Endo-xylanases as tools for production of substituted xylooligosaccharides with prebiotic properties

Advances of microbial xylanases in the application of flour industries: A comprehensive review

Microbial xylanase has a wide range of applications, and many researchers favoring its utilization as an alternative to improve flour products. Wheat flour is the main raw material of flour products, although the content of arabinoxylan is not high in flour products, but it has a great influence on the quality of flour products, microbial xylanase can act on wheat arabinoxylan, so as to play the role of flour product improvement. This review carries out a description of the research progress on the application of xylanases in flour products in terms of xylanase properties, different families of xylanases and improvement mechanisms of xylanases in flour products. According to the properties of various microbial sources of xylanases, the suitable xylanase can be added to flour products, and the effect of xylanase towards wheat arabinoxylan in flour can be used to improve the quality of flour products. The molecular modification based on the properties of xylanase and the crystal structure of different families of xylanase and their substrate specificity toward wheat arabinoxylan are discussed. The article reviews the information about microbial xylanases in order to achieve better results in flour products and to provide a theoretical basis for their industrial application.

Exploring the Structural and Dynamic Properties of a Chimeric Glycoside Hydrolase Protein in the Presence of Calcium Ions

GH10 xylanases and GH62 Arabinofuranosidases play key roles in the breakdown of arabinoxylans and are important tools in various industrial and biotechnological processes, such as renewable biofuel production, the paper industry, and the production of short-chain xylooligosaccharides (XOS) from plant biomass. However, the use of these enzymes in industrial settings is often limited due to their relatively low thermostability and reduced catalytic efficiency. To overcome these limitations, strategies based on enzymatic chimera construction and the use of metal ions and other cofactors have been proposed to produce new recombinant enzymes with improved catalytic activity and thermostability. Here, we examine the conformational dynamics of a GH10-GH62 chimera at different calcium ion concentrations through molecular dynamics simulations. While experimental data have demonstrated improved activity and thermostability in GH10-GH62 chimera, the mechanistic basis for these enhancements remains unclear. We explored the structural details of the binding subsites of Ca2+ in the parental enzymes GH62 from Aspergillus fumigatus (Afafu62) and a recombinant GH10 from Cryptococcus flavescens (Xyn10cf), as well as their chimeric combination, and how negatively charged electron pairing located at the protein surface affects Ca2+ capture. The results indicate that Ca2+ binding significantly contributes to structural stability and catalytic cavity modulation in the chimera, particularly evident at a concentration of 0.01 M. This effect, not observed in the parental GH10 and GH62 enzymes, highlights how Ca2+ enhances stability in the overall chimeric enzyme, while supporting a larger cavity volume in the chimera GH62 subunit. The increased catalytic site volume and reduced structural flexibility in response to Ca2+ suggest that calcium binding minimizes non-productive conformational states, which could potentially improve catalytic turnover. The findings presented here may aid in the development of more thermostable and efficient catalytic systems.

Homologous expression, purification, and characterization of a recombinant acetylxylan esterase from Aspergillus nidulans

Acetylxylan esterases (AXEs) are essential enzymes that break down the acetyl groups in acetylated xylan found in plant cell walls polysaccharides. They work synergistically with backbone-depolymerizing xylanolytic enzymes to accelerate the degradation of complex polysaccharides. In this study, we cloned the gene axeA, which encodes the acetylxylan esterase from Aspergillus nidulans FGSC A4 (AxeAN), into the pEXPYR expression vector and introduced it into the high protein-producing strain A. nidulans A773. The purified AxeAN, with a molecular weight of 33.5 kDa as confirmed by SDS-PAGE, was found to be active on ρ-nitrophenyl acetate (ρNPA), exhibiting a remarkably high specific activity (170 U mg-1) at pH 7.0 and 55 °C. AxeAN demonstrated stability over a wide pH range (5.5-9.0), retaining >80% of its initial activity after 24 h. The KM and Vmax were 0.098 mmol L-1 and 320 U mg-1, respectively, using ρNPA as a substrate. We also evaluated the synergistic effect of AxeAN with an endo-1,4-β-xylanase from Malbranchea pulchella (MpXyn10) in the hydrolysis of four different xylans (Birchwood, Beechwood, Oat spelt, and Arabinoxylan) to produce xylooligosaccharides (XOS). The best results were obtained using Birchwood xylan as substrate and MpXyn10-AxeAN as biocatalysts after 24 h of reaction (50 °C), with a XOS-yield of 91%, value 41% higher when compared to MpXyn10 (XOS-yield of 63%). These findings showed the potential of the application of AxeAN, together with other xylanases, to produce xylooligosaccharides with high purity and other products with high added value in the field of lignocellulosic biorefinery.

Halosquirtibacter laminarini gen. nov., sp. nov. and Halosquirtibacter xylanolyticus sp. nov., marine anaerobic laminarin and xylan degraders in the phylum Bacteroidota

The bacterial group of the phylum Bacteroidota greatly contributes to the global carbon cycle in marine ecosystems through its specialized ability to degrade marine polysaccharides. In this study, it is proposed that two novel facultative anaerobic strains, DS1-an-13321T and DS1-an-2312T, which were isolated from a sea squirt, represent a novel genus, Halosquirtibacter, with two novel species in the family Prolixibacteraceae. The 16S rRNA sequence similarities of these two strains were 91.26% and 91.37%, respectively, against Puteibacter caeruleilacunae JC036T, which is the closest recognized neighbor. The complete genomes of strains DS1-an-13321T and DS1-an-2312T each consisted of a single circular chromosome with a size of 4.47 and 5.19 Mb, respectively. The average amino acid identity and the percentage of conserved proteins against the type species of the genera in the family Prolixibacteraceae ranged from 48.33 to 52.35% and 28.34-37.37%, respectively, which are lower than the threshold for genus demarcation. Strains DS1-an-13321T and DS1-an-2312T could grow on galactose, glucose, maltose, lactose, sucrose, laminarin, and starch, and only DS1-an-2312T could grow on xylose and xylan under fermentation conditions. These strains produced acetic acid and propionic acid as the major fermentation products. Genome mining of the genomes of the two strains revealed 27 and 34 polysaccharide utilization loci, which included 155 and 249 carbohydrate-active enzymes (CAZymes), covering 57 and 65 CAZymes families, respectively. The laminarin-degrading enzymes in both strains were cell-associated, and showed exo-hydrolytic activity releasing glucose as a major product. The xylan-degrading enzymes of strain DS1-an-2312T was also cell-associated, and had endo-hydrolytic activities, releasing xylotriose and xylotetraose as major products. The evidence from phenotypic, biochemical, chemotaxonomic, and genomic characteristics supported the proposal of a novel genus with two novel species in the family Prolixibacteraceae, for which the names Halosquirtibacter laminarini gen. nov., sp. nov. and Halosquirtibacter xylanolyticus sp. nov. are proposed. The type strain of Halosquirtibacter laminarini is DS1-an-13321T (= KCTC 25031T = DSM 115329T) and the type strain of Halosquirtibacter xylanolyticus is DS1-an-2312T (= KCTC 25032T = DSM 115328T).

Arabinoxylo-oligosaccharides production from unexploited agro-industrial sesame (Sesamum indicum L.) hulls waste

This work demonstrates that sesame (Sesamum indicum L.) hull, an unexploited food industrial waste, can be used as an efficient source for the extraction of hemicellulose and/or pectin polysaccharides to further obtain functional oligosaccharides. Different polysaccharides extraction methods were surveyed including alkaline and several enzymatic treatments. Based on the enzymatic release of xylose, arabinose, glucose, and galacturonic acid from sesame hull by using different enzymes, Celluclast®1.5 L, Pectinex®Ultra SP-L, and a combination of them were selected for the enzymatic extraction of polysaccharides at 50 °C, pH 5 up to 24 h. Once the polysaccharides were extracted, Ultraflo®L was selected to produce arabinoxylo-oligosaccharides (AXOS) at 40 °C up to 24 h. Apart from oligosaccharides production from extracted polysaccharides, alternative approaches for obtaining oligosaccharides were also explored. These were based on the analysis of the supernatants resulting from the polysaccharide extraction, alongside a sequential hydrolysis performed with Celluclast®1.5 L and Ultraflo®L of the starting raw sesame hull. The different fractions obtained were comprehensively characterized by determining low molecular weight carbohydrates and monomeric compositions, average Mw and dispersity, and oligosaccharide structure by MALDI-TOF-MS. The results indicated that sesame hull can be a useful source for polysaccharides extraction (pectin and hemicellulose) and derived oligosaccharides, especially AXOS.

Assessing the Impact of Arabinoxylans on Dough Mixing Properties and Noodle-Making Performance through Xylanase Treatment

This study examined the impact of xylanases, focusing on the hydrolysis of water-extractable (WE-AX) and water-unextractable arabinoxylans (WU-AX) and on the quality and noodle-making performance of flours with varying gluten strengths. Flours categorized as strong (S), medium (M), and weak (W) were treated with two xylanases (WE and WU) at concentrations ranging from 0.01% to 0.2%. Parameters such as solvent retention capacity (SRC), SDS sedimentation volume, dough mixing properties, and noodle characteristics were measured. The SRC revealed that flour S had the highest water-holding capacity, gluten strength, and arabinoxylan content. Xylanase treatment reduced water SRC values in flour S and increased the SDS sedimentation volume, with a greater effect from xylanase WU, indicating the potential enhancement of gluten strength. The impact of xylanases was pronounced at higher enzyme concentrations, with differences in dough mixing properties, resistance, and extensibility of fresh noodles, producing softer and stretchable noodles. Cooked noodles made from flours treated with xylanase were softer and had decreased firmness and chewiness, especially those made from flours S and M. This study concludes that WE-AX and WU-AX influence noodle texture; therefore, controlling their degradation with xylanases can produce noodles with varied textures, depending on the gluten strength of the flour.

Enzymatic production of xylooligosaccharide from lignocellulosic and marine biomass: A review of current progress, challenges, and its applications in food sectors

Over the last decade, xylooligosaccharides (XOS) have attracted great attentions because of their unique chemical properties and excellent prebiotic effects. Among the current strategies for XOS production, enzymatic hydrolysis is preferred due to its green and safe process, simplicity in equipment, and high control of the degrees of polymerization. This paper comprehensively summarizes various lignocellulosic biomass and marine biomass employed in enzymatic production of XOS. The importance and advantages of enzyme immobilization in XOS production are also discussed. Many novel immobilization techniques for xylanase are presented. In addition, bioinformatics techniques for the mining and designing of new xylanase are also described. Moreover, XOS has exhibited great potential applications in the food industry as diverse roles, such as a sugar replacer, a fat replacer, and cryoprotectant. This review systematically summarizes the current research progress on the applications of XOS in food sectors, including beverages, bakery products, dairy products, meat products, aquatic products, food packaging film, wall materials, and others. It is anticipated that this paper will act as a reference for the further development and application of XOS in food sectors and other fields.

A new halotolerant xylanase from Aspergillus clavatus expressed in Escherichia coli with catalytic efficiency improved by site-directed mutagenesis

Daily agro-industrial waste, primarily cellulose, lignin, and hemicellulose, poses a significant environmental challenge. Harnessing lignocellulolytic enzymes, particularly endo-1,4-β-xylanases, for efficient saccharification is a cost-effective strategy, transforming biomass into high-value products. This study focuses on the cloning, expression, site-directed mutagenesis, purification, three-dimensional modeling, and characterization of the recombinant endo-1,4-β-xylanase (XlnA) from Aspergillus clavatus in Escherichia coli. This work includes evaluation of the stability at varied NaCl concentrations, determining kinetic constants, and presenting the heterologous expression of XlnAΔ36 using pET22b(+). The expression led to purified enzymes with robust stability across diverse pH levels, exceptional thermostability at 50 °C, and 96-100% relative stability after 24 h in 3.0 M NaCl. Three-dimensional modeling reveals a GH11 architecture with catalytic residues Glu 132 and 22. XlnAΔ36 demonstrates outstanding kinetic parameters compared to other endo-1,4-β-xylanases, indicating its potential for industrial enzymatic cocktails, enhancing saccharification. Moreover, its ability to yield high-value compounds, such as sugars, suggests a promising and ecologically positive alternative for the food and biotechnology industries.

Structural and molecular insights into a bifunctional glycoside hydrolase 30 xylanase specific to glucuronoxylan

Glycoside hydrolase (GH) 30 family xylanases are enzymes of biotechnological interest due to their capacity to degrade recalcitrant hemicelluloses, such as glucuronoxylan (GX). This study focuses on a subfamily 7 GH30, TtXyn30A from Thermothelomyces thermophilus, which acts on GX in an "endo" and "exo" mode, releasing methyl-glucuronic acid branched xylooligosaccharides (XOs) and xylobiose, respectively. The crystal structure of inactive TtXyn30A in complex with 23-(4-O-methyl-α-D-glucuronosyl)-xylotriose (UXX), along with biochemical analyses, corroborate the implication of E233, previously identified as alternative catalytic residue, in the hydrolysis of decorated xylan. At the -1 subsite, the xylose adopts a distorted conformation, indicative of the Michaelis complex of TtXyn30AEE with UXX trapped in the semi-functional active site. The most significant structural rearrangements upon substrate binding are observed at residues W127 and E233. The structures with neutral XOs, representing the "exo" function, clearly show the nonspecific binding at aglycon subsites, contrary to glycon sites, where the xylose molecules are accommodated via multiple interactions. Last, an unproductive ligand binding site is found at the interface between the catalytic and the secondary β-domain which is present in all GH30 enzymes. These findings improve current understanding of the mechanism of bifunctional GH30s, with potential applications in the field of enzyme engineering.

Xylanases and high-degree wet milling improve soluble dietary fibre content in liquid oat base

The growth of plant-based food and drink substitutes has led to increased interest in oat-based milk substitute as a dairy milk alternative. Conventional liquid oat base (LOB) production results in a fibre-rich insoluble by-product and loss of valuable macronutrients. This study investigates the use of xylanase enzymes to release insoluble arabinoxylan (AX) fibre and employs different degrees of milling in the LOB manufacturing process, with the aim to reduce insoluble waste and simultaneously increase soluble dietary fibre in oat-based milk substitutes. The combination of decreased mill gap space from 1 to 0.05 mm and addition of GH10 xylanase, resulted in a homogenous LOB product and solubilization of all available AX. Potential prebiotic arabinoxylooligosaccharides of DP3-7 from GH10 hydrolysis were identified using HPAEC-PAD and MS analysis. These findings demonstrate the value of utilizing xylanases and fine-milling in LOB manufacturing, offering a sustainable approach to maximize health benefits of oat-based beverages.

A novel glycoside hydrolase 43-like enzyme from Clostridium boliviensis is an endo-xylanase and a candidate for xylooligosaccharide production from different xylan substrates

An uncharacterized gene encoding a glycoside hydrolase family 43-like enzyme from Clostridium boliviensis strain E-1 was identified from genomic sequence data, and the encoded enzyme, CbE1Xyn43-l, was produced in Escherichia coli. CbE1Xyn43-l (52.9 kDa) is a two-domain endo-β-xylanase consisting of a C-terminal CBM6 and a GH43-like catalytic domain. The positions of the catalytic dyad conserved in GH43, the catalytic base (Asp74), and proton donor (Glu240) were identified in alignments including GH43-enzymes of known 3D-structure from different subfamilies. CbE1Xyn43-l is active at pH 7.0-9.0, with optimum temperature at 65°C, and a more than 7 days' half-life in irreversible deactivation studies at this temperature. The enzyme hydrolyzed birchwood xylan, quinoa stalks glucuronoarabinoxylan, and wheat arabinoxylan with xylotriose and xylotetraose as major hydrolysis products. CbE1Xyn43-l also released xylobiose from pNPX2 with low turnover (kcat of 0.044 s-1) but was inactive on pNPX, showing that a degree of polymerization of three (DP3) was the smallest hydrolyzable substrate. Divalent ions affected the specific activity on xylan substrates, which dependent on the ion could be increased or decreased. In conclusion, CbE1Xyn43-l from C. boliviensis strain E-1 is the first characterized member of a large group of homologous hypothetical proteins annotated as GH43-like and is a thermostable endo-xylanase, producing xylooligosaccharides of high DP (xylotriose and xylotetraose) producer.

IMPORTANCE

The genome of Clostridium boliviensis strain E-1 encodes a number of hypothetical enzymes, annotated as glycoside hydrolase-like but not classified in the Carbohydrate Active Enzyme Database (CAZy). A novel thermostable GH43-like enzyme is here characterized as an endo-β-xylanase of interest in the production of prebiotic xylooligosaccharides (XOs) from different xylan sources. CbE1Xyn43-l is a two-domain enzyme composed of a catalytic GH43-l domain and a CBM6 domain, producing xylotriose as main XO product. The enzyme has homologs in many related Clostridium strains which may indicate a similar function and be a previously unknown type of endo-xylanase in this evolutionary lineage of microorganisms.

Structure-dependent stimulation of gut bacteria by arabinoxylo-oligosaccharides (AXOS): a review

Arabinoxylo-oligosaccharides (AXOS) are non-digestible dietary fibers that potentially confer a health benefit by stimulating beneficial bacteria in the gut. Still, a detailed overview of the diversity of gut bacteria and their specificity to utilize structurally different AXOS has not been provided to date and was aimed for in this study. Moreover, we assessed the genetic information of summarized bacteria, and we extracted genes expected to encode for enzymes that are involved in AXOS hydrolysis (based on the CAZy database). The taxa involved in AXOS fermentation in the gut display a large variety of AXOS-active enzymes in their genome and consequently utilize AXOS to a highly different extent. Clostridia and Bacteroidales are generalists that consume many structurally diverse AXOS, whereas Bifidobacterium are specialists that specifically consume AXOS with a low degree of polymerization. Further complexity is evident from the fact that the exact bacterial species, and in some cases even the bacterial strains (e.g. in Bifidobacterium longum) that are stimulated, highly depend on the specific AXOS molecular structure. Furthermore, certain species in Bifidobacterium and Lactobacillaceae are active as cross-feeders and consume monosaccharides and unbranched short xylo-oligosaccharides released from AXOS. Our review highlights the possibility that (enzymatic) fine-tuning of specific AXOS structures leads to improved precision in targeting growth of specific beneficial bacterial species and strains in the gut.

Discovery of novel alkaline-tolerant xylanases from fecal microbiota of dairy cows

Xylo-oligosaccharides (XOS) are considered as a promising type of prebiotics that can be used in foods, feeds, and healthcare products. Xylanases play a key role in the production of XOS from xylan. In this study, we conducted a metagenomic analysis of the fecal microbiota from dairy cows fed with different types of fodders. Despite the diversity in their diets, the main phyla observed in all fecal microbiota were Firmicutes and Bacteroidetes. At the genus level, one group of dairy cows that were fed probiotic fermented herbal mixture-containing fodders displayed decreased abundance of Methanobrevibacter and increased growth of beneficial Akkermansia bacteria. Additionally, this group exhibited a high microbial richness and diversity. Through our analysis, we obtained a comprehensive dataset comprising over 280,000 carbohydrate-active enzyme genes. Among these, we identified a total of 163 potential xylanase genes and subsequently expressed 34 of them in Escherichia coli. Out of the 34 expressed genes, two alkaline xylanases with excellent temperature stability and pH tolerance were obtained. Notably, CDW-xyl-8 exhibited xylanase activity of 96.1 ± 7.5 U/mg protein, with an optimal working temperature of 55 ℃ and optimal pH of 8.0. CDW-xyl-16 displayed an activity of 427.3 ± 9.1 U/mg protein with an optimal pH of 8.5 and an optimal temperature at 40 ℃. Bioinformatic analyses and structural modeling suggest that CDW-xyl-8 belongs to GH10 family xylanase, and CDW-xyl-16 is a GH11 family xylanase. Both enzymes have the ability to hydrolyze beechwood xylan and produce XOS. In conclusion, this metagenomic study provides valuable insights into the fecal microbiota composition of dairy cows fed different fodder types, revealing main microbial groups and demonstrating the abundance of xylanases. Furthermore, the characterization of two novel xylanases highlights their potential application in XOS production.

The Potential of Xylooligosaccharides as Prebiotics and Their Sustainable Production from Agro-Industrial by-Products

In recent years, concerns about a good-quality diet have increased. Food supplements such as prebiotics have great nutritional and health benefits. Within the diverse range of prebiotics, xylooligosaccharides (XOs) show high potential, presenting exceptional properties for the prevention of systemic disorders. XOs can be found in different natural sources; however, their production is limited. Lignocellulosic biomasses present a high potential as a source of raw material for the production of XOs, making the agro-industrial by-products the perfect candidates for production on an industrial scale. However, these biomasses require the application of physicochemical pretreatments to obtain XOs. Different pretreatment methodologies are discussed in terms of increasing the production of XOs and limiting the coproduction of toxic compounds. The advance in new technologies for XOs production could decrease their real cost (USD 25-50/kg) on an industrial scale and would increase the volume of market transactions in the prebiotic sector (USD 4.5 billion). In this sense, new patents and innovations are being strategically developed to expand the use of XOs as daily prebiotics.

Structural determinants underlying high-temperature adaptation of thermophilic xylanase from hot-spring microorganisms

Thermophilic xylanases from hot-spring microorganisms play potential biological and industrial applications for renewable and sustainable social development. However, high-temperature adaptation mechanisms of these thermophilic xylanases remain elusive at the molecular and evolutionary levels. Here, two recently reported xylanases, named XynDRTY1 and XynM1, from hot springs were subjected to molecular dynamics (MD) simulations at a series of temperature gradients and comparatively analyzed in comparison with the evolutionary background of the xylanase family. Comparative analysis of MD trajectories revealed that the XynM1 exhibits smaller structural dynamics and greater thermal stability than the XynDRTY1, although both share a similar fold architecture with structural differences in the βα_loops. Local regions whose conformational flexibility and regular secondary structure exhibited differences as temperature increases were closely related to the high-temperature adaptation of xylanase, implying that stabilization of these regions is a feasible strategy to improve the thermal stability of xylanases. Furthermore, coevolutionary information from the xylanase family further specified the structural basis of xylanases. Thanks to these results about the sequence, structure, and dynamics of thermophilic xylanases from hot springs, a series of high-temperature-related structural determinants were resolved to promote understanding of the molecular mechanism of xylanase high-temperature adaptation and to provide direct assistance in the improvement of xylanase thermal stability.

Analysing the dynamics of the bacterial community in pozol, a Mexican fermented corn dough

Pozol is a traditional prehispanic Mexican beverage made from fermented nixtamal dough; it is still part of everyday life in many communities due to its nutritional properties. It is the product of spontaneous fermentation and has a complex microbiota composed primarily of lactic acid bacteria (LAB). Although this is a beverage that has been used for centuries, the microbial processes that participate in this fermented beverage are not well understood. We fermented corn dough to produce pozol and sampled it at four key times to follow the community and metabolic changes (0, 9 24 and 48 h) by shotgun metagenomic sequencing to determine structural changes in the bacterial community, as well as metabolic genes used for substrate fermentation, nutritional properties and product safety. We found a core of 25 abundant genera throughout the 4 key fermentation times, with the genus Streptococcus being the most prevalent throughout fermentation. We also performed an analysis focused on metagenomic assembled genomes (MAGs) to identify species from the most abundant genera. Genes involving starch, plant cell wall (PCW), fructan and sucrose degradation were found throughout fermentation and in MAGs, indicating the metabolic potential of the pozol microbiota to degrade these carbohydrates. Complete metabolic modules responsible for amino acid and vitamin biosynthesis increased considerably during fermentation, and were also found to be abundant in MAG, highlighting the bacterial contribution to the well-known nutritional properties attributed to pozol. Further, clusters of genes containing CAZymes (CGCs) and essential amino acids and vitamins were found in the reconstructed MAGs for abundant species in pozol. The results of this study contribute to our understanding of the metabolic role of micro-organisms in the transformation of corn to produce this traditional beverage and their contribution to the nutritional impact that pozol has had for centuries in the traditional cuisine of southeast Mexico.

Yeasts Have Evolved Divergent Enzyme Strategies To Deconstruct and Metabolize Xylan

Together with bacteria and filamentous fungi, yeasts actively take part in the global carbon cycle. Over 100 yeast species have been shown to grow on the major plant polysaccharide xylan, which requires an arsenal of carbohydrate active enzymes. However, which enzymatic strategies yeasts use to deconstruct xylan and what specific biological roles they play in its conversion remain unclear. In fact, genome analyses reveal that many xylan-metabolizing yeasts lack expected xylanolytic enzymes. Guided by bioinformatics, we have here selected three xylan-metabolizing ascomycetous yeasts for in-depth characterization of growth behavior and xylanolytic enzymes. The savanna soil yeast Blastobotrys mokoenaii displays superior growth on xylan thanks to an efficient secreted glycoside hydrolase family 11 (GH11) xylanase; solving its crystal structure revealed a high similarity to xylanases from filamentous fungi. The termite gut-associated Scheffersomyces lignosus, in contrast grows more slowly, and its xylanase activity was found to be mainly cell surface-associated. The wood-isolated Wickerhamomyces canadensis, surprisingly, could not utilize xylan as the sole carbon source without the addition of xylooligosaccharides or exogenous xylanases or even co-culturing with B. mokoenaii, suggesting that W. canadensis relies on initial xylan hydrolysis by neighboring cells. Furthermore, our characterization of a novel W. canadensis GH5 subfamily 49 (GH5_49) xylanase represents the first demonstrated activity in this subfamily. Our collective results provide new information on the variable xylanolytic systems evolved by yeasts and their potential roles in natural carbohydrate conversion. IMPORTANCE Microbes that take part in the degradation of the polysaccharide xylan, the major hemicellulose component in plant biomass, are equipped with specialized enzyme machineries to hydrolyze the polymer into monosaccharides for further metabolism. However, despite being found in virtually every habitat, little is known of how yeasts break down and metabolize xylan and what biological role they may play in its turnover in nature. Here, we have explored the enzymatic xylan deconstruction strategies of three underexplored yeasts from diverse environments, Blastobotrys mokoenaii from soil, Scheffersomyces lignosus from insect guts, and Wickerhamomyces canadensis from trees, and we show that each species has a distinct behavior regarding xylan conversion. These findings may be of high relevance for future design and development of microbial cell factories and biorefineries utilizing renewable plant biomass.

Glycomic profiling identifies key-structural differences in three arabinoxylan fractions from sugarcane culms

Sugarcane is an important food and bioenergy crop, and although the residual biomass is potentially available for biorefinery and biofuels production the complex plant cell wall matrix requires pretreatment prior to enzymatic hydrolysis. Arabinoxylans require multiple enzymes for xylose backbone and saccharide side-branch hydrolysis to release xylooligosaccharides and pentoses. The effect of arabinoxylan structure on xylooligosaccharide release by combinations of up to five xylanolytic enzymes was studied using three arabinoxylan fractions extracted from sugarcane culms by sodium chlorite, DMSO and alkaline treatments. Reducing sugar release and LC-MS detection with chemometric analysis identified different xylooligosaccharide profiles between extracts following enzyme treatments. The position and degree of side-branch decorations are determinants of enzyme activity and xylooligosaccharide diversity with the alkaline and post‑sodium chlorite extracts as the most accessible and most recalcitrant, respectively, indicating acetyl substituents as a major recalcitrance factor. The complex xylooligosaccharide profile with the DMSO extract suggests regions with different levels of branching. Chemometric analysis identified GH10 xylanase hydrolysis products that act as substrates for other enzymes, such as α-glucuronidase. The strategy reported here can identify specific enzyme combinations to overcome barriers for biomass processing such as pretreatment selection, recalcitrance to enzyme digestion and optimization of reducing sugar release.

Endo-1,4-β-xylanase-containing glycoside hydrolase families: Characteristics, singularities and similarities

Endo-1,4-β-xylanases (EC 3.2.1.8) are O-glycoside hydrolases that cleave the internal β-1,4-D-xylosidic linkages of the complex plant polysaccharide xylan. They are produced by a vast array of organisms where they play critical roles in xylan saccharification and plant cell wall hydrolysis. They are also important industrial biocatalysts with widespread application. A large and ever growing number of xylanases with wildly different properties and functionalites are known and a better understanding of these would enable a more effective use in various applications. The Carbohydrate-Active enZYmes database (CAZy), which classifies evolutionarily related proteins into a glycoside hydrolase family-subfamily organisational scheme has proven powerful in understanding these enzymes. Nevertheless, ambiguity currently exists as to the number of glycoside hydrolase families and subfamilies harbouring catalytic domains with true endoxylanase activity and as to the specific characteristics of each of these families/subfamilies. This review seeks to clarify this, identifying 9 glycoside hydrolase families containing enzymes with endo-1,4-β-xylanase activity and discussing their properties, similarities, differences and biotechnological perspectives. In particular, substrate specificities and hydrolysis patterns and the structural determinants of these are detailed, with taxonomic aspects of source organisms being also presented. Shortcomings in current knowledge and research areas that require further clarification are highlighted and suggestions for future directions provided. This review seeks to motivate further research on these enzymes and especially of the lesser known endo-1,4-β-xylanase containing families. A better understanding of these enzymes will serve as a foundation for the knowledge-based development of process-fitted endo-1,4-β-xylanases and will accelerate their development for use with even the most recalcitrant of substrates in the biobased industries of the future.

Nondigestible Functional Oligosaccharides: Enzymatic Production and Food Applications for Intestinal Health

Nondigestible functional oligosaccharides are of particular interest in recent years because of their unique prebiotic activities, technological characteristics, and physiological effects. Among different types of strategies for the production of nondigestible functional oligosaccharides, enzymatic methods are preferred owing to the predictability and controllability of the structure and composition of the reaction products. Nondigestible functional oligosaccharides have been proved to show excellent prebiotic effects as well as other benefits to intestinal health. They have exhibited great application potential as functional food ingredients for various food products with improved quality and physicochemical characteristics. This article reviews the research progress on the enzymatic production of several typical nondigestible functional oligosaccharides in the food industry, including galacto-oligosaccharides, xylo-oligosaccharides, manno-oligosaccharides, chito-oligosaccharides, and human milk oligosaccharides. Moreover, their physicochemical properties and prebiotic activities are discussed as well as their contributions to intestinal health and applications in foods.

Debranching enzymes decomposed corn arabinoxylan into xylooligosaccharides and achieved prebiotic regulation of gut microbiota in broiler chickens

BACKGROUND

Corn arabinoxylan (AX) is a complicated and multibranched antinutritional factor, thereby proving the use of endo-xylanase (EX) to be marginally valid. This study focused on specific types of AX-degrading enzymes (ADEs) to exert the synergy of debranching enzymes and track the prebiotic potential of enzymatic hydrolysates. This study investigated the effects of ADEs on the growth performance, intestinal histomorphology, absorption functions, changes in polysaccharide components, fermentation, and gut microbiota of broiler chickens. Five hundred seventy-six five-day-old Arbor Acres male broiler chickens were randomly allocated into eight treatments with six replicates each. Corn basal diets supplemented with or without enzymes were fed for a 21-day period, specifically including EX, its compatible use with arabinofuranosidase (EXA) or ferulic acid esterase (EXF), and compound groups with the above three enzymes (XAF).

RESULTS

Specific ADEs stimulated the jejunal villus height and goblet cell number and evidently decreased the crypt depth (P < 0.05), while the ratio of ileal villus height to crypt depth was significantly increased in EXF (P < 0.05). Maltase activities of ileal mucosa in XAF groups were extremely enhanced (P < 0.01), and EX boosted the activity of Na⁺-K⁺ ATPase in the small intestine (P < 0.01). The insoluble AX concentrations comparatively lessened, thereby notably raising the sundry xylooligosaccharide (XOS) yield in the ileal chyme (P < 0.05), which was dominant in xylobiose and xylotriose. Improvements in the abundance and diversity of ileal microbial communities within the EXA, EXF, and XAF treatments were observed (P < 0.05). Positive correlations between microbiota and XOS were revealed, with xylobiose and xylotriose being critical for ten beneficial bacteria (P < 0.05). EXF increased the BWG and FCR of broiler chickens in this phase (P < 0.05), which was attributed to the thriving networks modified by Lactobacillus. The intracecal contents of acetic acid, butyric acid, and propionic acid were greatly enhanced in most ADE groups, such as EXF (P < 0.05).

CONCLUSIONS

Debranching enzymes appreciably targeted corn AX to release prebiotic XOS in the posterior ileum and facilitated intracaecal fermentation. It was beneficial for improving gut development, digestion and absorption and modulating the microflora to promote the early performance of broiler chickens.

Functional identification of two novel carbohydrate-binding modules of glucuronoxylanase CrXyl30 and their contribution to the lignocellulose saccharification

BACKGROUND

Glycoside hydrolase (GH) family 30 xylanases are a distinct group of xylanases, most of which have a highly specific catalytic activity for glucuronoxylan. Since GH30 xylanases do not normally carry carbohydrate-binding modules (CBMs), our knowledge of the function of their CBMs is lacking.

RESULTS

In this work, the CBM functions of CrXyl30 were investigated. CrXyl30 was a GH30 glucuronoxylanase containing tandem CBM13 (CrCBM13) and CBM2 (CrCBM2) at its C terminus, which was identified in a lignocellulolytic bacterial consortium previously. Both CBMs could bind insoluble and soluble xylan, with CrCBM13 having binding specificity for the xylan with L-arabinosyl substitutions, whereas CrCBM2 targeted L-arabinosyl side chains themselves. Such binding abilities of these two CBMs were completely different from other CBMs in their respective families. Phylogenetic analysis also suggested that both CrCBM13 and CrCBM2 belong to novel branches. Inspection of the simulated structure of CrCBM13 identified a pocket that just accommodates the side chain of 3(2)-alpha-L-arabinofuranosyl-xylotriose, which forms hydrogen bonds with three of the five amino acid residues involved in ligand interaction. The truncation of either CrCBM13 or CrCBM2 did not alter the substrate specificity and optimal reaction conditions of CrXyl30, whereas truncation of CrCBM2 decreased the kcat/Km value by 83% (± 0%). Moreover, the absence of CrCBM2 and CrCBM13 resulted in a 5% (± 1%) and a 7% (± 0%) decrease, respectively, in the amount of reducing sugar released by the synergistic hydrolysis of delignified corncob whose hemicellulose is arabinoglucuronoxylan, respectively. In addition, fusion of CrCBM2 with a GH10 xylanase enhanced its catalytic activity against the branched xylan and improved the synergistic hydrolysis efficiency by more than fivefold when delignified corncob was used as substrate. Such a strong stimulation of hydrolysis resulted from the enhancement of hemicellulose hydrolysis on the one hand, and the cellulose hydrolysis is also improved according to the lignocellulose conversion rate measured by HPLC.

CONCLUSIONS

This study identifies the functions of two novel CBMs in CrXyl30 and shows the good potential of such CBMs specific for branched ligands in the development of efficient enzyme preparations.

Immobilization of α-amylase from Aspergillus fumigatus using adsorption method onto zeolite

The stability of enzymes which play an important role as biocatalysts in many industrial processes is a persistent challenge with significant impact on production costs. In this study, improvement of the stability of α-amylase obtained from Aspergillus fumigatus was attempted by immobilizing the enzyme onto zeolite using adsorption method. For purification, the isolated enzyme was subsequently subjected to centrifugation, fractionation, and dialysis. The native enzyme was found to have an optimum temperature of 50 °C, while the immobilized enzyme, the optimum temperature of 60 °C was found. The immobilized enzyme was found to have the K M value of 11.685 ± 0.183 mg mL−1 substrate and V max of 1.406 ± 0.049 μmol mL−1 min−1, while for the native enzyme, the K M value of 3.478 ± 0.271 mg mL−1 substrate and the V max of 2.211 ± 0.096 μmol mL−1 min−1 were obtained. Furthermore, the immobilized enzyme displays the ΔGi of 106.76 ± 0.00 kJ mol−1 and t ½ of 90.40 ± 0.00 min, while the native enzyme, the values obtained are ΔGi of 104.35 ± 1.09 kJ mol−1 and t½ of 38.75 ± 1.53 min. As can be seen, the t ½ of immobilized enzyme is 2.38 times longer than that of native enzyme, justifying a very significant stability enhancement of the enzyme as a result of. Another important finding is that the immobilized α-amylase enzyme was able to retain its activity as high as 13.80 ± 1.19% activity after five cycles, indicating its potential for industrial use.

Novel Function of CtXyn5A from Acetivibrio thermocellus: Dual Arabinoxylanase and Feruloyl Esterase Activity in the Same Active Site

Enzymes' uncharacterised side activities can have significant effects on reaction products and yields. Hence, their identification and characterisation are crucial for the development of successful reaction systems. Here, we report the presence of feruloyl esterase activity in CtXyn5A from Acetivibrio thermocellus, besides its well-known arabinoxylanase activity, for the first time. Activity analysis of enzyme variants mutated in the catalytic nucleophile, Glu279, confirmed removal of all activity for E279A and E279L, and increased esterase activity while removing xylanase activity for E279S, thus allowing the proposal that both reaction types are catalysed in the same active site in two subsequential steps. The ferulic acid substituent is cleaved off first, followed by hydrolysis of the xylan backbone. The esterase activity on complex carbohydrates was found to be higher than that of a designated ferulic acid esterase (E-FAERU). Therefore, we conclude that the enzyme exhibits a dual function rather than an esterase side activity.

Engineering of xylanases for the development of biotechnologically important characteristics

Xylanases are the main biocatalysts used for the reduction of the xylan backbone from hemicellulose, randomly splitting off β-1,4-glycosidic linkages between xylopyranosyl residues. Xylanase market has been annually estimated at 500 million US Dollars and they are potentially used in broad industrial process ranges such as paper pulp biobleaching, xylo-oligosaccharide production, and biofuel manufacture from lignocellulose. The highly stable xylanases are preferred in the downstream procedure of industrial processes because they can tolerate severe conditions. Almost all native xylanases can not endure adverse conditions thus they are industrially not proper to be utilized. Protein engineering is a powerful technology for developing xylanases, which can effectively work in adverse conditions and can meet requirements for industrial processes. This study considered state-of-the-art strategies of protein engineering for creating the xylanase gene diversity, high-throughput screening systems toward upgraded traits of the xylanases, and the prediction and comprehensive analysis of the target mutations in xylanases by in silico methods. Also, key molecular factors have been elucidated for industrial characteristics (alkaliphilic enhancement, thermal stability, and catalytic performance) of GH11 family xylanases. The present review explores industrial characteristics improved by directed evolution, rational design, and semi-rational design as protein engineering approaches for pulp bleaching process, xylooligosaccharides production, and biorefinery & bioenergy production.

Enzymatic production of xylooligosaccharides from corn cobs: Assessment of two different pretreatment strategies

Corn cobs (CCs) are abundant xylan-rich agricultural wastes. Here, we compared CCs XOS yields obtained via two different pretreatment routs, alkali and hydrothermal, using a set of recombinant endo- and exo-acting enzymes from GH10 and GH11 families, which have different restrictions for xylan substitutions. Furthermore, impacts of the pretreatments on chemical composition and physical structure of the CCs samples were evaluated. We demonstrated that alkali pretreatment route rendered 59 mg of XOS per gram of initial biomass, while an overall XOS yield of 115 mg/g was achieved via hydrothermal pretreatment using a combination of GH10 and GH11 enzymes. These results hold a promise of ecologically sustainable enzymatic valorization of CCs via "green" and sustainable XOS production.

PACER: a novel 3D plant cell wall model for the analysis of non-catalytic and enzymatic responses

Background

Substrate accessibility remains a key limitation to the efficient enzymatic deconstruction of lignocellulosic biomass. Limited substrate accessibility is often addressed by increasing enzyme loading, which increases process and product costs. Alternatively, considerable efforts are underway world-wide to identify amorphogenesis-inducing proteins and protein domains that increase the accessibility of carbohydrate-active enzymes to targeted lignocellulose components.

Results

We established a three-dimensional assay, PACER (plant cell wall model for the analysis of non-catalytic and enzymatic responses), that enables analysis of enzyme migration through defined lignocellulose composites. A cellulose/azo-xylan composite was made to demonstrate the PACER concept and then used to test the migration and activity of multiple xylanolytic enzymes. In addition to non-catalytic domains of xylanases, the potential of loosenin-like proteins to boost xylanase migration through cellulose/azo-xylan composites was observed.

Conclusions

The PACER assay is inexpensive and parallelizable, suitable for screening proteins for ability to increase enzyme accessibility to lignocellulose substrates. Using the PACER assay, we visualized the impact of xylan-binding modules and loosenin-like proteins on xylanase mobility and access to targeted substrates. Given the flexibility to use different composite materials, the PACER assay presents a versatile platform to study impacts of lignocellulose components on enzyme access to targeted substrates.

Hydrolysates containing xylooligosaccharides produced by different strategies: Structural characterization, antioxidant and prebiotic activities

This study explores the structural characterization, antioxidant and prebiotic activities of hydrolysates containing xylooligosaccharides (XOS) produced by different strategies: direct fermentation of beechwood xylan (FermBX) and enzymatic treatment of beechwood (EnzBX) and rice husk (EnzRH) xylans. EnzBX and EnzRH showed XOS with a backbone of (1 → 4)-linked-xylopyranosyl residues and branches of arabinose, galactose, and uronic acids. FermBX presented the highest content of total phenolic compounds (14 mg GAE/g) and flavonoids (0.6 mg QE/g), which may contribute to its antioxidant capacity -39.1 μmol TE/g (DPPH), 45.7 μmol TE/g (ABTS), and 79.9 μmol Fe II/g (FRAP). The fermentation of hydrolysates decreased the abundance of microorganisms associated with intestinal diseases from Eubacteriales, Desulfovibrionales and Methanobacteriales orders, while stimulating the growth of organisms belonging to Bacteroides, Megamonas and Limosilactobacillus genera. The production of short-chain fatty acids, ammonia, and CO₂ suggested the prebiotic potential. In conclusion, hydrolysates without previous purification and obtained from non-chemical approaches demonstrated promising biological activities for further food applications.

Effects of Site-Directed Mutations on the Communicability between Local Segments and Binding Pocket Distortion of Engineered GH11 Xylanases Visualized through Network Topology Analysis

Mutations occurred within the binding pocket of enzymes directly modified the interaction network between an enzyme and its substrate. However, some mutations affecting the catalytic efficiency occurred far from the binding pocket and the explanation regarding mechanisms underlying the transmission of the mechanical signal from the mutated site to the binding pocket was lacking. In this study, network topology analysis was used to characterize and visualize the changes of interaction networks caused by site-directed mutations on a GH11 xylanase from our previous study. For each structure, coordinates from molecular dynamics (MD) trajectory were obtained to create networks of representative atoms from all protein and xylooligosaccharide substrate residues, in which edges were defined between pairs of residues within a cutoff distance. Then, communicability matrices were extracted from the network to provide information on the mechanical signal transmission from the number of possible paths between any residue pairs or local protein segments. The analysis of subgraph centrality and communicability clearly showed that site-direct mutagenesis at non-reducing or reducing ends caused binding pocket distortion close to the opposite ends and created denser interaction networks. However, site-direct mutagenesis at both ends cancelled the binding pocket distortion, while enhancing the thermostability. Therefore, the network topology analysis tool on the atomistic simulations of engineered proteins could play some roles in protein design for the minimization to the correction of binding pocket tilting, which could affect the functionality and efficacy of enzymes.

Optimization of Compound Ratio of Exogenous Xylanase and Debranching Enzymes Supplemented in Corn-Based Broiler Diets Using In Vitro Simulated Gastrointestinal Digestion and Response Surface Methodology

This experiment aimed to explore the zymogram of endo-xylanase (EX) and debranching enzymes (arabinofuranosidase [EA] and ferulic acid esterase [EF]) supplemented in the corn−soybean meal-based diet of broilers. An in vitro simulated gastrointestinal digestion model was adopted. According to single-factor, completely random design, the optimal supplemental levels of individual carbohydrase were determined by reducing sugars (RS) and in vitro dry matter digestibility (IVDMD). Response surface method (RSM) was used to predict the proper compound ratio of three carbohydrases. Results showed that shifts were different for feedstuffs such as corn−soybean meal−distillers dried grains with solubles, corn hull, and wheat bran, revealing that the net increase of RS or IVDMD distinctly dropped when degrading corn and related by-products by EX (p < 0.05). There was a significant quadratic relationship between the above response metrics and addition levels of each enzyme (p < 0.05). The determined dosage was 54 U/g EX, 5.0 U/g EA, and 0.4 U/g of EF, respectively. The optimistic zymogram of carbohydrases in corn basal substrates was judged by the IVDMD screening (R2 = 0.9089, p < 0.001). Conclusively, the in vitro assay and RSM were convenient and rapid methods for the optimization of xylan-degrading zymogram, and also testified asthenic hydrolysis of corn arabinoxylan by EX, thus highlighting the synergistic combinations with debranching enzymes.

Expression of an extremophilic xylanase in Nicotiana benthamiana and its use for the production of prebiotic xylooligosaccharides

A gene construct encoding a xylanase, which is active in extreme conditions of temperature and alkaline pH (90 °C, pH 10.5), has been transitorily expressed with high efficiency in Nicotiana benthamiana using a viral vector. The enzyme, targeted to the apoplast, accumulates in large amounts in plant tissues in as little as 7 days after inoculation, without detrimental effects on plant growth. The properties of the protein produced by the plant, in terms of resistance to temperature, pH, and enzymatic activity, are equivalent to those observed when Escherichia coli is used as a host. Purification of the plant-produced recombinant xylanase is facilitated by exporting the protein to the apoplastic space. The production of this xylanase by N. benthamiana, which avoids the hindrances derived from the use of E. coli, namely, intracellular production requiring subsequent purification, represents an important step for potential applications in the food industry in which more sustainable and green products are continuously demanded. As an example, the use of the enzyme producing prebiotic xylooligosdaccharides from xylan is here reported.

Xylan Prebiotics and the Gut Microbiome Promote Health and Wellbeing: Potential Novel Roles for Pentosan Polysulfate

This narrative review highlights the complexities of the gut microbiome and health-promoting properties of prebiotic xylans metabolized by the gut microbiome. In animal husbandry, prebiotic xylans aid in the maintenance of a healthy gut microbiome. This prevents the colonization of the gut by pathogenic organisms obviating the need for dietary antibiotic supplementation, a practice which has been used to maintain animal productivity but which has led to the emergence of antibiotic resistant bacteria that are passed up the food chain to humans. Seaweed xylan-based animal foodstuffs have been developed to eliminate ruminant green-house gas emissions by gut methanogens in ruminant animals, contributing to atmospheric pollution. Biotransformation of pentosan polysulfate by the gut microbiome converts this semi-synthetic sulfated disease-modifying anti-osteoarthritic heparinoid drug to a prebiotic metabolite that promotes gut health, further extending the therapeutic profile and utility of this therapeutic molecule. Xylans are prominent dietary cereal components of the human diet which travel through the gastrointestinal tract as non-digested dietary fibre since the human genome does not contain xylanolytic enzymes. The gut microbiota however digest xylans as a food source. Xylo-oligosaccharides generated in this digestive process have prebiotic health-promoting properties. Engineered commensal probiotic bacteria also have been developed which have been engineered to produce growth factors and other bioactive factors. A xylan protein induction system controls the secretion of these compounds by the commensal bacteria which can promote gut health or, if these prebiotic compounds are transported by the vagal nervous system, may also regulate the health of linked organ systems via the gut–brain, gut–lung and gut–stomach axes. Dietary xylans are thus emerging therapeutic compounds warranting further study in novel disease prevention protocols.

Preparation and nutritional properties of xylooligosaccharide from agricultural and forestry byproducts: A comprehensive review

Xylooligosaccharide (XOS) are functional oligosaccharides with prebiotic activities, which originate from lignocellulosic biomass and have attracted extensive attention from scholars in recent years. This paper summarizes the strategies used in the production of XOS, and introduces the raw materials, preparation methods, and purification technology of XOS. In addition, the biological characteristics and applications of XOS are also presented. The most commonly recommended XOS production strategy is the two-stage method of alkaline pre-treatment and enzymatic hydrolysis; and further purification by membrane filtration to achieve the high yield of XOS is required for prebiotic function. At the same time, new strategies and technologies such as the hydrothermal and steam explosion have been used as pre-treatment methods combined with enzymatic hydrolysis to prepare XOS. XOS have many critical physiological activities, especially in regulating blood glucose, reducing blood lipid, and improving the structure of host intestinal flora.

Heterologous Expression of Xylanase xAor from Aspergillus oryzae in Komagataella phaffii T07

Xylanases (EC 3.2.1.8) hydrolyze the hemicellulose of plant cell walls. Xylanases are used in the food and paper industries and for bioconversion of lignocellulose to biofuel. In this work, the producer-strain with four copies of the xAor xylanase gene was organized in two tandem copies for optimal expression in Komagataella phaffii T07 yeast. The secreted 35 kDa xylanase was purified from culture medium by gel filtration on Sephadex G-25 and anion exchange chromatography on DEAE-Sepharose 6HF. Tryptic peptides of the recombinant enzyme were analyzed by liquid chromatography-tandem mass spectrometry where the amino acid sequence corresponded to Protein Accession # O94163 for Endo-1,4-beta-xylanase from Aspergillus oryzae RIB40. The recombinant xylanase was produced in a bioreactor where the secreted enzyme hydrolyzed oat xylane with an activity of 258240 IU/mL. High activity in the culture medium suggested xylanase could be used for industrial applications without being purified or concentrated. The pH optimum for xylanase xAor was 7.5, though the enzyme was active from pH 2.5 to pH 10. Xylanase was active at temperatures from 35 °C to 85 °C with a maximum at 60 °C. In conclusion, this protocol yields soluble, secreted xylanase suitable for industrial scale production.

Development of a Multi-Enzymatic Approach for the Modification of Biopolymers with Ferulic Acid

A series of polymers, including chitosan (CS), carboxymethylcellulose (CMC) and a chitosan-gelatin (CS-GEL) hybrid polymer, were functionalized with ferulic acid (FA) derived from the enzymatic treatment of arabinoxylan through the synergistic action of two enzymes, namely, xylanase and feruloyl esterase. Subsequently, the ferulic acid served as the substrate for laccase from Agaricus bisporus (AbL) in order to enzymatically functionalize the above-mentioned polymers. The successful grafting of the oxidized ferulic acid products onto the different polymers was confirmed through ultraviolet-visible (UV-Vis) spectroscopy, attenuated total reflectance (ATR) spectroscopy, scanning electron microscopy (SEM) and nuclear magnetic resonance (NMR) spectroscopy. Additionally, an enhancement of the antioxidant properties of the functionalized polymers was observed according to the DDPH and ABTS protocols. Finally, the modified polymers exhibited strong antimicrobial activity against bacterial populations of Escherichia coli BL21DE3 strain, suggesting their potential application in pharmaceutical, cosmeceutical and food industries.

Cellulolytic and Xylanolytic Enzymes from Yeasts: Properties and Industrial Applications

Lignocellulose, the main component of plant cell walls, comprises polyaromatic lignin and fermentable materials, cellulose and hemicellulose. It is a plentiful and renewable feedstock for chemicals and energy. It can serve as a raw material for the production of various value-added products, including cellulase and xylanase. Cellulase is essentially required in lignocellulose-based biorefineries and is applied in many commercial processes. Likewise, xylanases are industrially important enzymes applied in papermaking and in the manufacture of prebiotics and pharmaceuticals. Owing to the widespread application of these enzymes, many prokaryotes and eukaryotes have been exploited to produce cellulase and xylanases in good yields, yet yeasts have rarely been explored for their plant-cell-wall-degrading activities. This review is focused on summarizing reports about cellulolytic and xylanolytic yeasts, their properties, and their biotechnological applications.

Genetic Determinants of Xylan Utilization in Humisphaera borealis M1803T, a Planctomycete of the Class Phycisphaerae

Abstract—

Planctomycetes of the class Phycisphaerae are aerobic and anaerobic heterotrophic bacteria that colonize a wide range of marine and terrestrial habitats. Their functional roles in the environment, however, are still poorly understood. Humisphaera borealis M1803T is one of the very few characterized planctomycetes of this class. It is also the first described representative of the previously uncultured group WD2101, which is commonly detected in soils and peatlands. This work analyzed the genetic determinants that define the ability of Humisphaera borealis M1803T to grow on xylan, one of the plant cell wall polymers. The whole genome sequence analysis of this planctomycete resulted in identification of five genes encoding the proteins homologous to previously described endo-β-xylanases. For two of these proteins, evolutionarily closer experimentally characterized homologs with other substrate specificities were found. In a member of the GH10 family of glycoside hydrolases, the active center of the enzyme was destroyed. We consider two proteins from GH62 and GH141 families as the most likely candidates for the role of β-xylanase responsible for xylan utilization. Phylogenetic analysis of proteins of GH10, GH62, and GH141 families was carried out. The role of lateral transfers in the evolution of the genes for glycoside hydrolases and their close homologs is discussed.

Application of oligosaccharides in meat processing and preservation

In recent decades, consumer preference and attention to foodstuff presented as healthy and with desirable nutritional information, has increased significantly. In this field, the meat industry has a challenging task since meat and meat products have been related to various chronic diseases. Functional ingredients have emerged in response to the increasing demand for healthier and more nutritious foods. On this matter, oligosaccharides such as fructooligosaccharides (FOS), xylooligosaccharides (XOS), galactooligosaccharides (GOS), and chitooligosaccharides (COS) have been presented as suitable ingredients for the meat industry with the aim of obtaining healthier meat derivatives (e.g. with low fat or sugar content, reduced amount of additives, and desirable functional properties, etc.). However, studies considering application of such oligomers in the meat sector are scarce. In addition, a large number of issues remain to be solved related both to obtaining and characterizing the oligosaccharides available in the industry and to the effect that these ingredients have on the features of meat products (mainly physicochemical and sensory). The study of new oligosaccharides, the methodologies for obtaining them, and their application to new meat products should be promoted, as well as improving knowledge about their effects on the properties of functional meat foods.

Prebiotic effect of sorghum biomass xylooligosaccharides employing immobilized endoxylanase from Thermomyces lanuginosus PC7S1T

Purified endoxylanase from Thermomyces lanuginosus PC7S1T was immobilized in calcium alginate, resulting in a yield of 78.5% and a reusability for 11 cycles. The stability of the immobilized enzyme was given for a pH range of 4 to 9 for 96 h. Endoxylanase immobilized in calcium alginate at 65 °C exhibited thermal stability equal to the soluble enzyme for 5 h, and at high temperatures of 75 °C and 85 °C showed half-lives of 4 and 3 h, respectively. Both soluble endoxylanase and immobilized forms were able to hydrolyze hemicellulose, obtained from low-lignin sorghum biomass pretreated with 5% H₂O₂ and 2% NaOH, after 1 h of incubation at 65 °C, releasing a mixture of short-chain xylooligosaccharides (X2-X6). The highest amounts of XOS generated were those for X5 (24 to 40%), X4 (33 to 39%), and X3 (11 to 22%). These XOS acted as prebiotics, promoting the growth of the probiotic L. acidophilus, similar to glucose in the MRS broth. These results show the potential of low-lignin sorghum to generate XOS with prebiotic activity, suggesting the application of these compounds in the food industry.

The Emergence of New Catalytic Abilities in an Endoxylanase from Family GH10 by Removing an Intrinsically Disordered Region

Endoxylanases belonging to family 10 of the glycoside hydrolases (GH10) are versatile in the use of different substrates. Thus, an understanding of the molecular mechanisms underlying substrate specificities could be very useful in the engineering of GH10 endoxylanases for biotechnological purposes. Herein, we analyzed XynA, an endoxylanase that contains a (β/α)₈-barrel domain and an intrinsically disordered region (IDR) of 29 amino acids at its amino end. Enzyme activity assays revealed that the elimination of the IDR resulted in a mutant enzyme (XynAΔ29) in which two new activities emerged: the ability to release xylose from xylan, and the ability to hydrolyze p-nitrophenyl-β-d-xylopyranoside (pNPXyl), a substrate that wild-type enzyme cannot hydrolyze. Circular dichroism and tryptophan fluorescence quenching by acrylamide showed changes in secondary structure and increased flexibility of XynAΔ29. Molecular dynamics simulations revealed that the emergence of the pNPXyl-hydrolyzing activity correlated with a dynamic behavior not previously observed in GH10 endoxylanases: a hinge-bending motion of two symmetric regions within the (β/α)₈-barrel domain, whose hinge point is the active cleft. The hinge-bending motion is more intense in XynAΔ29 than in XynA and promotes the formation of a wider active site that allows the accommodation and hydrolysis of pNPXyl. Our results open new avenues for the study of the relationship between IDRs, dynamics and activity of endoxylanases, and other enzymes containing (β/α)₈-barrel domain.

One-step fermentation for producing xylo-oligosaccharides from wheat bran by recombinant Escherichia coli containing an alkaline xylanase

BACKGROUND

One-step fermentation is a cheap way to produce xylo-oligosaccharides (XOS), where production of xylanases and XOS is integrated into a single process. In spite of cost advantage, one-step fermentation is still short in yield so far due to the limited exploration. To cope with this issue, production of XOS from wheat bran by recombinant Escherichia coli through one-step fermentation was investigated in this study.

RESULTS

An endo-β-1,4-xylanase gene belonging to glycoside hydrolase family 11 of Bacillus agaradhaerens was employed to construct recombinant E. coli. This xylanase showed maximal activity at 60 °C and pH 8.0-8.5. Its activity retained more than 60% after incubation at 70 °C for 4 h, showing a good stability. The recombinant E. coli BL21(DE3) could secreted xylanases that directly hydrolyzed de-starched wheat bran to XOS in fermentation medium. The XOS generated from hydrolysis consisted of xylose, xylobiose and xylotriose accounting for 23.1%, 37.3% and 39.6%, respectively. Wheat bran concentration was found to be the most crucial factor affecting XOS production. The XOS concentration reached 5.3 mg/mL at 10% loading of wheat bran, which is higher than those of previous researches. Nitrogen source type could also affect production of XOS by changing extracellular xylanase activity, and glycine was found to be the best one for fermentation. Optimal fermentation conditions were finally studied using response surface optimization. The maximal concentration emerged at 44.3 °C, pH 7.98, which is affected by characteristics of the xylanase as well as growth conditions of E. coli.

CONCLUSIONS

This work indicates that the integrated fermentation using recombinant E. coli is highly competitive in cost and final concentration for producing XOS. Results can also provide theoretical basis for large-scale production and contribute to the wide adoption of XOS.

Investigation into the effects of CbXyn10C and Xyn11A on xylooligosaccharide profiles produced from sugarcane bagasse and rice straw and their impact on probiotic growth

This comparative study investigated the effects of CbXyn10C and Xyn11A on xylooligosaccharide profiles produced from sugarcane bagasse (SCB) and rice straw (RS) and their impact on probiotic growth. Generally, CbXyn10C produced more xylose and a higher total phenolic content than Xyn11A. Interestingly, XOS obtained from SCB with CbXyn10C contained significantly more gallic acid than that produced by Xn11A. All selected probiotics thrived in RS-derived XOS, regardless of the enzyme used. However, probiotics grew differently on SCB-derived XOS depending on the enzyme used. All probiotics thrived in Xyn11A-derived XOS from SCB. Only Lactobacillus plantarum thrived on CbXyn10C-derived XOS, while the other two were inhibited. Gallic acid in CbXyn10C-derived XOS from SCB has been linked to probiotic retardation, and gallic acid-enriched broth has been found to inhibit Bifidobacterium longum and Bacillus subtilis, but not L. plantarum. Consequently, the selection of enzymes and plant biomass is crucial for XOS properties and prebiotic effects.

Glycoside Hydrolase family 30 harbors fungal subfamilies with distinct polysaccharide specificities

Efficient bioconversion of agro-industrial side streams requires a wide range of enzyme activities. Glycoside Hydrolase family 30 (GH30) is a diverse family that contains various catalytic functions and has so far been divided into ten subfamilies (GH30_1-10). In this study, a GH30 phylogenetic tree using over 150 amino acid sequences was contructed. The members of GH30 cluster into four subfamilies and eleven candidates from these subfamilies were selected for biochemical characterization. Novel enzyme activities were identified in GH30. GH30_3 enzymes possess β-(1→6)-glucanase activity. GH30_5 targets β-(1→6)-galactan with mainly β-(1→6)-galactobiohydrolase catalytic behavior. β-(1→4)-Xylanolytic enzymes belong to GH30_7 targeting β-(1→4)-xylan with several activities (e.g. xylobiohydrolase, endoxylanase). Additionally, a new fungal subfamily in GH30 was proposed, i.e. GH30_11, which displays β-(1→6)-galactobiohydrolase. This study confirmed that GH30 fungal subfamilies harbor distinct polysaccharide specificity and have high potential for the production of short (non-digestible) di- and oligosaccharides.

Improved Production of Streptomyces sp. FA1 Xylanase in a Dual-Plasmid Pichia pastoris System

Methanol is considered as a potential hazard in the methanol-induced yeast expression of food-related enzymes. To increase the production efficiency of recombinant proteins in Pichia&nbsp;pastoris without methanol induction, a novel dual-plasmid system was constructed, for the first time, by a combining the strategies of genomic integration and episomal expression. To obtain a high copy number of the target gene, the autonomously replicating sequence derived from Kluyveromyces lactis (PARS) was used to construct episomal vectors carrying the constitutive promoters P_GAP and P_GCW14. In addition, an integrative vector carrying the P_GCW14 promoter was constructed by replacing the P_GAP promoter sequence with a partial P_GCW14 promoter. Next, using xylanase XynA from Streptomyces sp. FA1 as the model enzyme, recombination strains were transformed with different combinations of integrating and episomal vectors that were constructed to investigate the changes in the protein yield. Results in shake flasks indicated that the highest enzyme yield was achieved when integrated P_GAP and episomal P_GCW14 were simultaneously transformed into the host strain. Meanwhile, the copy number of xynA increased from 1.14 ± 0.46 to 3.06 ± 0.35. The yield of XynA was successfully increased to 3925 U·mL^-1 after 102 h of fermentation in a 3.6 L fermenter, which was 16.7-fold and 2.86-fold of the yields that were previously reported for the constitutive expression and methanol-induced expression of the identical protein, respectively. Furthermore, the high-cell-density fermentation period was shortened from 132 h to 102 h compared to that of methanol-induced system. Since the risk of methanol toxicity is removed, this novel expression system would be suitable for the production of proteins related to the food and pharmaceutical industries.