodes the majority of these proteins, all harbouring carbohydrate-binding module 6 or carbohydrate-binding module 22 xylan-binding modules along dockerins. This newly identified xyl-doc gene cluster, specialised in hemicellulose degradation, comes in addition of the cip-cel operon for plant cell wall degradation. Hydrolysis efficiencies determined on the different substrates corroborates the finding that cellulosome composition is adapted to the growth substrate.
Identification and characterization of plant cell wall degrading enzymes from three glycoside hydrolase families in the cerambycid beetle Apriona japonica.
Pauchet, Y., Kirsch, R., Giraud, S., Vogel, H. & Heckel, D. G. (2014). Insect Biochemistry and Molecular Biology, 49, 1-13.
Xylophagous insects have evolved to thrive in a highly challenging environment. For example, wood-boring beetles from the family Cerambycidae feed exclusively on woody tissues, and to efficiently access the nutrients present in this sub-optimal environment, they have to cope with the lignocellulose barrier. Whereas microbes of the insect's gut flora were hypothesized to be responsible for the degradation of lignin, the beetle itself depends heavily on the secretion of a range of enzymes, known as plant cell wall degrading enzymes (PCWDEs), to efficiently digest both hemicellulose and cellulose networks. Here we sequenced the larval gut transcriptome of the Mulberry longhorn beetle, Apriona japonica (Cerambycidae, Lamiinae), in order to investigate the arsenal of putative PCWDEs secreted by this species. We combined our transcriptome with all available sequencing data derived from other cerambycid beetles in order to analyze and get insight into the evolutionary history of the corresponding gene families. Finally, we heterologously expressed and functionally characterized the A. japonica PCWDEs we identified from the transcriptome. Together with a range of endo-β-1,4-glucanases, we describe here for the first time the presence in a species of Cerambycidae of (i) a xylanase member of the subfamily 2 of glycoside hydrolase family 5 (GH5 subfamily 2), as well as (ii) an exopolygalacturonase from family GH28. Our analyses greatly contribute to a better understanding of the digestion physiology of this important group of insects, many of which are major pests of forestry worldwide.
Comprehensive multidetector HPSEC study on solution properties of cereal arabinoxylans in aqueous and DMSO solutions.
Pitkänen, L., Virkki, L., Tenkanen, M. & Tuomainen, P. (2009). Biomacromolecules, 10(7), 1962-1969.
The water-soluble arabinoxylans from wheat flour (high, medium, and low viscosity samples) and rye flour (high viscosity sample) were characterized by 1H NMR spectroscopy and HPSEC with refractive index, light scattering, and viscometric detectors. These cereal arabinoxylans have recently been used as model arabinoxylans in various studies, but their solution properties have not been previously investigated. In this study, two HPSEC eluent systems were used: the water-based system and DMSO-based system. DMSO seemed to be a better solvent than water, especially for arabinoxylans containing a low amount of arabinose substituents. 1H NMR spectroscopy indicated the structural differences between the analyzed arabinoxylan samples that also affected the hydrodynamic parameters obtained with HPSEC. Influence of arabinose side groups on the solution conformation of arabinoxylans could not be excluded based on our data, despite the role of arabinose substituents being questioned in previous investigations concerning arabinoxylan conformation in solution.
Mode of action of glycoside hydrolase family 5 glucuronoxylan xylanohydrolase from Erwinia chrysanthemi.
Vršanská, M., Kolenová, K., Puchart, V. & Biely, P. (2007). FEBS Journal, 274(7), 1666-1677.
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.
Activity of an Aspergillus terreus α-arabinofuranosidase on phenolic-substituted oligosaccharides.
Luonteri, E., Kroon, P. A., Tenkanen, M., Teleman, A. & Williamson, G. (1999). Journal of Biotechnology, 67(1), 41-48.
The effect of phenolic substitutions on the activity of an α-arabinofuranosidase from Aspergillus terreus was investigated using feruloylated oligosaccharides isolated from plant cell walls, equivalent oligosaccharides obtained through treatment with specific ferulic acid esterases, and a synthetic lignin-carbohydrate complex (LCC). Feruloyl substituents limited the hydrolysis of arabinoxylan and arabinan oligosaccharides but only if the feruloyl group was esterified to the terminal non-reducing arabinose. Somewhat surprisingly, the LCC-model compound, in which the arabinose residue is substituted with a bulky dilignol group, was degraded by the enzyme. This indicated that the enzyme is able to approach this linkage from the xylose side.
Production of xylobiose from the autohydrolysis explosion liquor of corncob using Thermotoga maritima ylanase B (XynB) immobilized on nickel-chelated Eupergit C.
Tan, S. S., Li, D. Y., Jiang, Z. Q., Zhu, Y. P., Shi, B. & Li, L. T. (2008). Bioresource Technology, 99(1), 200-204.
In this study, a thermostable recombinant xylanase B (XynB) from Thermotoga maritima MSB8 was immobilized on nickel-chelated Eupergit C 250L. This immobilized XynB was then used to hydrolyze the autohydrolysis explosion liquor of corncob (AELC) in a packed-bed enzyme reactor for continuous production of xylooligosaccharides, especially xylobiose. When tested in batch hydrolysis of AELC, the immobilized XynB still retained its relative activity of 92.5% after 10 cycles of hydrolysis at 90°C. The immobilized XynB retained 83.6% of its initial hydrolysis activity even after 168 h of hydrolysis reaction at 90°C and demonstrated a half-life time of 577.6 h (24 days) for continuous hydrolysis. HPLC showed that xylobiose (49.8%) and xylose (22.6%) were the main hydrolysis products yielded during continuous hydrolysis. Xylobiose was adsorbed on an activated charcoal column and eluted with a linear gradient of 15% (v/v) ethanol to yield xylobiose with 84.7% of recovery. Also, the purity of xylobiose was up to 97.2% as determined by HPLC. Therefore, the immobilized XynB was suitable for the efficient production of xylobiose from AELC. This is the first report on the immobilization of xylanase for xylobiose production.
Evidence for the presence of arabinoxylan hydrolysing enzymes in European wheat flours.
Cleemput, G., Bleukx, W., Van Oort, M., Hessing, M. & Delcour, J. A. (1995). Journal of Cereal Science, 22(2), 139-145.
Water extracts of flour samples prepared from six sound European wheat varieties hydrolyse p-nitrophenyl-β-D-xylopyranoside and p-nitrophenyl-α-L-arabino-furanoside and, in addition, release soluble, dyed fragments from azurine crosslinked xylan. Incubation of water soluble wheat arabinoxylan with water extracts of flour results in the release of low molecular weight fractions consisting mainly of arabinose and xylose and small proportions of oligosaccharides as detected by high performance anion exchange chromatography. Gel permeation profiles of the incubation mixtures show a clear breakdown of the arabinoxylan.
Extractive bioconversion of xylan for production of xylobiose and xylotriose using a PEG6000/sodium citrate aqueous two-phase system.
Li, X., Lian, Z., Dong, B., Xu, Y., Yong, Q. & Yu, S. (2011). Korean Journal of Chemical Engineering, 28(9), 1897-1901.
Aqueous two-phase system (ATPS) was applied for extraction bioconversion of xylan by xylanase from Trichoderma viride. Phase diagrams for poly (ethylene glycol) (PEG) and sodium citrate were determined at room temperature. The ATPS composed of 12.99% (w/w) PEG6000 and 12.09% (w/w) sodium citrate was favorable for partition of xylanase and used for extraction bioconversion of xylan. Batch hydrolysis demonstrated that higher concentrations of xylobiose and xylotriose were obtained in the PEG6000/sodium citrate ATPS compared to those in the aqueous system. These results present the potential feasibility of production of xylo-oligosaccharides by extraction bioconversion in ATPS.
Purification and characterization of Thermobifida fusca xylanase 10B.
Kim, J. H., Irwin, D. & Wilson, D. B. (2004). Canadian Journal of Microbiology, 50(10), 835-843.
Thermobifida fusca grows well on cellulose and xylan, and produces a number of cellulases and xylanases. The gene encoding a previously unstudied endoxylanase, xyl10B, was overexpressed in E. coli, and the protein was purified and characterized. Mature Xyl10B is a 43-kDa glycohydrolase with a short basic domain at the C-terminus. It has moderate thermostability, maintaining 50% of its activity after incubation for 16 h at 62°C, and is most active between pH 5 and 8. Xyl10B is produced by growth of T. fusca on xylan or Solka Floc but not on pure cellulose. Mass spectroscopic analysis showed that Xyl10B produces xylobiose as the major product from birchwood and oat spelts xylan and that its hydrolysis products differ from those of T. fusca Xyl11A. Xyl10B hydrolyzes various p-nitrophenyl-sugars, including p-nitrophenyl α-D-arabinofuranoside, p-nitrophenyl-β-D-xylobioside, p-nitrophenyl-β-D-xyloside, and p-nitrophenyl-β-D-cellobioside. Xyl11A has higher activity on xylan substrates, but Xyl10B produced more reducing sugars from corn fiber than did Xyl11A.
Xylanase, β-glucanase, and other side enzymatic activities have greater effects on the viscosity of several feedstuffs than xylanase and β-glucanase used alone or in combination.
Mathlouthi, N., Saulnier, L., Quemener, B. & Larbier, M. (2002). Journal of Agricultural and Food Chemistry, 50(18), 5121-5127.
This study was carried out to evaluate the effects of a pure xylanase, a pure β-glucanase, a mix of the two pure enzymes, and a commercial enzyme preparation (Quatrazyme HP, Nutri-Tomen Les Ulis, France) on the viscosity exhibited by water-soluble nonstarch polysaccharides of several feedstuffs (Rialto wheat, Sidéral wheat, Isengrain wheat, triticale, rye, barley, oats, corn, wheat bran, rice bran, wheat screenings, soybean meal, rapeseed meal, sunflower meal, and peas). The viscosity depended on the feedstuffs and varieties of the same feedstuff. There was a correlation (R2 = 0.86) between viscosity of cereals and their arabinoxylan and β-glucan contents. The correlation was greater (R2 = 0.99) when the type of cereal was taken into account. The addition of pure xylanase significantly decreased the viscosity of all feedstuffs except sunflower meal (P≤ 0.05). However, pure β-glucanase was unable significantly to decrease the viscosity of Isengrain wheat, corn, rice bran, wheat screenings, soybean meal, and sunflower meal. There was a greater decrease in viscosity with the combination of xylanase and β-glucanase than with addition of xylanase or β-glucanase alone. This synergistic action of xylanase and β-glucanase was observed only in Rialto wheat, Sidéral wheat, triticale, rye, barley, oats, and peas. Finally, the commercial enzyme preparation produced a greater reduction (P≤ 0.05) in viscosity for all feedstuffs compared to xylanase or β-glucanase used alone or in combination. The greater effectiveness of the commercial enzyme preparation was due to the presence of side enzymatic activities (arabinofuranosidase, xylosidase, glucosidase, galactosidase, cellulase, and polygalacturonase).
In vitro fermentation of cereal dietary fibre carbohydrates by probiotic and intestinal bacteria.
Crittenden, R., Karppinen, S., Ojanen, S., Tenkanen, M., Fagerström, R., Mättö, J., Saarela, M., Mattila-Sandholm, T. & Poutanen, K. (2002). Journal of the Science of Food and Agriculture, 82(8), 781-789.
A range of probiotic and other intestinal bacteria were examined for their ability to ferment the dietary fibre carbohydrates β-glucan, xylan, xylo-oligosaccharides (XOS) and arabinoxylan. β-Glucan was fermented by Bacteroides spp and Clostridium beijerinckii but was not fermented by lactobacilli, bifidobacteria, enterococci or Escherichia coli. Unsubstituted xylan was not fermented by any of the probiotic bacteria examined. However, many Bifidobacterium species and Lactobacillus brevis were able to grow to high yields using XOS. XOS were also efficiently fermented by some Bacteroides isolates but not by E coli, enterococci, Clostridium difficile, Clostridium perfringens or by the majority of intestinal Lactobacillus species examined. Bifidobacterium longum strains were able to grow well using arabinoxylan as the sole carbon source. These organisms hydrolysed and fermented the arabinosyl residues from arabinoxylan but did not substantially utilise the xylan backbone of the polysaccharide. Arabinoxylan was not fermented by lactobacilli, enterococci, E coli, C perfringens or C difficile and has potential to be an applicable carbohydrate to complement probiotic Bif longum strains in synbiotic combinations.
HPAEC-PAD for oligosaccharide analysis—novel insights into analyte sensitivity and response stability.
Mechelke, M., Herlet, J., Benz, J. P., Schwarz, W. H., Zverlov, V. V., Liebl, W. & Kornberger, P. (2017). Analytical and Bioanalytical Chemistry, 1-13.
The rising importance of accurately detecting oligosaccharides in biomass hydrolyzates or as ingredients in food, such as in beverages and infant milk products, demands for the availability of tools to sensitively analyze the broad range of available oligosaccharides. Over the last decades, HPAEC-PAD has been developed into one of the major technologies for this task and represents a popular alternative to state-of-the-art LC-MS oligosaccharide analysis. This work presents the first comprehensive study which gives an overview of the separation of 38 analytes as well as enzymatic hydrolyzates of six different polysaccharides focusing on oligosaccharides. The high sensitivity of the PAD comes at cost of its stability due to recession of the gold electrode. By an in-depth analysis of the sensitivity drop over time for 35 analytes, including xylo- (XOS), arabinoxylo- (AXOS), laminari- (LOS), manno- (MOS), glucomanno- (GMOS), and cellooligosaccharides (COS), we developed an analyte-specific one-phase decay model for this effect over time. Using this model resulted in significantly improved data normalization when using an internal standard. Our results thereby allow a quantification approach which takes the inevitable and analyte-specific PAD response drop into account.