Towards enzymatic breakdown of complex plant xylan structures: State of the art

Xylan, Xylooligosaccharides, and Aromatic Structures With Antioxidant Activity Released by Xylanase Treatment of Alkaline-Sulfite–Pretreated Sugarcane Bagasse

Xylanase enzymes are useful to fractionate plant biomass, producing xylan, xylooligosaccharides (XOS), and antioxidant-derived XOS. In a biorefinery, pretreated biomass can be digested with xylanase prior to cellulose saccharification, enhancing the product portfolio in the process. With this vision, this study highlighted a wide range of new products attainable from alkaline-sulfite–pretreated sugarcane bagasse by treatments with endo-xylanase under controlled conditions. The developed process provided a crude extract corresponding to 29.7% (w/w) of pretreated sugarcane bagasse. The crude extract included a relatively polymeric glucuronoarabinoxylan fraction, DP2-DP6 xylooligosaccharides, and aromatic compounds. The enzymatically produced extract was fractionated with increasing ethanol concentrations [up to 90% (v/v)], providing precipitation of varied polymeric xylan fractions (48% (w/w) of the crude extract) with average molar masses ranging from 28 kDa to 3.6 kDa. The fraction soluble in 90% ethanol was subjected to adsorption on 4% (w/v) activated charcoal and eluted with an ethanol gradient from 10% to 70% (v/v), thus providing xylooligosaccharides and aromatic fractions. Most of the xylooligosaccharides (74% of the eluted sugars) were washed out in 10%–30% ethanol. DP2 and DP3 structures predominated in the 10% ethanol fraction, while DP5 structures were significantly enriched in the 30% ethanol fraction. Higher ethanol concentrations desorbed xylooligosaccharides associated with higher amounts of aromatic compounds. Total aromatics, phenolic structures, and p-hydroxycinnamates predominated in the fractions desorbed with 60% and 70% ethanol. The antioxidant activity of produced fractions correlated with their phenolic contents. Compiled results indicate that a wide variety of products can be prepared from pretreated biomass using xylanase-aided extraction procedures. Recovered fractions presented different features and specific application prospects. Beyond polymeric xylan with low lignin contamination, xylooligosaccharides or even lignin-carbohydrate complexes with antioxidant activity can be included in the biorefinery portfolio based on the currently developed fractionation studies.

Changes in the Metagenome-Encoded CAZymes of the Rumen Microbiome Are Linked to Feed-Induced Reductions in Methane Emission From Holstein Cows

Enteric methane (CH4) emission from cattle is strongly linked to the feeding regime and the rumen microbial community structure. Here, we report that feed-induced CH4-reducing effects correlate with specific alterations in the profile of the microbiome-encoded carbohydrate-active enzymes predicted from the rumen fluid metagenome. Rumen microbiome samples were obtained by mouth-tube sampling from 12 lactating Holstein cows after 3-4 weeks of feeding with three different concentrate-to-forage-ratio diets, i.e., standard, high, and extremely high levels of concentrate (4 cows per group; constant dry matter intake in the three groups). Increased inclusion of concentrate involved increased starch levels in the diet at the expense of fiber. The extreme diet resulted in 48% reduction of the CH4 emission per kg dry matter intake compared to the standard diet. From metagenome sequencing of the rumen fluid samples from each cow, 561 different microbial strains (bins) could be derived from analysis of 260 billion DNA base pairs. In the cows fed, the extreme diet, the relative abundance of the majority of the bins, was significantly altered compared to the other groups. Fibrobacterota and Verrucomicrobiota were less abundant in the Extreme group. Surprisingly, no significant abundance changes were observed among Archaea and Bacteroidota, although abundance changes of individual bins of these phyla were found. For each of the 561 bins, the functions of the metagenome-encoded carbohydrate-active enzymes were predicted by bioinformatics using conserved unique peptide pattern (CUPP) analysis. By linking each of the predicted molecular functions of the enzymes to their substrates, changes were found in the predicted abundance of the different enzyme types. Notably, the decreased CH4 emission of the extreme diet group was concurrent with a profound decrease in the xylan-active enzymes, targeting the xylan backbone β-1,4-linkages, acetyl-, feruloyl-, and methyl-glucuronoyl substitutions in xylan. This work provides a first enzyme-conversion-based characterization of how extreme feeding, i.e., lowered forage, can drive rumen microbiome changes that support decreased CH4 emission via a changed carbohydrate-active enzyme profile. The data, furthermore, provide a metagenome-wide catalog of enzymes, underpinning the microbial conversion of different feed fibers (the enzymes attacking specific carbohydrate linkages) in the rumen of Holstein cows.

Whey Beverage Emulsified System as Carrying Matrix of Fennel Seed Extract Obtained by Supercritical CO2 Extraction: Impact of Thermosonication Processing and Addition of Prebiotic Fibers

Whey beverages that were enriched with fructooligosaccharides (FOS) and xylooligosaccharides (XOS) were used for carrying Foeniculum vulgare extract that was obtained by the supercritical CO₂ extraction technique to produce novel functional products. Fennel-based whey beverages were subjected to thermosonication processing (100, 200, and 300 W at 60 °C for 15 min) to verify the performance of the dairy colloidal system for protecting the bioactive fennel compounds. The impacts of thermosonication processing on the quality attributes of the functional whey beverages were examined according to their droplet size distribution, microstructure, kinetic stability, color parameters, browning index, total phenolic content (TPC), and antioxidant capacity by DPPH (2,2-diphenyl-1-picrylhydrazyl) and ABTS (2,2-Azino-bis-(3-ethylbenzothiazoline)-6-sulphonic acid) assays. The enrichment of the whey beverages with FOS and XOS did not affect their kinetic stability. However, the addition of prebiotic dietary fibers contributed to reducing the mean droplet size due to the formation of whey protein–FOS/XOS conjugates. The thermosonication treatments did not promote color changes that were discernible to the human eye. On the other hand, the thermosonication processing reduced the kinetic stability of the beverages. Overall, the colloidal dairy systems preserved the antioxidant capacity of the fennel seed extract, regardless of thermosonication treatment intensity. The whey beverages enriched with FOS and XOS proved to be effective carrying matrices for protecting the lipophilic bioactive fennel compounds.

Functional Specificity of Three α-Arabinofuranosidases from Different Glycoside Hydrolase Families in Aspergillus niger An76

α-l-Arabinofuranosidase (Abf), a debranching enzyme that can remove arabinose substituents from arabinoxylan, promotes the hydrolysis of hemicellulose in plant biomass. However, the functional specificity of Abfs from different glycoside hydrolase (GH) families on the digestion of arabinoxylan and their synergistic interaction with xylanase have not been systematically studied. In this work, we characterized three Abfs (AxhA, AbfB, and AbfC) from GH62, GH54, and GH51 families in Aspergillus niger An76. Quantitative transcriptional analysis showed that expression of the axhA gene was upregulated as a result of induction by xylose substrates, whereas expression of the abfB gene was mainly induced by arabinose. Recombinant AxhA, AbfB, and AbfC exhibited different hydrolytic performances. AxhA showed the highest catalytic activity toward wheat arabinoxylan (WAX) and tended to hydrolyze monosubstituted arabinofuranose units, whereas AbfB had higher catalytic activity on AN and debranched arabinan (DAN), having the ability to cope with mono- and disubstituted arabinofuranose units. Furthermore, AbfC had greater arabinofuranosidase activity on p-nitrophenyl-α-l-arabinofuranoside (pNP-AraF) than on other substrates. Moreover, three Abfs displayed obvious synergistic action with GH11 xylanase XynB against WAX and barley husk residues. The elucidation of the degradation mechanisms of Abfs will lay a theoretical foundation for the efficient industrialized transformation of arabinoxylans.

Elucidating Sequence and Structural Determinants of Carbohydrate Esterases for Complete Deacetylation of Substituted Xylans

Acetylated glucuronoxylan is one of the most common types of hemicellulose in nature. The structure is formed by a β-(1→4)-linked D-xylopyranosyl (Xylp) backbone that can be substituted with an acetyl group at O-2 and O-3 positions, and α-(1→2)-linked 4-O-methylglucopyranosyluronic acid (MeGlcpA). Acetyl xylan esterases (AcXE) that target mono- or doubly acetylated Xylp are well characterized; however, the previously studied AcXE from Flavobacterium johnsoniae (FjoAcXE) was the first to remove the acetyl group from 2-O-MeGlcpA-3-O-acetyl-substituted Xylp units, yet structural characteristics of these enzymes remain unspecified. Here, six homologs of FjoAcXE were produced and three crystal structures of the enzymes were solved. Two of them are complex structures, one with bound MeGlcpA and another with acetate. All homologs were confirmed to release acetate from 2-O-MeGlcpA-3-O-acetyl-substituted xylan, and the crystal structures point to key structural elements that might serve as defining features of this unclassified carbohydrate esterase family. Enzymes comprised two domains: N-terminal CBM domain and a C-terminal SGNH domain. In FjoAcXE and all studied homologs, the sequence motif around the catalytic serine is Gly-Asn-Ser-Ile (GNSI), which differs from other SGNH hydrolases. Binding by the MeGlcpA-Xylp ligand is directed by positively charged and highly conserved residues at the interface of the CBM and SGNH domains of the enzyme.

Crucial Residues of C-Terminal Oligopeptide C60 to Improve the Yield of Prebiotic Xylooligosaccharides by Truncated Mutation

Increasing the yields of short xylooligosaccharides by enzymatic production is efficient to improve prebiotic effects. Previously, C-terminal oligopeptide C60 was found to accelerate short xylooligosaccharides. Herein, in order to further understand the molecular mechanism of C60, the sequence analysis firstly showed that C60 displays typical properties of a linker (rich in proline/alanine/glycine/glutamine/arginine, 8.33–20.00%). C60 shared the highest identity with the N-terminal region of esterase (98.33%) and high identity with the linker between xylanase and esterase from Prevotella sp. (56.50%), it is speculated to originate from an early linker between XynA and another domain. Besides, structure simulation showed that C60 enhances the molecular interactions between substrate and active residues to improve catalytic efficiency. Moreover, three truncated variants with different lengths of C-terminal regions were successfully generated in Escherichia coli. The specific activities of variants were 6.44–10.24 fold of that of XynA-Tr, and their optimal temperature and pH were the same as XynA-Tr. Three truncated variants released more xylooligosaccharides, especially xylobiose (46.33, 43.41, and 49.60%), than XynA-Tr (32.43%). These results are helpful to understand the molecular mechanism of C60, and also provide new insight to improve the yields of short xylooligosaccharides by molecular modification at the terminal of xylanases.

Acetylated xylan degradation by glycoside hydrolase family 10 and 11 xylanases from the white-rot fungus <i>Phanerochaete chrysosporium</i>

Endo-type xylanases are key enzymes in microbial xylanolytic systems, and xylanases belonging to glycoside hydrolase (GH) families 10 or 11 are the major enzymes degrading xylan in nature. These enzymes have typically been characterized using xylan prepared by alkaline extraction, which removes acetyl sidechains from the substrate, and thus the effect of acetyl groups on xylan degradation remains unclear. Here, we compare the ability of GH10 and 11 xylanases, PcXyn10A and PcXyn11B, from the white-rot basidiomycete Phanerochaete chrysosporium to degrade acetylated and deacetylated xylan from various plants. Product quantification revealed that PcXyn10A effectively degraded both acetylated xylan extracted from Arabidopsis thaliana and the deacetylated xylan obtained by alkaline treatment, generating xylooligosaccharides. In contrast, PcXyn11B showed limited activity towards acetyl xylan, but showed significantly increased activity after deacetylation of the xylan. Polysaccharide analysis using carbohydrate gel electrophoresis showed that PcXyn11B generated a broad range of products from native acetylated xylans extracted from birch wood and rice straw, including large residual xylooligosaccharides, while non-acetylated xylan from Japanese cedar was readily degraded into xylooligosaccharides. These results suggest that the degradability of native xylan by GH11 xylanases is highly dependent on the extent of acetyl group substitution. Analysis of 31 fungal genomes in the Carbohydrate-Active enZymes database indicated that the presence of GH11 xylanases is correlated to that of carbohydrate esterase (CE) family 1 acetyl xylan esterases (AXEs), while this is not the case for GH10 xylanases. These findings may imply co-evolution of GH11 xylanases and CE1 AXEs.

Hydrolysis of Arabinoxylo-oligosaccharides by α-L-Arabinofuranosidases and β-D-Xylosidase from Bifidobacterium dentium

Two α-L-arabinofuranosidases (BfdABF1 and BfdABF3) and a β-D-xylosidase (BfdXYL2) genes were cloned from Bifidobacterium dentium ATCC 27679, and functionally expressed in E. coli BL21(DE3). BfdABF1 showed the highest activity in 50 mM sodium acetate buffer at pH 5.0 and 25°C. This exo-enzyme could hydrolyze p-nitrophenyl arabinofuranoside, arabino-oligosaccharides (AOS), arabinoxylo-oligosaccharides (AXOS) such as 3²-α-L-arabinofuranosyl-xylobiose (A³X), and 2³-α-Larabinofuranosyl-xylotriose (A²XX), whereas hardly hydrolyzed polymeric substrates such as debranched arabinan and arabinoxylans. BfdABF1 is a typical exo-ABF with the higher specific activity on the oligomeric substrates than the polymers. It prefers to α-(1,2)-L-arabinofuranosidic linkages compared to α-(1,3)-linkages. Especially, BfdABF1 could slowly hydrolyze 2³,3³-di-α-L-arabinofuranosyl-xylotriose (A²⁺³XX). Meanwhile, BfdABF3 showed the highest activity in sodium acetate at pH 6.0 and 50°C, and it has the exclusively high activities on AXOS such as A³X and A²XX. BfdABF3 mainly catalyzes the removal of L-arabinose side chains from various AXOS. BfdXYL2 exhibited the highest activity in sodium citrate at pH 5.0 and 55°C, and it specifically hydrolyzed p-nitrophenyl xylopyranoside and xylo-oligosaccharides (XOS). Also, BfdXYL2 could slowly hydrolyze AOS and AXOS such as A³X. Based on the detailed hydrolytic modes of action of three exo-hydrolases (BfdABF1, BfdABF3, and BfdXYL2) from Bf. dentium, their probable roles in the hemiceulloseutilization system of Bf. dentium are proposed in the present study. These intracellular exo-hydrolases can synergistically produce L-arabinose and D-xylose from various AOS, XOS, and AXOS.

Metatranscriptome Profiling of a Specialized Microbial Consortium during the Degradation of Nixtamalized Maize Pericarp

Lignocellulose degradation by microbial consortia is multifactorial; hence, it must be analyzed from a holistic perspective. In this study, the temporal transcriptional activity of consortium PM-06, a nixtamalized maize pericarp (NMP) degrader, was determined and related to structural and physicochemical data to give insights into the mechanism used to degrade this substrate. Transcripts were described in terms of metabolic profile, carbohydrate-active enzyme (CAZyme) annotation, and taxonomic affiliation. The PM-06 gene expression pattern was closely related to the differential rates of degradation. The environmental and physiological conditions preceding high-degradation periods were crucial for CAZyme expression. The onset of degradation preceded the period with the highest degradation rate in the whole process, and in this time, several CAZymes were upregulated. Functional analysis of expressed CAZymes indicated that PM-06 overcomes NMP recalcitrance through modular enzymes operating at the proximity of the insoluble substrate. Increments in the diversity of expressed modular CAZymes occurred in the last stages of degradation where the substrate is more recalcitrant and environmental conditions are stressing. Taxonomic affiliation of CAZyme transcripts indicated that Paenibacillus macerans was fundamental for degradation. This microorganism established synergistic relationships with Bacillus thuringiensis for the degradation of cellulose and hemicellulose and with Microbacterium, Leifsonia, and Nocardia for the saccharification of oligosaccharides. IMPORTANCE Nixtamalized maize pericarp is an abundant residue of the tortilla industry. Consortium PM-06 efficiently degraded this substrate in 192 h. In this work, the temporal transcriptional profile of PM-06 was determined. Findings indicated that differential degradation rates are important sample selection criteria since they were closely related to the expression of carbohydrate-active enzymes (CAZymes). The initial times of degradation were crucial for the consumption of nixtamalized pericarp. A transcriptional profile at the onset of degradation is reported for the first time. Diverse CAZyme genes were rapidly transcribed after inoculation to produce different enzymes that participated in the stage with the highest degradation rate in the whole process. This study provides information about the regulation of gene expression and mechanisms used by PM-06 to overcome recalcitrance. These findings are useful in the design of processes and enzyme cocktails for the degradation of this abundant substrate.

Xylo-Oligosaccharide Utilization by Engineered Saccharomyces cerevisiae to Produce Ethanol

The engineering of xylo-oligosaccharide-consuming Saccharomyces cerevisiae strains is a promising approach for more effective utilization of lignocellulosic biomass and the development of economic industrial fermentation processes. Extending the sugar consumption range without catabolite repression by including the metabolism of oligomers instead of only monomers would significantly improve second-generation ethanol production This review focuses on different aspects of the action mechanisms of xylan-degrading enzymes from bacteria and fungi, and their insertion in S. cerevisiae strains to obtain microbial cell factories able of consume these complex sugars and convert them to ethanol. Emphasis is given to different strategies for ethanol production from both extracellular and intracellular xylo-oligosaccharide utilization by S. cerevisiae strains. The suitability of S. cerevisiae for ethanol production combined with its genetic tractability indicates that it can play an important role in xylan bioconversion through the heterologous expression of xylanases from other microorganisms.

Gut microbiome of the largest living rodent harbors unprecedented enzymatic systems to degrade plant polysaccharides

The largest living rodent, capybara, can efficiently depolymerize and utilize lignocellulosic biomass through microbial symbiotic mechanisms yet elusive. Herein, we elucidate the microbial community composition, enzymatic systems and metabolic pathways involved in the conversion of dietary fibers into short-chain fatty acids, a main energy source for the host. In this microbiota, the unconventional enzymatic machinery from Fibrobacteres seems to drive cellulose degradation, whereas a diverse set of carbohydrate-active enzymes from Bacteroidetes, organized in polysaccharide utilization loci, are accounted to tackle complex hemicelluloses typically found in gramineous and aquatic plants. Exploring the genetic potential of this community, we discover a glycoside hydrolase family of β-galactosidases (named as GH173), and a carbohydrate-binding module family (named as CBM89) involved in xylan binding that establishes an unprecedented three-dimensional fold among associated modules to carbohydrate-active enzymes. Together, these results demonstrate how the capybara gut microbiota orchestrates the depolymerization and utilization of plant fibers, representing an untapped reservoir of enzymatic mechanisms to overcome the lignocellulose recalcitrance, a central challenge toward a sustainable and bio-based economy.

Comparison of Glycoside Hydrolase family 3 β-xylosidases from basidiomycetes and ascomycetes reveals evolutionarily distinct xylan degradation systems

Xylan is the most common hemicellulose in plant cell walls, though the structure of xylan polymers differs between plant species. Here, to gain a better understanding of fungal xylan degradation systems, which can enhance enzymatic saccharification of plant cell walls in industrial processes, we conducted a comparative study of two glycoside hydrolase family 3 (GH3) β-xylosidases (Bxls), one from the basidiomycete Phanerochaete chrysosporium (PcBxl3), and the other from the ascomycete Trichoderma reesei (TrXyl3A). A comparison of the crystal structures of the two enzymes, both with saccharide bound at the catalytic center, provided insight into the basis of substrate binding at each subsite. PcBxl3 has a substrate-binding pocket at subsite -1, while TrXyl3A has an extra loop that contains additional binding subsites. Furthermore, kinetic experiments revealed that PcBxl3 degraded xylooligosaccharides faster than TrXyl3A, while the K_M values of TrXyl3A were lower than those of PcBxl3. The relationship between substrate specificity and degree of polymerization of substrates suggested that PcBxl3 preferentially degrades xylobiose (X₂), while TrXyl3A degrades longer xylooligosaccharides. Moreover, docking simulation supported the existence of extended positive subsites of TrXyl3A in the extra loop located at the N-terminus of the protein. Finally, phylogenetic analysis suggests that wood-decaying basidiomycetes use Bxls such as PcBxl3 that act efficiently on xylan structures from woody plants, whereas molds use instead Bxls that efficiently degrade xylan from grass. Our results provide added insights into fungal efficient xylan degradation systems.

Improved Release of Monosaccharides and Ferulic Acid Using Enzyme Blends From Aspergillus Niger and Eupenicillium Parvum

Supplementing commercial xylanase and cellulase with selected debranching enzymes only resulted in slight enhancement of the enzymatic hydrolysis of wheat bran autohydrolysis residues (WBAR) which was obtained at 160°C over a 30-min period of autohdyrolysis, while a blend of enzymes from Aspergillus niger and Eupenicillium parvum achieved synergistic efficacy in this context. Using an equal mixture blend of these enzymes at a 0.5% (w/w) enzyme loading dosage with the addition of ferulic acid esterase (1 U/g substrate), the obtained hydrolysis yields were desirable, including 84.98% of glucose, 84.74% of xylose, 80.24% of arabinose, and 80.86% of ferulic acid. Following further separation using an HP-20 resin, the final ferulic acid recovery levels were as high as 62.5% of the esterified ferulic acid present within the initial WBAR input. Together, these data suggest that a combination of autohydrolysis and enzymatic hydrolysis using crude enzyme blends can efficiently achieve wheat bran enzymatic saccharification and associated ferulic acid release.

Mass spectrometry imaging of oligosaccharides following in situ enzymatic treatment of maize kernels

In recent years enzymatic treatment of maize has been utilized in the wet-milling process to increase the yield of extracted starch, proteins, and other constituents. One of the strategies to obtain this goal is to add enzymes that break down insoluble cell-wall polysaccharides which would otherwise entrap starch granules. Due to the high complexity of maize polysaccharides, this goal is not easily achieved and more knowledge about the substrate and enzyme performances is needed. To gather information of both enzyme performance and increase substrate understanding, a method was developed using mass spectrometry imaging (MSI) to analyze degradation products from polysaccharides following enzymatic treatment of the maize endosperm. Different enzymes were spotted onto cryosections of maize kernels which had been pre-treated with an amylase to remove starch. The cryosections were then incubated for 17 h. before mass spectrometry images were generated with a MALDI-MSI setup. The images showed varying degradation products for the different enzymes observed as pentose oligosaccharides differing with regards to sidechains and the number of linked pentoses. The method proved suitable for identifying the reaction products formed after reaction with different xylanases and arabinofuranosidases and for characterization of the complex arabinoxylan substrate in the maize kernel. HYPOTHESES: Mass spectrometry imaging can be a useful analytical tool for obtaining information of polysaccharide constituents and enzyme performance from maize samples.

Paludibacter propionicigenes GH10 xylanase as a tool for enzymatic xylooligosaccharides production from heteroxylans

Bioconversion of lignocellulosic biomass into value-added products relies on polysaccharides depolymerization by carbohydrate active enzymes. This work reports biochemical characterization of Paludibacter propionicigenes xylanase from GH10 (PpXyn10A) and its application for enzymatic xylooligosaccharides (XOS) production from commercial heteroxylans and liquor of hydrothermally pretreated corn cobs (PCC). PpXyn10A is tolerant to ethanol and NaCl, and releases xylobiose (X2) and xylotriose (X3) as the main hydrolytic products. The conversion rate of complex substrates into short XOS was approximately 30% for glucuronoxylan and 8.8% for rye arabinoxylan, after only 4 h; while for PCC, PpXyn10A greatly increased unbranched XOS yields. B. adolescentis fermentation with XOS from beechwood glucuronoxylan produced mainly acetic and lactic acids. Structural analysis shows that while the glycone region of PpXyn10A active site is well preserved, the aglycone region has aromatic interactions in the +2 subsite that may explain why PpXyn10A does not release xylose.

Fungal xylanolytic enzymes: Diversity and applications

As important polysaccharide degraders in nature, fungi can diversify their extensive set of carbohydrate-active enzymes to survive in ecological habitats of various composition. Among these enzymes, xylanolytic ones can efficiently and sustainably degrade xylans into (fermentable) monosaccharides to produce valuable chemicals or fuels from, for example relevant for upgrading agro-food industrial side streams. Moreover, xylanolytic enzymes are being used in various industrial applications beyond biomass saccharification, e.g. food, animal feed, biofuel, pulp and paper. As a reference for researchers working in related areas, this review summarized the current knowledge on substrate specificity of xylanolytic enzymes from different families of the Carbohydrate-Active enZyme database. Additionally, the diversity of enzyme sets in fungi were discussed by comparing the number of genes encoding xylanolytic enzymes in selected fungal genomes. Finally, to support bio-economy, the current applications of fungal xylanolytic enzymes in industry were reviewed.

Functional characterization of a GH62 family α-L-arabinofuranosidase from Eupenicillium parvum suitable for monosaccharification of corncob arabinoxylan in combination with key enzymes

Corncob rich in arabinoxylan is an important raw material widely used in bio-refinery. Complete saccharification of arabinoxylan depends on the synergism of different enzymes including α-L-arabinofuranosidase (ABF). This study aimed to investigate the functional characteristics of a new ABF EpABF62A belonging to glycoside hydrolase (GH) 62 family from the fungus Eupenicillium parvum, and to explore its potential in the saccharification of corncob arabinoxylan. The recombinant EpABF62A showed high activity against wheat arabinoxylan and rye arabinoxylan, with the optimal temperature of 55 °C and pH of 4.5. The protein contains an N-terminal cellulose-binding domain family 1 (CBM_1) domain, and displayed a 59.5% absorption rate to phosphoric acid swollen cellulose. Regioselectivity analysis indicated that the enzyme selectively removed α-1,2 or α-1,3 linked arabinofuranosyl residues on mono-substituted xylose residues on arabinoxylan. Corncob arabinoxylans (CAX1 or CAX2) with different (low or high) branching degrees were extracted from the raw material by alkaline hydrogen peroxide pretreatment and graded ethanol precipitation. Single EpABF62A removed 69.5% or 67.1% arabinose from CAX1 or CAX2, respectively. EpABF62A combined with a GH10 xylanase, a GH43 β-D-xylosidase and a GH67 α-glucuronidase released 75.0% or 64.5% xylose from CAX1 or CAX2, respectively. The addition of the four hemicellulases enhanced the saccharification the solid fraction of the pretreated corncob by the commercial cellulase Cellic® CTec2, and the conversion ratios of glucose, xylose and arabinose were up to 94.0%, 91.8% and 82.6%, respectively.

Unique features of the bifunctional GH30 from Thermothelomyces thermophila revealed by structural and mutational studies

Fungal xylanases belonging to family GH30_7, initially categorized as endo-glucuronoxylanases, are now known to differ both in terms of substrate specificity, as well as mode of action. Recently, TtXyn30A, a GH30_7 xylanase from Thermothelomyces thermophila, was shown to possess dual activity, acting on the xylan backbone in both an endo- and an exo- manner. Here, in an effort to identify the structural characteristics that append these functional properties to the enzyme, we present the biochemical characterization of various TtXyn30A mutants as well as its crystal structure, alone, and in complex with the reaction product. An auxiliary catalytic amino acid has been identified, while it is also shown that glucuronic acid recognition is not mediated by a conserved arginine residue, as shown by previously determined GH30 structures.

Production of xylooligosaccharides, bioethanol, and lignin from structural components of barley straw pretreated with a steam explosion

Barley straw (BS) is a potential source to obtain bioethanol and value-added products such as xylooligosaccharides (XOS) and lignin for application in diverse industries. In this study, BS was submitted to steam explosion pretreatment to valorize the main components of this lignocellulose biomass. For hemicellulose fraction valorization, different combinations of endo-β-(1,4)-D-xylanase enzyme with accessory enzymes (α-L-arabinofuranosidase, feruloy -esterase and acetylxylan-esterase) have been studied to produce XOS with a low degree of polymerization. The application of accessory enzymes combined with endo-β-(1,4)-D-xylanase enzymes turned out to be the most effective strategy for the formation of XOS. The solid fraction obtained after the pretreatment was submitted to presacharification and simultaneous saccharification and fermentation process for bioethanol production. The resulting lignin-rich residue was characterized. In this integrated process, 13.0 g XOS (DP2-DP6), 12.6 g ethanol and 16.6 g lignin were obtained from 100 g of BS, achieving the goal of valorizing this agricultural residue.

Recent advances on key enzymatic activities for the utilisation of lignocellulosic biomass

The field of enzymatic degradation of lignocellulose is actively growing and the recent updates of the last few years indicate that there is still much to learn. The growing number of protein sequences with unknown function in microbial genomes indicates that there is still much to learn on the mechanisms of lignocellulose degradation. In this review, a summary of the progress in the field is presented, including recent discoveries on the nature of the structural polysaccharides, new technologies for the discovery and functional annotation of gene sequences including omics technologies, and the novel lignocellulose-acting enzymes described. Novel enzymatic activities and enzyme families as well as accessory enzymes and their synergistic relationships regarding biomass breakdown are described. Moreover, it is shown that all the valuable knowledge of the enzymatic decomposition of plant biomass polymers can be employed towards the decomposition and upgrading of synthetic polymers, such as plastics.

Unraveling Synergism between Various GH Family Xylanases and Debranching Enzymes during Hetero-Xylan Degradation

Enzymes classified with the same Enzyme Commission (EC) that are allotted in different glycoside hydrolase (GH) families can display different mechanisms of action and substrate specificities. Therefore, the combination of different enzyme classes may not yield synergism during biomass hydrolysis, as the GH family allocation of the enzymes influences their behavior. As a result, it is important to understand which GH family combinations are compatible to gain knowledge on how to efficiently depolymerize biomass into fermentable sugars. We evaluated GH10 (Xyn10D and XT6) and GH11 (XynA and Xyn2A) β-xylanase performance alone and in combination with various GH family α-l-arabinofuranosidases (GH43 AXH-d and GH51 Abf51A) and α-d-glucuronidases (GH4 Agu4B and GH67 AguA) during xylan depolymerization. No synergistic enhancement in reducing sugar, xylose and glucuronic acid released from beechwood xylan was observed when xylanases were supplemented with either one of the glucuronidases, except between Xyn2A and AguA (1.1-fold reducing sugar increase). However, overall sugar release was significantly improved (≥1.1-fold reducing sugar increase) when xylanases were supplemented with either one of the arabinofuranosidases during wheat arabinoxylan degradation. Synergism appeared to result from the xylanases liberating xylo-oligomers, which are the preferred substrates of the terminal arabinofuranosyl-substituent debranching enzyme, Abf51A, allowing the exolytic β-xylosidase, SXA, to have access to the generated unbranched xylo-oligomers. Here, it was shown that arabinofuranosidases are key enzymes in the efficient saccharification of hetero-xylan into xylose. This study demonstrated that consideration of GH family affiliations of the carbohydrate-active enzymes (CAZymes) used to formulate synergistic enzyme cocktails is crucial for achieving efficient biomass saccharification.

Contributions and characteristics of two bifunctional GH43 β-xylosidase /α-L-arabinofuranosidases with different structures on the xylan degradation of Paenibacillus physcomitrellae strain XB

Xylan is one of the major polymeric hemicellulosic constituents of lignocellulosic biomass, and its effective utilization by microorganisms is crucial for the economical production of biofuels. In this study, Paenibacillus physcomitrellae XB exhibited different xylan degradation ability on different substrates of corncob xylan (CCX), oat spelt xylan (OSX), wheat flour arabinoxylan (AX) and beech wood xylan (BWX). The RT-QPCR result showed that two genes (Pph_0602 and Pph_2344) belonging to the glycoside hydrolase family 43 were up-regulated more than 5-fold on CCX and xylose. Substrate-specific assays with purified proteins Ppxyl43A (Pph_0602) and Ppxyl43B (Pph_2344) revealed that both exhibited β-xylosidase activity toward the chromogenic substrate p-nitrophenyl-β-D-xylopyranoside, and α-L-arabinofuranosidase activity toward p-nitrophenyl-α-L-arabinofuranoside, indicating their bifunctionality. By testing their degradation characteristics on different natural substrates, it was found that both Ppxyl43A and Ppxyl43B showed similar degradation ability on CCX and OSX. Both enzymes could hydrolyze xylohexaose and xylobiose completely to xylose, but could not hydrolyze BWX and AX, suggesting they mainly hydrolyze xylo-oligosaccharides by β-xylosidase activity. Further analysis showed that both of them displayed very high pH stability and thermostability on the β-xylosidase activity, but Ppxy143B exhibited wider pH and temperature ranges, higher pH and temperature stability, was less influenced by metal ions, and had a slower start-up response than Ppxyl43A. Given their predicted structure, it is likely that the enzymatic differences between Ppxyl43A and Ppxyl43B might be related to the extra C-terminus domain (GH43_C2) in Ppxyl43B, which could enhance the enzymatic stability while restricting the substrates' or metal ions' access to the active sites of Ppxyl43B. In conclusion, both Ppxyl43A and Ppxyl43B were β-xylosidase/α-L-arabinofuranosidase bifunctional enzymes and might be useful in xylan biomass conversion, especially in the hydrolysis of xylo-oligosaccharides into xylose.

Enzymatic Fibre Modification During Production of Dissolving Wood Pulp for Regenerated Cellulosic Materials

The production of regenerated cellulosic fibres, such as viscose, modal and lyocell, is based mainly on the use of dissolving wood pulp as raw material. Enzymatic processes are an excellent alternative to conventional chemical routes in the production of dissolving pulp, in terms of energy efficiency, reagent consumption and pulp yield. The two main characteristics of a dissolving pulp are the cellulose purity and the molecular weight, both of which can be controlled with the aid of enzymes. A purification process for paper-grade kraft pulp has been proposed, based on the use of xylanases in combination with hot and cold caustic extraction, without the conventional pre-hydrolysis step before kraft pulping. This enzyme aided purification allowed the production of a dissolving pulp that met the specifications for the manufacture of viscose, < 3% xylan, > 92% ISO brightness and 70% Fock's reactivity. Endoglucanases (EGs) can efficiently reduce the average molecular weight of the cellulose while simultaneously increasing the pulp reactivity for viscose production. It is shown in this study that lytic polysaccharide monooxygenases act synergistically with EGs in the modification of bleached dissolving pulp.

A New Subfamily of Glycoside Hydrolase Family 30 with Strict Xylobiohydrolase Function

The Acetivibrio clariflavus (basonym: Clostridium clariflavum) glycoside hydrolase family 30 cellulosomal protein encoded by the Clocl_1795 gene was highly represented during growth on cellulosic substrates. In this report, the recombinantly expressed protein has been characterized and shown to be a non-reducing terminal (NRT)-specific xylobiohydrolase (AcXbh30A). Biochemical function, optimal biophysical parameters, and phylogeny were investigated. The findings indicate that AcXbh30A strictly cleaves xylobiose from the NRT up until an α-1,2-linked glucuronic acid (GA)-decorated xylose if the number of xyloses is even or otherwise a single xylose will remain resulting in a penultimate GA-substituted xylose. Unlike recently reported xylobiohydrolases, AcXbh30A has no other detectable hydrolysis products under our optimized reaction conditions. Sequence analysis indicates that AcXbh30A represents a new GH30 subfamily. This new xylobiohydrolase may be useful for commercial production of industrial quantities of xylobiose.

Recent advances in the enzymatic production and applications of xylooligosaccharides

The majority of lignocellulosic biomass on the planet originates from plant cell walls, which are complex structures build up mainly by cellulose, hemicellulose and lignin. The largest part of hemicellulose, xylan, is a polymer with a β-(1→4)-linked xylose residues backbone decorated with α-D-glucopyranosyl uronic acids and/or L-arabinofuranose residues. Xylan is the second most abundant biopolymer in nature, which can be sustainably and efficiently degraded into decorated and undecorated xylooligosaccharides (XOS) using combinations of thermochemical pretreatments and enzymatic hydrolyses, that have broad applications in the food, feed, pharmaceutical and cosmetic industries. Endo-xylanases from different complex carbohydrate-active enzyme (CAZyme) families can be used to cleave the backbone of arabino(glucurono)xylans and xylooligosaccharides and degrade them into short XOS. It has been shown that XOS with a low degree of polymerization have enhanced prebiotic effects conferring health benefits to humans and animals. In this review we describe recent advances in the enzymatic production of XOS from lignocellulosic biomass arabino- and glucuronoxylans and their applications as food and feed additives and health-promoting ingredients. Comparative advantages of xylanases from different CAZy families in XOS production are discussed and potential health benefits of different XOS are presented.

Hemicellulosic biomass conversion by Moroccan hot spring Bacillus paralicheniformis CCMM B940 evidenced by glycoside hydrolase activities and whole genome sequencing

Thermophilic bacteria, especially from the genus Bacillus, constitute a huge potential source of novel enzymes that could be relevant for biotechnological applications. In this work, we described the cellulose and hemicellulose-related enzymatic activities of the hot spring Bacillus aerius CCMM B940 from the Moroccan Coordinated Collections of Microorganisms (CCMM), and revealed its potential for hemicellulosic biomass utilization. Indeed, B940 was able to degrade complex polysaccharides such as xylan and lichenan and exhibited activity towards carboxymethylcellulose. The strain was also able to grow on agriculture waste such as orange and apple peels as the sole carbon source. Whole-genome sequencing allowed the reclassification of CCMM B940 previously known as B. aerius into Bacillus paralicheniformis since the former species name has been rejected. The draft genome reported here is composed of 38 contigs resulting in a genome of 4,315,004 bp and an average G + C content of 45.87%, and is an important resource for illuminating the molecular mechanisms of carbohydrate metabolism. The annotated genomic sequences evidenced more than 52 genes encoding glycoside hydrolases and pectate lyases belonging to 27 different families of CAZymes that are involved in the degradation of plant cell wall carbohydrates. Genomic predictions in addition to in vitro experiments have revealed broad hydrolytic capabilities of the strain, thus reinforcing its relevance for biotechnology applications.

Non-Specific GH30_7 Endo-β-1,4-xylanase from Talaromyces leycettanus

This study describes the catalytic properties of a GH30_7 xylanase produced by the fungus Talaromyces leycettanus. The enzyme is an ando-β-1,4-xylanase, showing similar specific activity towards glucuronoxylan, arabinoxylan, and rhodymenan (linear β-1,3-β-1,4-xylan). The heteroxylans are hydrolyzed to a mixture of linear as well as branched β-1,4-xylooligosaccharides that are shorter than the products generated by GH10 and GH11 xylanases. In the rhodymenan hydrolyzate, the linear β-1,4-xylooligosaccharides are accompanied with a series of mixed linkage homologues. Initial hydrolysis of glucuronoxylan resembles the action of other GH30_7 and GH30_8 glucuronoxylanases, resulting in a series of aldouronic acids of a general formula MeGlcA²Xyl_n. Due to the significant non-specific endoxylanase activity of the enzyme, these acidic products are further attacked in the unbranched regions, finally yielding MeGlcA²Xyl_2-3. The accommodation of a substituted xylosyl residue in the −2 subsite also applies in arabinoxylan depolymerization. Moreover, the xylose residue may be arabinosylated at both positions 2 and 3, without negatively affecting the main chain cleavage. The catalytic properties of the enzyme, particularly the great tolerance of the side-chain substituents, make the enzyme attractive for biotechnological applications. The enzyme is also another example of extraordinarily great catalytic diversity among eukaryotic GH30_7 xylanases.

Enzymatic upgrading of heteroxylans for added-value chemicals and polymers

Xylan is one of the most abundant, natural polysaccharides, and much recent interest focuses on upgrading heteroxylan to make use of its unique structures and chemistries. Significant progress has been made in the discovery and application of novel enzymes for debranching and modifying heteroxylans. Debranching enzymes include acetylxylan esterases, α-l-arabinofuranosidases and α-dglucuronidases that release side groups from the xylan backbone to recover both biochemicals and less substituted xylans for polymer applications in food packaging or drug delivery systems. Besides esterases and hydrolases, many oxidoreductases including carbohydrate oxidases, lytic polysaccharide monooxygenases, laccases and peroxidases have been also applied to alter different types of xylans for improved physical and chemical properties. This review will highlight the recent discovery and application of enzymes for upgrading xylans for use as added-value chemicals and in functional polymers.

Characterization of Two α-l-Arabinofuranosidases from Acetivibrio mesophilus and Their Synergistic Effect in Degradation of Arabinose-Containing Substrates

Arabinofuranosidases are important accessory enzymes involved in the degradation of arabinose-containing poly- and oligosaccharides. Two arabinofuranosidases from the recently described novel anaerobic cellulolytic bacterium Acetivibrio mesophilus, designated AmAraf51 and AmAraf43, were heterologously expressed in Escherichia coli and biochemically characterized. AmAraf51 not only removed arabinose moieties at O-3, O-2 and terminal O-5 positions of arabinose-containing oligosaccharides, but also exhibited exo-β-xylosidase side activity. In comparison, AmAraf43 preferably cleaved 1,3-linkages from arabinosyl disubstitutions. AmAraf51 and AmAraf43 demonstrated maximum activity at 70 °C and 57 °C, respectively. Judging from the genetic context and substrate specificity, AmAraf51 may decompose internalized arabino/xylo-oligosaccharides. The embedding of the AmAraf43 gene between genes for several putative xylanolytic enzymes, along with its enzymatic properties suggests that AmAraf43 cleaves arabinose decorations from heteroxylans extracellularly. The enzymes revealed completely converse activity profiles towards arabinan/arabinoxylan: AmAraf51 displayed strong activity on arabinan, while AmAraf43 prefers arabinoxylan. AmAraf51 dramatically stimulated the saccharification level of wheat arabinoxylan (WAX-RS) and sugar beet arabinan when administered along with xylanase M_Xyn10 or arabinanase PpAbn43, respectively. For WAX-RS degradation, the yield of arabinose and xylose was boosted 13.77-fold and 4.96-fold, respectively. The bifunctional activity, thermostability and high catalytic efficiency make AmAraf51 an interesting candidate for industrial applications.

Characterization and Phylogenetic Analysis of a Novel GH43 β-Xylosidase From Neocallimastix californiae

Degradation of lignocellulosic materials to release fermentable mono- and disaccharides is a decisive step toward a sustainable bio-based economy, thereby increasing the demand of robust and highly active lignocellulolytic enzymes. Anaerobic fungi of the phylum Neocallimastigomycota are potent biomass degraders harboring a huge variety of such enzymes. Compared to cellulose, hemicellulose degradation has received much less attention; therefore, the focus of this study has been the enzymatic xylan degradation of anaerobic fungi as these organisms produce some of the most effective known hydrolytic enzymes. We report the heterologous expression of a GH43 xylosidase, Xyl43Nc, and a GH11 endoxylanase, X11Nc, from the anaerobic fungus Neocallimastix californiae in Escherichia coli. The enzymes were identified by screening of the putative proteome. Xyl43Nc was highly active against 4-Nitrophenol-xylopyranosides with a Km of 0.72 mM, a kcat of 29.28 s-1, a temperature optimum of 32°C and a pH optimum of 6. When combined, Xyl43Nc and X11Nc released xylose from beechwood xylan and arabinoxylan from wheat. Phylogenetic analysis revealed that Xyl43Nc shares common ancestry with enzymes from Spirochaetes and groups separately from Ascomycete sequences in our phylogeny, highlighting the importance of horizontal gene transfer in the evolution of the anaerobic fungi.

Unlocking the structural features for the xylobiohydrolase activity of an unusual GH11 member identified in a compost-derived consortium

The heteropolysaccharide xylan is a valuable source of sustainable chemicals and materials from renewable biomass sources. A complete hydrolysis of this major hemicellulose component requires a diverse set of enzymes including endo-β-1,4-xylanases, β-xylosidases, acetylxylan esterases, α-l-arabinofuranosidases, and α-glucuronidases. Notably, the most studied xylanases from glycoside hydrolase family 11 (GH11) have exclusively been endo-β-1,4- and β-1,3-xylanases. However, a recent analysis of a metatranscriptome library from a microbial lignocellulose community revealed GH11 enzymes capable of releasing solely xylobiose from xylan. Although initial biochemical studies clearly indicated their xylobiohydrolase mode of action, the structural features that drive this new activity still remained unclear. It was also not clear whether the enzymes acted on the reducing or nonreducing end of the substrate. Here, we solved the crystal structure of MetXyn11 in the apo and xylobiose-bound forms. The structure of MetXyn11 revealed the molecular features that explain the observed pattern on xylooligosaccharides released by this nonreducing end xylobiohydrolase.

ANALYSIS OF CARBOHYDRATES AND GLYCOCONJUGATES BY MATRIX-ASSISTED LASER DESORPTION/IONIZATION MASS SPECTROMETRY: AN UPDATE FOR 2015-2016

This review is the ninth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2016. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented over 30 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show no sign of deminishing. © 2020 Wiley Periodicals, Inc.

Identification and spatio-temporal expression analysis of barley genes that encode putative modular xylanolytic enzymes

Arabinoxylans are cell wall polysaccharides whose re-modelling and degradation during plant development are mediated by several classes of xylanolytic enzymes. Here, we present the identification and new annotation of twelve putative (1,4)-β-xylanase and six β-xylosidase genes, and their spatio-temporal expression patterns during vegetative and reproductive growth of barley (Hordeum vulgare cv. Navigator). The encoded xylanase proteins are all predicted to contain a conserved carbohydrate-binding module (CBM) and a catalytic glycoside hydrolase (GH) 10 domain. Additional domains in some xylanases define three discrete phylogenetic clades: one clade contains proteins with an additional N-terminal signal sequence, while another clade contains proteins with multiple CBMs. Homology modelling revealed that all fifteen xylanases likely contain a third domain, a β-sandwich folded from two non-contiguous sequence segments that bracket the catalytic GH domain, which may explain why the full length protein is required for correct folding of the active enzyme. Similarly, predicted xylosidase proteins share a highly conserved domain structure, each with an N-terminal signal peptide, a split GH 3 domain, and a C-terminal fibronectin-like domain. Several genes appear to be ubiquitously expressed during barley growth and development, while four newly annotated xylanase and xylosidase genes are expressed at extremely high levels, which may be of broader interest for industrial applications where cell wall degradation is necessary.

The Effect of a Modified GH11 Xylanase on Live Performance, Gut Health, and Clostridium perfringens Excretion of Broilers Fed Corn-Soy Diets

Xylanase enzymes and other feed additives are being used more commonly in poultry feed to reduce feed cost, improve performance, and maintain gut health. Five corn-soy-based dietary treatments were designed to compare the effect of different inclusion levels of high-efficiency GH11 xylanase on live performance, gut lesions, and Clostridium perfringens excretion in littler samples of broiler chickens. Diets were the standard diet (positive control; PC); a diet of reduced energy by 130 kcal/kg diet (negative control; NC); NC with xylanase at 10 XU/g of feed (NC + 10); NC with xylanase at 12.5 XU/g of feed (NC + 12.5); NC with xylanase at 15 XU/g of feed (NC + 15). Data were analyzed with one-way ANOVA. At 42 d, birds fed NC + 12.5 and NC + 15 were heavier (P < 0.05) than NC and comparable improvement to birds fed PC. Significant Improvement in FCR (P = 0.0001) was observed from 1 to 42 d for NC + 12.5 and NC + 15 compared with NC. Supplementation of xylanase reduced (P < 0.005) 21 d intestinal lesion score at 21 d with further improvement (P < 0.0001) at 42 d. NC + 15 reduced lesion scores by 24% compared with NC. Xylanase supplementations reduced litter C. perfringens cell forming unit per gram (CFU/g) compared with NC with the highest reduction of NC + 15 treatment by ~27%. In conclusion, xylanase can be included in reduced-energy diets up to 15 XU/g of feed to improve live performance, energy digestibility, and reduce intestinal lesion scores in broilers.

Polysaccharide utilization loci-driven enzyme discovery reveals BD-FAE: a bifunctional feruloyl and acetyl xylan esterase active on complex natural xylans

BACKGROUND

Nowadays there is a strong trend towards a circular economy using lignocellulosic biowaste for the production of biofuels and other bio-based products. The use of enzymes at several stages of the production process (e.g., saccharification) can offer a sustainable route due to avoidance of harsh chemicals and high temperatures. For novel enzyme discovery, physically linked gene clusters targeting carbohydrate degradation in bacteria, polysaccharide utilization loci (PULs), are recognized 'treasure troves' in the era of exponentially growing numbers of sequenced genomes.

RESULTS

We determined the biochemical properties and structure of a protein of unknown function (PUF) encoded within PULs of metagenomes from beaver droppings and moose rumen enriched on poplar hydrolysate. The corresponding novel bifunctional carbohydrate esterase (CE), now named BD-FAE, displayed feruloyl esterase (FAE) and acetyl esterase activity on simple, synthetic substrates. Whereas acetyl xylan esterase (AcXE) activity was detected on acetylated glucuronoxylan from birchwood, only FAE activity was observed on acetylated and feruloylated xylooligosaccharides from corn fiber. The genomic contexts of 200 homologs of BD-FAE revealed that the 33 closest homologs appear in PULs likely involved in xylan breakdown, while the more distant homologs were found either in alginate-targeting PULs or else outside PUL contexts. Although the BD-FAE structure adopts a typical α/β-hydrolase fold with a catalytic triad (Ser-Asp-His), it is distinct from other biochemically characterized CEs.

CONCLUSIONS

The bifunctional CE, BD-FAE, represents a new candidate for biomass processing given its capacity to remove ferulic acid and acetic acid from natural corn and birchwood xylan substrates, respectively. Its detailed biochemical characterization and solved crystal structure add to the toolbox of enzymes for biomass valorization as well as structural information to inform the classification of new CEs.

A novel fungal metal-dependent α-L-arabinofuranosidase of family 54 glycoside hydrolase shows expanded substrate specificity

Trichoderma genus fungi present great potential for the production of carbohydrate-active enzymes (CAZYmes), including glycoside hydrolase (GH) family members. From a renewability perspective, CAZYmes can be biotechnologically exploited to convert plant biomass into free sugars for the production of advanced biofuels and other high-value chemicals. GH54 is an attractive enzyme family for biotechnological applications because many GH54 enzymes are bifunctional. Thus, GH54 enzymes are interesting targets in the search for new enzymes for use in industrial processes such as plant biomass conversion. Herein, a novel metal-dependent GH54 arabinofuranosidase (ThABF) from the cellulolytic fungus Trichoderma harzianum was identified and biochemically characterized. Initial in silico searches were performed to identify the GH54 sequence. Next, the gene was cloned and heterologously overexpressed in Escherichia coli. The recombinant protein was purified, and the enzyme's biochemical and biophysical properties were assessed. GH54 members show wide functional diversity and specifically remove plant cell substitutions including arabinose and galactose in the presence of a metallic cofactor. Plant cell wall substitution has a major impact on lignocellulosic substrate conversion into high-value chemicals. These results expand the known functional diversity of the GH54 family, showing the potential of a novel arabinofuranosidase for plant biomass degradation.

Significantly improving the thermostability of a hyperthermophilic GH10 family xylanase XynAF1 by semi-rational design

Xylanases have a broad range of applications in industrial biotechnologies, which require the enzymes to resist the high-temperature environments. The majority of xylanases have maximum activity at moderate temperatures, which limited their potential applications in industries. In this study, a thermophilic GH10 family xylanase XynAF1 from the high-temperature composting strain Aspergillus fumigatus Z5 was characterized and engineered to further improve its thermostability. XynAF1 has the optimal reaction temperature of 90 °C. The crystal structure of XynAF1 was obtained by X-ray diffraction after heterologous expression, purification, and crystallization. The high-resolution X-ray crystallographic structure of the protein-product complex was obtained by soaking the apo-state crystal with xylotetraose. Structure analysis indicated that XynAF1 has a rigid skeleton, which helps to maintain the hyperthermophilic characteristic. The homologous structure analysis and the catalytic center mutant construction of XynAF1 indicated the conserved catalytic center contributed to the high optimum catalytic temperature. The amino acids in the surface of xylanase XynAF1 which might influence the enzyme thermostability were identified by the structure analysis. Combining the rational design with the saturation mutation at the high B-value regions, the integrative mutant XynAF1-AC with a 6-fold increase of thermostability was finally obtained. This study efficiently improved the thermostability of a GH10 family xylanase by semi-rational design, which provided a new biocatalyst for high-temperature biotechnological applications. KEY POINTS: • Obtained the crystal structure of GH10 family hyperthermophilic xylanase XynAF1. • Shed light on the understanding of the GH10 family xylanase thermophilic mechanism. • Constructed a 6-fold increased thermostability recombinant xylanase.

Microbial lipid production from crude glycerol and hemicellulosic hydrolysate with oleaginous yeasts

BACKGROUND

Crude glycerol (CG) and hemicellulose hydrolysate (HH) are low-value side-products of biodiesel transesterification and pulp-and paper industry or lignocellulosic ethanol production, respectively, which can be converted to microbial lipids by oleaginous yeasts. This study aimed to test the ability of oleaginous yeasts to utilise CG and HH and mixtures of them as carbon source.

RESULTS

Eleven out of 27 tested strains of oleaginous yeast species were able to grow in plate tests on CG as sole carbon source. Among them, only one ascomycetous strain, belonging to Lipomyces starkeyi, was identified, the other 10 strains were Rhodotorula spec. When yeasts were cultivated in mixed CG/ HH medium, we observed an activation of glycerol conversion in the Rhodotorula strains, but not in L. starkeyi. Two strains-Rhodotorula toruloides CBS 14 and Rhodotorula glutinis CBS 3044 were further tested in controlled fermentations in bioreactors in different mixtures of CG and HH. The highest measured average biomass and lipid concentration were achieved with R. toruloides in 10% HH medium mixed with 55 g/L CG-19.4 g/L and 10.6 g/L, respectively, with a lipid yield of 0.25 g lipids per consumed g of carbon source. Fatty acid composition was similar to other R. toruloides strains and comparable to that of vegetable oils.

CONCLUSIONS

There were big strain differences in the ability to convert CG to lipids, as only few of the tested strains were able to grow. Lipid production rates and yields showed that mixing GC and HH have a stimulating effect on lipid accumulation in R. toruloides and R. glutinis resulting in shortened fermentation time to reach maximum lipid concentration, which provides a new perspective on converting these low-value compounds to microbial lipids.

Biochemical and Biotechnological Studies on Xylanase and β‐xylosidase Enzymes Produced by Trichoderma viride Under Solid State Fermentation

The current study concerns with enhancement of xylanase and β-xylosidase activities from lignocellulosic materials by soil derived fungi Trichoderma viride under solid state fermentation (SSF). Xylanase and β-xylosidase activities were found to affected by variety of factors. In this study, some agricultural wastes were selected and used as sources for carbon. Sugar beet pulp (SBP) was at the forefront of these types. Also, various sources for nitrogen were selected to determine the best one. Yeast extract was the best organic source. Maximum xylanase activity took place by using inoculum size 1.8 × 105 spores / ml at 30°C when the pH was 5.5 for eight days of incubation with the addition of 0.1 % of Tween 40. Moreover, spores of Trichoderma viride were irradiated with gamma–rays. The maximum activity was observed upon using 0.7 kilo-gray (kGy). Furthermore, mixed cultures of Trichoderma viride and Penicillium janthenellum (wt / wt) were enhanced xylanase degrading capability. From another standpoint, ammonium sulphate and gel filtration chromatography were the best methods for xylanase purification. Characterizations of the purified enzyme were also selected and studied. It was found that, β-xylosidase enzyme exhibited its maximum activity and stability when the pH was 6 at 40°C by the addition of CaCl2 metal ion. On the other hand, total protein contents and volatile constituents of Trichoderma viride and Penicillium janthenellum were separated and investigated using high performance liquid chromatography (HPLC) and gas chromatography/mass spectrometry (GC/MS) techniques. It was found that, total protein contents for Trichoderma viride and Penicillium janthenellum were represented by fifteen and sixteen amino acids respectively. Also,29 compounds of the total volatile compounds for both Trichoderma viride and Penicillium janthenellum were identified. On the practical and applied field, crude enzyme was a good analyzer for agricultural residues as well showed antifungal and antibacterial effects.

Xylan Decomposition in Plant Cell Walls as an Inducer of Surfactin Synthesis by Bacillus subtilis

Hemicellulose is the second most abundant plant heterogenous biopolymer. Among products obtained from a wide range of agro-residues, biosurfactants, e.g., surfactin (SU), are gaining increasing interest. Our previous studies have shown that a Bacillus subtilis strain can successfully produce a significant amount of SU using a rapeseed cake. This work aimed to investigate plant hemicellulose components as substrates promoting SU's efficient production by B. subtilis 87Y. Analyses of SU production, enzymatic activity and cell wall composition of hulled oat caryopses suggest that the main ingredients of plant hemicellulose, in particular xylan and its derivatives, may be responsible for an increased biosurfactant yield.

Debranching enzymes in corn/soybean meal-based poultry feeds: a review

This review discusses the complex nature of the primary nonstarch polysaccharide (NSP) in corn with respect to the merit of debranching enzymes. Celluloses, hemicelluloses, and pectins comprise the 3 major categories of NSP that make up nearly 90% of plant cell walls. Across cereals, the hemicellulose arabinoxylan exists as the primary NSP, followed by cellulose, glucans, and others. Differences in arabinoxylan structure among cereals and cereal fractions are facilitated by cereal type, degree and pattern of substitution along the xylan backbone, phenol content, and cross-linkages. In particular, arabinoxylan (also called glucuronoarabinoxylan) in corn is heavily fortified with substituents, being more populated than in wheat and other cereal grains. Feed-grade xylanases - almost solely of the glycoside hydrolase (GH) 10 and GH 11 families - require at least 2 or 3 contiguous xylose units to be free of attachments to effectively attack the xylan chain. This canopy of attachments, along with a high phenol content and the insoluble nature of corn glucuronoarabinoxylan, confers a significant resistance to xylanase attack. Both in vitro and in vivo studies demonstrate that debranching enzymes appreciably increase xylanase access and fiber degradability by removing these attachments and breaking phenolic linkages. The enzymatic degradation of the highly branched arabinoxylan can facilitate disassembly of other fibers by increasing exposure to pertinent carbohydrases. For cereals, the arabinofuranosidases, α-glucuronidases, and esterases are some of the more germane debranching enzymes. Enzyme composites beyond the simple core mixes of xylanases, cellulases, and glucanases can exploit synergistic benefits generated by this class of enzymes. A broad scope of enzymatic activity in customized mixes can more effectively target the resilient NSP construct of cereal grains in commercial poultry diets, particularly those in corn-based feeds.

Plant cell wall architecture guided design of CBM3-GH11 chimeras with enhanced xylanase activity using a tandem repeat left-handed β-3-prism scaffold

Effective use of plant biomass as an abundant and renewable feedstock for biofuel production and biorefinery requires efficient enzymatic mobilization of cell wall polymers. Knowledge of plant cell wall composition and architecture has been exploited to develop novel multifunctional enzymes with improved activity against lignocellulose, where a left-handed β-3-prism synthetic scaffold (BeSS) was designed for insertion of multiple protein domains at the prism vertices. This allowed construction of a series of chimeras fusing variable numbers of a GH11 β-endo-1,4-xylanase and the CipA-CBM3 with defined distances and constrained relative orientations between catalytic domains. The cellulose binding and endoxylanase activities of all chimeras were maintained. Activity against lignocellulose substrates revealed a rapid 1.6- to 3-fold increase in total reducing saccharide release and increased levels of all major oligosaccharides as measured by polysaccharide analysis using carbohydrate gel electrophoresis (PACE). A construct with CBM3 and GH11 domains inserted in the same prism vertex showed highest activity, demonstrating interdomain geometry rather than number of catalytic sites is important for optimized chimera design. These results confirm that the BeSS concept is robust and can be successfully applied to the construction of multifunctional chimeras, which expands the possibilities for knowledge-based protein design.