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.

Arabinoxylan hydrolysates (AXH) are the hydrolyzed products of the major components of the dietary fiber arabinoxylan. AXH include diverse oligosaccharides varying in xylose polymerization and side residue modifications with arabinose at the O-2 and/or O-3 position of the xylose unit. Previous studies have reported that AXH exhibit prebiotic properties on gut bifidobacteria; moreover, several adult-associated bifidobacterial species (e.g., Bifidobacterium adolescentis and Bifidobacterium longum subsp. longum) are known to utilize AXH. In this study, we tried to elucidate the molecular mechanisms of AXH utilization by Bifidobacterium pseudocatenulatum, which is a common bifidobacterial species found in adult feces. We performed transcriptomic analysis of B. pseudocatenulatum YIT 4072^T, which identified three upregulated gene clusters during AXH utilization. The gene clusters encoded three sets of ATP-binding cassette (ABC) transporters and five enzymes belonging to glycoside hydrolase family 43 (GH43). By characterizing the recombinant proteins, we found that three solute-binding proteins of ABC transporters showed either broad or narrow specificity, two arabinofuranosidases hydrolyzed either single- or double-decorated arabinoxylooligosaccharides, and three xylosidases exhibited functionally identical activity. These data collectively suggest that the transporters and glycoside hydrolases, encoded in the three gene clusters, work together to utilize AXH of different sizes and with different side residue modifications. Thus, our study sheds light on the overall picture of how these proteins collaborate for the utilization of AXH in B. pseudocatenulatum and may explain the predominance of this symbiont species in the adult human gut.

Advancement in industrial biotechnology offers potential opportunities for economic utilization of agro industrial biomass for the production of value-added products. Xylooligosaccharides (XOS) are non-digestible food ingredients with prebiotic properties for selectively promoting the growth of probiotics providing many health benefits and several applications on food and pharmaceutical industry. The present study deal with enzymatic production of XOS from xylan extracted from different agroindustrial wastes, namely sugarcane straw (SS) and coffee husk (CH) using an optimized enzymatic mixture with endo-xylanase (GH11), α-l-arabinofuranosidase (GH51) and Feruloyl Esterase (CE1). The XOS profile concentration was quantified by HPAEC-PAD using standard (X2-X6) from Megazyme^®. The efficient enzymatic mixture achieved a high total XOS concentration using SS xylan (10.23 ± 0.56 g/L) and CH xylan (8.45 ± 0.65 g/L). Three of four probiotic cultures of Lactobacillus and Bifidobacterium tested were able to utilize XOS produced from agricultural wastes and showed remarkable growth in the media containing XOS, consuming preferentially the X2 and X3 fractions as the sole source of carbon. The XOS produced also exhibited a considerable resistance to hydrolysis of digestive enzymes, as well as an concentration dependent anti-oxidant activity achieving until 78% in a XOS concentration of 2 g. L⁻¹. Thus, the results showed that XOS produced from these agricultural residues have great prebiotic potential and good antioxidant activity; therefore, it can be used in food-related applications as functional ingredients.

Cross-Linked Enzyme Aggregates (CLEAs) technologies for enzyme immobilization are influenced by mass transference problems as the degree of molecular crosslinking achieved strongly affects the enzyme exposure to the substrates. Therefore, this work seeks to improve the accessibility of high molecular weight substrates by using macromolecular cross-linkers to the synthesis of a xylanolytic biocatalyst. After confirming that commercial polymers used as macromolecular cross-linkers significantly upgraded the xylanase activity from a crude preparation, a novel biopolymer/amyloid protein complex (BPAP) extracted from a microbial biofilm was used producing a remarkable recovery (83%) of the enzyme activity. A response surface methodology was applied to contrast the features of a previously developed biocatalyst with glutaraldehyde (GA@Xyl-CLEAs) and a novel one synthesized with BPAP combined with functionalized magnetic nanoparticles: mBPAP@Xyl-CLEAs. It was observed that the crosslinking agent used was the factor that most affected the enzyme activity. Also, the mBPAP system showed a similar and higher hydrolytic activity than those synthesized with GA, which was not affected by the mNPs/protein ratio. Finally, the mBPAP@Xyl-CLEAs were successfully tested for xylooligosaccharides production from agroindustrial-derived substrates, making this technology a promising practice to obtain green and suitable biocatalysts.

Alkali-extracted xylan from lignocellulosics is a promising feedstock for production of prebiotic xylooligosaccharides (XOS). An integrated process was established combining autohydrolysis, nanofiltration and xylanase hydrolysis. Results show that after autohydrolysis 48.37% of xylan was degraded into oligomers and dissolved into the autohydrolysate, of which 57.83% were XOS. By-products and xylose were removed by nanofiltration with discontinuous diafiltration, while high recovery yields of XOS (84.15%) and xylan (87.45%) were obtained. High yields of XOS were obtained by adding xylanase to the autohydrolysates; after enzymatic hydrolysis an XOS yield of 96-98% was obtained. The enzymatic hydrolysates showed positive prebiotic effects on B. adolescentis with an increase in cell concentration by 4.8-fold after fermentation for 24 h. The main products were short-chain fatty acids with carbon balanced during the whole fermentation process. This integrated strategy resulted in a final XOS conversion of 41.22% contrasted to the initial xylan in raw alkali-extracted xylan.

Wheat bran arabinoxylan can be converted by enzymatic hydrolysis into short arabinoxylo-oligosaccharides (AXOS) with prebiotic potential. Alkali extraction of arabinoxylan from wheat-bran offers advantages in terms of yield and results in arabinoxylan with highly-substituted regions which has been a challenge to hydrolyse using endoxylanases. We show that this hurdle can be overcome by selecting an arabinoxylanase that attacks these regions. The yield of AXOS can be increased by enzyme synergy, involving the hydrolysis of some arabinoxylan side groups. Thus, arabinoxylanase (CtXyl5At) from Clostridium thermocellum, belonging to subfamily 34 of glycoside hydrolase (GH) family 5 was investigated pertaining to its specificity for highly-substituted regions in the arabinoxylan-backbone. CtXyl5At preferentially hydrolysed the water-soluble fraction of alkali-extracted arabinoxylan. AXOS with DP 2-4 were determined as major products from CtXyl5At catalyzed hydrolysis. Increase in AXOS yield was observed with enzyme synergy, involving an initial treatment of soluble arabinoxylan with a GH43 α-l-arabinofuranosidase from Bifidobacterium adolescentis termed BaAXHd3 (30°C, 6h), followed by hydrolysis with CtXyl5At (50°C, 24h). The prebiotic potential of AXOS was shown by growth analysis using the human gut bacteria Bifidobacterium adolescentis ATCC 15703 and Roseburia hominis DSM 6839. Importantly, AXOS were utilized by the bacteria and short-chain fatty acids were produced.

Objective: We previously described the structure and activity of a glycoside hydrolase family 30 subfamily 8 (GH30-8) endoxylanase, CaXyn30A, from Clostridium acetobutylicum which exhibited novel glucuronic acid (GA)-independent activity. Immediately downstream from CaXyn30A is encoded another GH30-8 enzyme, CaXyn30B. While CaXyn30A deviated substantially in the highly conserved β7-α7 and β8-α8 loop regions of the catalytic cleft which are responsible for GA-dependence, CaXyn30B maintains these conserved subfamily 8 amino acid residues thus predicting canonical GA-dependent activity. In this report, we show that CaXyn30B functions as a canonical GA-dependent GH30-8 endoxylanase in contrast to its GA-independent neighbor, CaXyn30A. Results: A clone expressing the catalytic domain of CaXyn30B (CaXyn30B-CD) exhibited GA-dependent endoxylanase activity. Digestion of glucuronoxylan generated a ladder of aldouronate limit products as anticipated for canonical GA-dependent GH30-8 enzymes. Unlike the previously described CaXyn30A-CD, CaXyn30B-CD showed no activity on arabinoxylan or the generation of appreciable neutral oligosaccharides from glucuronoxylan substrates. These results are consistent with amino acid sequence comparisons of the catalytic cleft and phylogenetic analysis.

Hemicellulose-rich substrates produced in the lignocellulose biorefinery context can yield macromolecular xylan structures with assorted application in the chemical industry. Xylan presents natural affinity to cellulose and its incorporation onto fibers increases the physical processability of pulp; however, current studies diverge on how molar mass affects xylan interaction with cellulose. In the current work, xylans with varied structural characteristics were prepared from alkaline-sulfite pretreated sugarcane bagasse with aid of an alkaline-active xylanase and selective precipitations using different ethanol concentrations. Prepared xylan fractions, containing low levels of lignin contamination (4-9%) and molar masses ranging from 2.3 kDa to 34 kDa, were incorporated onto eucalyptus pulp fibers up to 4.7 g xylan/100 g pulp. The efficiency of xylan incorporation onto cellulosic fibers was dependent on the xylan structures, where low molar mass and low substitution degree favored high incorporation levels.

Xylooligosaccharides (XOS) are attracting an ever-increasing amount of interest for use as food prebiotics. In this study, we used efficient membrane separation technology to convert lignocellulosic materials into a renewable source of XOS. This study revealed a dual function of nanofiltration membranes by first achieving a high yield of xylobiose (a main component of XOS) from alkali-pretreated empty fruit bunch (EFB) hydrolysate, and then by achieving a high degree of separation for xylose as a monosaccharide product. Alkali pretreatment could increase the xylan content retention of raw EFB from 23.4% to 26.9%, which eventually contributed to higher yields of both xylobiose and xylose. Nanofiltration increased the total amount of XYN10Ks_480 endoxylanase produced from recombinant Streptomyces lividans 1326 without altering its specific activity. Concentrated XYN10Ks_480 endoxylanase was applied to the recovery of both xylobiose and xylose from alkali-pretreated EFB hydrolysate. Xylobiose and xylose yields reached 41.1% and 17.3%, respectively, and when unconcentrated XYN10Ks_480 endoxylanase was applied, those yields reached 35.1% and 8.3%, respectively. The last step in nanofiltration was to separate xylobiose over xylose, and 41.3 g.L⁻¹ xylobiose (90.1% purity over xylose) was achieved. This nanofiltration method should shorten the processes used to obtain XOS as a high-value end product from lignocellulosic biomass.

Nanoscale materials of carbon, silica and zirconia were used to immobilize a recombinant endo-1, 4-β-D-xylanase (XynC) of B. subtilis KCX006. The adsorption of endo-1, 4-β-D-xylanase on nanomaterials of carbon, silica and zirconia followed the pseudo-second-order kinetic model. The activation energies for adsorption of endoxylanase on carbon, silica and zirconia nanomaterials were 9.94 kJ mol⁻¹, 40.44 kJ mol⁻¹ and 16.33 kJ mol⁻¹ respectively. The recovered activity (RA) of endoxylanase immobilized on carbon, silica and zirconia nanomaterials was in the range of 52%–92%. The endoxylanase immobilized on zirconia nanoparticles showed maximum RA. All immobilized endoxylanase showed optimum activity at pH 6.6 similar to that of free/soluble endoxylanase. But compared to free endoxylanase, all immobilized endoxylanase had broad optimum temperature range (50-65°C) for catalytic activity. The Michaelis-Menten constant (K_m) increased for all immobilized endoxylanase due to substrate diffusion limit. The endoxylanase immobilized on above nanomaterials was used repeatedly for XOS production from xylan. All immobilized endoxylanase produced X2-X6 and substituted XOS similar to free endoxylanase from beechwood xylan and extracted crude xylans from sorghum and sugarcane bagasse. The endoxylanase immobilized on above nanoparticles did not lose activity after five batches of repeated use. The results showed that endoxylanase immobilized on carbon, silica and zirconia matrices would be useful for production of XOS by enzyme recycling.

The severe pretreatment of poplar makes xylan difficult to utilize efficiently. In this work, poplar was pretreated by hydrogen peroxide-acetic acid (HPAC) with H₂SO₄ as catalyst to remove lignin, and the solid residues were used to produce xylooligosaccharides (XOS) and monosaccharides by two-step xylanase and cellulase hydrolysis. The results indicated that higher H₂SO₄ concentrations in the HPAC pretreatment of poplar afforded stronger lignin removal ability. An increased XOS yield of 19.8% was obtained from 200 mM H₂SO₄-catalyzed poplar by xylanase and the XOS purity was high, with a very low xylose/XOS ratio of 0.14. Higher glucose (75.2%) and xylose (61.4%) yields were obtained from the HPAC-pretreated poplar using 50 mM H₂SO₄ as catalyst. Finally, 16.9 g XOS and 296.4 g glucose were produced from 1 kg poplar by xylanase and cellulase. This study provides a method for producing functional XOS and monosaccharides from poplar using a simple reduced-pollution strategy.

Plant cell wall polysaccharides, including xylan, glucomannan, xyloglucan and pectin, are often acetylated. Although a number of acetyltransferases responsible for the acetylation of some of these polysaccharides have been biochemically characterized, little is known about the source of acetyl donors and how acetyl donors are translocated into the Golgi, where these polysaccharides are synthesized. In this report, we investigated roles of ATP-citrate lyase (ACL) that generates cytosolic acetyl-CoA in cell wall polysaccharide acetylation and effects of simultaneous mutations of four Reduced Wall Acetylation (RWA) genes on acetyl-CoA transport into the Golgi in Arabidopsis thaliana. Expression analyses of genes involved in the generation of acetyl-CoA in different subcellular compartments showed that the expression of several ACL genes responsible for cytosolic acetyl-CoA synthesis was elevated in interfascicular fiber cells and induced by secondary wall-associated transcriptional activators. Simultaneous downregulation of the expression of ACL genes was demonstrated to result in a substantial decrease in the degree of xylan acetylation and a severe alteration in secondary wall structure in xylem vessels. In addition, the degree of acetylation of other cell wall polysaccharides, including glucomannan, xyloglucan and pectin, was also reduced. Moreover, Golgi-enriched membrane vesicles isolated from the rwa1/2/3/4 quadruple mutant were found to exhibit a drastic reduction in acetyl-CoA transport activity compared with the wild type. These findings indicate that cytosolic acetyl-CoA generated by ACL is essential for cell wall polysaccharide acetylation and RWAs are required for its transport from the cytosol into the Golgi.

Eucalyptus wood is the primary source of fibers to produce paper and cellulose in South American countries. The major by-product generated in the cellulose industry is sawdust derived from chip wood production, which is designated as Eucalyptus by-product (EB). The xylooligosaccharides (XOS) are xylose-based oligomers with proven effects over maintenance and stimulation of beneficial human gut bacteria. This study reported the EB extraction and characterization along with an assessment of hemicellulose hydrolysis using commercial xylanases to produce XOS. Hemicellulose derived from extracted and NaClO₂ pretreated (HEEBPT) presented xylan content of 55%, which was similar to 58.5% found in commercial Birchwood hemicellulose (CBH). The enzymatic hydrolysis of HEEBPT and CBH presented 30% as maximum conversion of xylan into XOS without significant difference among the enzymatic extracts evaluated. The XOS production from EB was proven as a technically feasible alternative to recover a value-added product from hemicellulosic fraction generated in the cellulose industry. However, lignin removal with NaClO₂ from EB affects the feasibility of an industrial process because they generate toxic compounds in the pretreatment step. Thus, further studies with alternative reagents, such as ionic liquids, are required to asses selectively lignin removal from EB.

The bacterial species living in the gut mediate many aspects of biological processes such as nutrition and activation of adaptive immunity. In addition, commensal fungi residing in the intestine also influence host health. Although the interaction of bacterium and fungus has been shown, its precise mechanism during colonization of the human intestine remains largely unknown. Here, we show interaction between bacterial and fungal species for utilization of dietary components driving their efficient growth in the intestine. Next generation sequencing of fecal samples from Japanese and Indian adults revealed differential patterns of bacterial and fungal composition. In particular, Indians, who consume more plant polysaccharides than Japanese, harbored increased numbers of Prevotella and Candida. Candida spp. showed strong growth responses to the plant polysaccharide arabinoxylan in vitro. Furthermore, the culture supernatants of Candida spp. grown with arabinoxylan promoted rapid proliferation of Prevotella copri. Arabinose was identified as a potential growth-inducing factor in the Candida culture supernatants. Candida spp. exhibited a growth response to xylose, but not to arabinose, whereas P. copri proliferated in response to both xylose and arabinose. Candida spp., but not P. copri, colonized the intestine of germ-free mice. However, P. copri successfully colonized mouse intestine already harboring Candida. These findings demonstrate a proof of concept that fungal members of gut microbiota can facilitate a colonization of the intestine by their bacterial counterparts, potentially mediated by a dietary metabolite.

Xylooligosaccharides (XOS) from woody biomass were evaluated as a substrate for secondary lactic acid bacteria (LAB) fermentation in sour beer production. XOS were extracted from birch (Betula pubescens) and added to beer to promote the growth of Lactobacillus brevis BSO 464. Growth, pH, XOS degradation, and metabolic products were monitored throughout fermentations, and the final beer was evaluated sensorically. XOS were utilized, metabolic compounds were produced (1800 mg/L lactic acid), and pH was reduced from 4.1 to 3.6. Secondary fermentation changed sensory properties significantly, and the resulting sour beer was assessed as similar to a commercial reference in multiple attributes, including acidic taste. Overall, secondary LAB fermentation induced by wood-derived XOS provided a new approach to successfully produce sour beer with reduced fermentation time (from 1-3 years to 4 weeks). The presented results demonstrate how hemicellulosic biomass can be valorized for beverage production and to obtain sour beer with improved process control.

The importance of inhibition sensitivity for xylanase functionality in bread making was investigated using mutants of the wild-type Bacillus subtilis xylanase (XBS_TAXI), sensitive to Triticum aestivum xylanase inhibitor (TAXI). XBS_NI, a mutant with reduced sensitivity to TAXI, and XBS_TI, a mutant sensitive to all wheat endogenous proteinaceous inhibitors (TAXI, Xylanase Inhibiting Protein and Thaumatin-like Xylanase Inhibitor) were used. The higher inhibition sensitivity of XBS_TAXI and XBS_TI compared to XBS_NI was associated with a respective 7- and 53-fold increase in enzyme dosage required for a maximal increase in bread loaf volume. XBS_TI and XBS_TAXI were only active during the mixing phase and the beginning of fermentation, while XBS_NI was able to hydrolyze arabinoxylan until the end of fermentation. In spite of this difference in activity profile, no differences in loaf volume were observed for the different xylanases at optimal concentrations. Dough extensional viscosity analysis suggests that increased water availability as a result of xylanase activity favors starch-starch and starch-gluten interactions and drives the improvement in bread loaf volume.

Prebiotic compounds are substrates selectively metabolized by beneficial gut microbiota causing a health-promoting effect. Despite some prebiotic carbohydrates have been largely studied, xylooligosaccharides (XOS) are important prebiotics derived from arabinoxylans, which are polysaccharides found in cereals. This study aimed to investigate the production of xylanolytic enzymes and XOS during bioprocessing of wheat middlings, a product derived from wheat flour production, using a probiotic Bacillus subtilis. The composition of XOS and the enzymatic and prebiotic activities of resulting B. subtilis cultures were evaluated. The activity of xylanolytic enzymes continuously enhanced during the 72 h bacterial growth, where β-xylosidase presented the highest value (70.31 U/mL). XOS profile and concentration varied considerably between control and bioprocessed samples and among these at different times. Maximum prebiotic activity score was found for the 24 h and 72 h bioprocessed samples (1.73 and 1.61, respectively) using the commercial probiotic Lactobacillus acidophilus LA-5. Wheat middlings showed to be a promising substrate for production of prebiotics like XOS and B. subtilis FTC01 appears to be a good source of xylanolytic enzymes.

A novel GH9 cellulase (AMOR_GH9A) was discovered by sequence-based mining of a unique metagenomic dataset collected at the Jan Mayen hydrothermal vent field. AMOR_GH9A comprises a signal peptide, a catalytic domain and a CBM3 cellulose-binding module. AMOR_GH9A is an exceptionally stable enzyme with a temperature optimum around 100°C and an apparent melting temperature of 105°C. The novel cellulase retains 64% of its activity after 4 hours of incubation at 95°C. The closest characterized homolog of AMOR_GH9A is TfCel9A, a processive endocellulase from the model thermophilic bacterium Thermobifida fusca (64.2% sequence identity). Direct comparison of AMOR_GH9A and TfCel9A revealed that AMOR_GH9A possesses higher activity on soluble and amorphous substrates (phosphoric acid swollen cellulose, konjac glucomannan) and has an ability to hydrolyse xylan that is lacking in TfCel9A.

Xylanases are in important class of industrial enzymes that are essential for the complete hydrolysis of lignocellulosic biomass into fermentable sugars. In the present study, we report the cloning of novel xylanases with interesting properties from compost metagenomics libraries. Controlled composting of lignocellulosic materials was used to enrich the microbial population in lignocellulolytic organisms. DNA extracted from the compost samples was used to construct metagenomics libraries, which were screened for xylanase activity. In total, 40 clones exhibiting xylanase activity were identified and the thermostability of the discovered xylanases was assayed directly from the library clones. Five genes, including one belonging to the more rare family GH8, were selected for subcloning and the enzymes were expressed in recombinant form in E. coli. Preliminary characterization of the metagenome-derived xylanases revealed interesting properties of the novel enzymes, such as high thermostability and specific activity, and differences in hydrolysis profiles. One enzyme was found to perform better than a standard Trichoderma reesei xylanase in the hydrolysis of lignocellulose at elevated temperatures.