Search Results (29)

Sorghum (Sorghum bicolor) is an essential bioenergy crop. Cellulosic and non-cellulosic polysaccharides, which can be transformed into biofuels, comprise most of its biomass. Many glycosyltransferases (GT) families, including GT43, are involved in the biosynthesis of xylan in plants’ primary and secondary cells. In this study, the GT43 gene family was identified, and its secondary structure and a three-dimensional (3D) model were constructed. Additionally, subcellular localization, detection of motifs, and analyses of its phylogenetic tree, physiochemical properties, protein–protein interaction network, gene structure, functional domain, gene duplication, Cis-acting elements, sequence logos, multiple sequence alignment, and gene expression profiles were performed based on RNA-sequence analyses. As a result, eleven members of the GT43 gene family were identified, and the phylogenetic tree of the GT43 gene family showed that all GT43 genes had evolutionary relationships with sorghum. Analyses of gene structure, motifs, sequence logos, and multiple sequence alignment showed that all members of the GT43 protein family were highly conserved. Subcellular localization showed all members of the GT43 protein family were localized in different compartments of sorghum. The secondary structure of the GT43 genes comprised different percentages of α-helices, random coils, β-turns, and extended strands. The tertiary structure model showed that all GT43 proteins had similar 3D structures. The results of the current study indicated that members of the GT43 gene family (Sobic.010G238800, Sobic.003G254700, and Sobic.001G409100) were highly expressed in internodes of the sorghum plant, based on RNA-Sequencing. The framework used in this study will be valuable for advancing research aligned with modern technology requirements and for enhancing understanding of the relationships among GT43 genes in Sorghum bicolor. Full article

This study was aimed at extracting, characterizing, and exploring the detoxification activity of the peptide-containing polysaccharide from Agaricus balchaschensis. An anion adsorption fraction was acquired through hot water extraction. Its structure was analyzed, and the potential protective effect against cadmium-intoxicated mice was explored. Structural analysis revealed that the principal component of the peptide-containing polysaccharide of A. balchaschensis (ABPCP) is polysaccharide, which consists of glucose, mannose, galactose, and xylose, containing (1 → 4)-linked α-D-glucan, (1 → 3)-linked β-D-Glcp, (1 → 4)-linked β-D-Glcp, (1 → 6)-linked β-D-Glcp, (1 → 6)-linked β-D-Manp, (1 → 3)-linked β-D-Galp, (1 → 6)-linked β-D-Galp, and (1 → 4)-linked β-D-xylan. The amino acid content of ABPCP is 11.747 mg/g. Threonine, serine, glutamate, glycine, alanine, cysteine, valine, methionine, lysine, and arginine were detected in ABPCP, among which the content of glutamate was the highest. The alleviating effect of ABPCP on cadmium poisoning in mice was investigated. ABPCP significantly reduced the cadmium content in serum and the heart, kidneys, and liver, which indicates that ABPCP could promote cadmium discharge. ABPCP also significantly decreased serum nitric oxide, endothelin-1, urea, uric acid, and serum creatinine, alleviating kidney and liver damage caused by cadmium. All these results manifest that ABPCP can lower the cadmium content in organs and alleviate the damage to kidneys and livers damaged by Cd. Full article

Lignin, a natural pol2ymer with a complex structure that is difficult to separate, is prone to C-C bond condensation during the separation process. To reduce the condensation of lignin, here, a novel method is proposed for separating the components by using a combination of maleic acid (MA)/ozone (O₃) to co-treat wheat straw. The removal of lignin, glucan, and xylan was 38.07 ± 0.2%, 31.44 ± 0.1%, and 71.98 ± 0.1%, respectively, under the conditions of ball-milling of wheat straw for 6 h, reaction temperature of 60 °C, and O₃ holding time of 9 min. Lignin-rich solutions were collected to extract the dissolved lignin (DL) after washing the treated samples. The DL obtained under MA/O₃ conditions had a carboxyl group (-COOH) content of 2.96 mmol/g. The carboxyl group of MA underwent esterification with the hydroxyl group (-OH) at the γ position of lignin and O₃ reacted on the positions of the lignin side chain or the phenolic ring, resulting in a break in the side chain and the opening of the phenolic ring to introduce the carboxyl group. The 2D-HSQC-NMR results revealed that the phenolic ring-opening reaction of lignin in the presence of O₃ was essentially free of β-β and β-5 condensation bonds. Full article

The endo-β-1,4-xylanase glycosyl hydrolase (GH11) decomposes the backbone of xylan into xylooligosaccharides or xylose. These enzymes are important for industrial applications in the production of biofuel, feed, food, and value-added materials. β-D-xylopyranose (XYP, also known as β-D-xylose) is the fundamental unit of the substrate xylan, and understanding its recognition is fundamental for the initial steps of GH11’s molecular mechanism. However, little is known about the recognition of a single XYP molecule by GH11. In this study, the crystal structures of GH11 from Thermoanaerobacterium saccharolyticum (TsaGH11) complexed with an XYP molecule were determined at a resolution of 1.7–1.9 Å. The XYP molecule binds to subsite −2 of the substrate-binding cleft. The XYP molecule is mainly stabilized by a π–π interaction with the conserved Trp36 residue. The O2 and O3 atoms of XYP are stabilized by hydrogen bond interactions with the hydroxyl groups of Tyr96 and Tyr192. The conformation of the thumb domain of TsaGH11 does not play a critical role in XYP binding, and XYP binding induces a shift in the thumb domain of TsaGH11 toward the XYP molecule. A structural comparison of TsaGH11 with other GH11 xylanases revealed that the XYP molecule forms π–π stacking with the center between the phenyl and indoline ring of Trp36, whereas the XYP molecule unit from xylobiose or xylotetraose forms π–π stacking with the indoline of Trp36, which indicates that the binding modes of the substrate and XYP differ. These structural results provide a greater understanding of the recognition of XYP by the GH11 family. Full article

This study aims to utilize the microbial resources found within Laphet-so, a traditional fermented tea in Myanmar. A total of 18 isolates of thermotolerant yeasts were obtained from eight samples of Laphet-so collected from southern Shan state, Myanmar. All isolates demonstrated the tannin tolerance, and six isolates were resistant to 5% (w/v) tannin concentration. All 18 isolates were capable of carboxy-methyl cellulose (CMC) degrading, but only the isolate DK showed ethanol production at 45 °C noticed by gas formation. This ethanol producing yeast was identified to be Cyberlindnera rhodanensis based on the sequence analysis of the D1/D2 domain on rRNA gene. C. rhodanensis DK produced 1.70 ± 0.01 U of thermostable extracellular β-glucosidase when cultured at 37 °C for 24 h using 0.5% (w/v) CMC as a carbon source. The best two carbon sources for extracellular β-glucosidase production were found to be either xylose or xylan, with β-glucosidase activity of 3.07–3.08 U/mL when the yeast was cultivated in the yeast malt extract (YM) broth containing either 1% (w/v) xylose or xylan as a sole carbon source at 37 °C for 48 h. The optimal medium compositions for enzyme production predicted by Plackett–Burman design and central composite design (CCD) was composed of yeast extract 5.83 g/L, peptone 10.81 g/L and xylose 20.20 g/L, resulting in a production of 7.96 U/mL, while the medium composed (g/L) of yeast extract 5.79, peptone 13.68 and xylan 20.16 gave 9.45 ± 0.03 U/mL for 48 h cultivation at 37 °C. Crude β-glucosidase exhibited a remarkable stability of 100%, 88% and 75% stable for 3 h at 35, 45 and 55 °C, respectively. Full article

Lignocellulose, the most abundant and renewable plant resource, is a complex of polymers mainly composed of polysaccharides (cellulose and hemicelluloses) and an aromatic polymer (lignin). Utilisation of lignocellulosic biomass for biotechnological applications has increased over the past few years. Xylan is the second most abundant carbohydrate in plant cell walls, and structurally, it is a heteropolysaccharide with a backbone composed of β-1,4-d-xylopyranosyl units connected with glycosidic bonds. Xylanases degrade this complex structure of xylan and can be produced by various microorganisms, including fungi, bacteria, and yeasts. Lignocellulosic biomass is the most economical substrate for the production of fungal xylanases. The bioconversion of lignocellulosic biomass to industrially important products, i.e., xylooligosaccharides and biofuels, is possible via the application of xylanases. These enzymes also play a key role in enhancing the nutrition of food and feed and the bio-bleaching of paper and kraft pulp. However, the demand for more potent and efficient xylanases with high activity has increased, which is fulfilled by involving recombinant DNA technology. Hence, in this review, we thoroughly discussed the biotechnological potential of lignocellulosic biomass for the production of fungal xylanases, their purification, molecular strategies for improving their efficiency, and their utilisation for the production of valuable products and in other industrial processes. Full article

The regulation of plant biomass degradation by fungi is critical to the carbon cycle, and applications in bioproducts and biocontrol. Trichoderma harzianum is an important plant biomass degrader, enzyme producer, and biocontrol agent, but few putative major transcriptional regulators have been deleted in this species. The T. harzianum ortholog of the transcriptional activator XYR1/XlnR/XLR-1 was deleted, and the mutant strains were analyzed through growth profiling, enzymatic activities, and transcriptomics on cellulose. From plate cultures, the Δxyr1 mutant had reduced growth on D-xylose, xylan, and cellulose, and from shake-flask cultures with cellulose, the Δxyr1 mutant had ~90% lower β-glucosidase activity, and no detectable β-xylosidase or cellulase activity. The comparison of the transcriptomes from 18 h shake-flask cultures on D-fructose, without a carbon source, and cellulose, showed major effects of XYR1 deletion whereby the Δxyr1 mutant on cellulose was transcriptionally most similar to the cultures without a carbon source. The cellulose induced 43 plant biomass-degrading CAZymes including xylanases as well as cellulases, and most of these had massively lower expression in the Δxyr1 mutant. The expression of a subset of carbon catabolic enzymes, other transcription factors, and sugar transporters was also lower in the Δxyr1 mutant on cellulose. In summary, T. harzianum XYR1 is the master regulator of cellulases and xylanases, as well as regulating carbon catabolic enzymes. Full article

β-xylosidases (4-β-d-xylan xylohydrolase, E.C. 3.2.1.37) are glycoside hydrolases (GH) catalyzing the hydrolysis of (1→4)-β-d-xylans, allowing for the removal of β-d-xylose residues from its non-reducing termini. Together with other xylan-degrading enzymes, β-xylosidases are involved in the enzymatic hydrolysis of lignocellulosic biomass, making them highly valuable in the biotechnological field. Whereas different GH families are deeply characterized from a structural point of view, the GH52 family has been barely described. In this work, we report the 2.25 Å resolution structure of Geobacillus stearothermophilus CECT43 XynB2, providing the second structural characterization for this GH family. A plausible dynamic loop closing the entrance of the catalytic cleft is proposed based on the comparison of the available GH52 structures, suggesting the relevance of a dimeric structure for members of this family. The glycone specificity at the −1 site for GH52 and GH116 members is also explained by our structural studies. Full article

Endoglucanases (EC 3.2.1.4) are important enzymes involved in the hydrolysis of cellulose, acting randomly in the β-1,4-glycosidic bonds present in the amorphous regions of the polysaccharide chain. These biocatalysts have been classified into 14 glycosyl hydrolase (GH) families. The GH7 family is of particular interest since it may act on a broad range of substrates, including cellulose, β-glucan, and xylan, an attractive feature for biotechnological applications, especially in the renewable energy field. In the current work, a gene from the thermophilic fungus Thermothielavioides terrestris, encoding an endoglucanase GH7 (TtCel7B), was cloned in the secretion vector pEXPYR and transformed into the high-protein-producing strain Aspergillus nidulans A773. Purified TtCel7B has a molecular weight of approximately 66 kDa, evidenced by SDS-PAGE. Circular dichroism confirmed the high β-strand content consistent with the canonical GH7 family β-jellyroll fold, also observed in the 3D homology model of TtCel7B. Biochemical characterization assays showed that TtCel7B was active over a wide range of pH values (3.5–7.0) and temperatures (45–70 °C), with the highest activity at pH 4.0 and 65 °C. TtCel7B also was stable over a wide range of pH values (3.5–9.0), maintaining more than 80% of its activity after 24 h. The K_M and Vmax values in low-viscosity carboxymethylcellulose were 9.3 mg mL⁻¹ and 2.5 × 10⁴ U mg⁻¹, respectively. The results obtained in this work provide a basis for the development of applications of recombinant TtCel7B in the renewable energy field. Full article

Endo-1,4-β-xylanase catalyzes the random hydrolysis of β-1,4-D-xylosidic bonds in xylan, resulting in the formation of oligomers of xylose. This study aims to demonstrate the promise of endoxylanases from alkaliphilic Bacillus halodurans for the production of xylooligosaccharides (XOS) from oil palm empty fruit bunch (EFB) at high pH. Two enzyme preparations were employed: recombinant endoxylanase Xyn45 (GH10 xylanase) and nonrecombinant endoxylanases, a mixture of two extracellular endo-1,4-β-xylanases Xyn45 and Xyn23 (GH11 xylanase) produced by B. halodurans. EFB was first treated with an alkaline solution. Then, the dissolved xylan-containing fraction was retained, and a prepared enzyme was added to react at pH 8 to convert xylan into XOS. Compared with the use of only Xyn45, the combined use of Xyn45 and Xyn23 resulted in a higher yield of XOS, suggesting the synergistic effect of the two endoxylanases. The yield of XOS obtained from EFB was as high as 46.77% ± 1.64% (w/w), with the xylobiose-to-xylotriose ratio being 6:5. However, when the enzyme activity dose was low, the product contained more xylotriose than xylobiose. Four probiotic lactobacilli and bifidobacteria grew well on a medium containing XOS from EFB. The presence of XOS increased cell mass and reduced pH, suggesting that XOS promoted the growth of probiotics. Full article

Sposisorium reilianum is the causal agent of corn ear smut disease. Eleven genes have been identified in its genome that code for enzymes that could constitute its hemicellulosic system, three of which have been associated with two Endo-β-1,4-xylanases and one with α-L-arabinofuranosidase activity. In this study, the native protein extracellular with β-xylosidase activity, called SRBX1, produced by this basidiomycete was analyzed by performing production kinetics and its subsequent purification by gel filtration. The enzyme was characterized biochemically and sequenced. Finally, its synergism with Xylanase SRXL1 was determined. Its activity was higher in a medium with corn hemicellulose and glucose as carbon sources. The purified protein was a monomer associated with the sr16700 gene, with a molecular weight of 117 kDa and optimal activity at 60 °C in a pH range of 4–7, which had the ability to hydrolyze the ρ-nitrophenyl β-D-xylanopyranoside and ρ-Nitrophenyl α-L-arabinofuranoside substrates. Its activity was strongly inhibited by silver ions and presented Km and Vmax values of 2.5 mM and 0.2 μmol/min/mg, respectively, using ρ-nitrophenyl β-D-xylanopyranoside as a substrate. The enzyme degrades corn hemicellulose and birch xylan in combination and in sequential synergism with the xylanase SRXL1. Full article

Salt–alkali stress threatens the resilience to variable environments and thus the grain yield of rice. However, how rice responds to salt–alkali stress at the molecular level is poorly understood. Here, we report isolation of a novel salt–alkali-tolerant rice (SATR) by screening more than 700 germplasm accessions. Using 93-11, a widely grown cultivar, as a control, we characterized SATR in response to strong salt–alkali stress (SSAS). SATR exhibited SSAS tolerance higher than 93-11, as indicated by a higher survival rate, associated with higher peroxidase activity and total soluble sugar content but lower malonaldehyde accumulation. A transcriptome study showed that cell wall biogenesis-related pathways were most significantly enriched in SATR relative to 93-11 upon SSAS. Furthermore, higher induction of gene expression in the cell wall matrix polysaccharide biosynthesis pathway, coupled with higher accumulations of hemicellulose and pectin as well as measurable physio-biochemical adaptive responses, may explain the strong SSAS tolerance in SATR. We mapped SSAS tolerance to five genomic regions in which 35 genes were candidates potentially governing SSAS tolerance. The 1,4-β-D-xylan synthase gene OsCSLD4 in hemicellulose biosynthesis pathway was investigated in details. The OsCSLD4 function-disrupted mutant displayed reduced SSAS tolerance, biomass and grain yield, whereas the OsCSLD4 overexpression lines exhibited increased SSAS tolerance. Collectively, this study not only reveals the potential role of cell wall matrix polysaccharides in mediating SSAS tolerance, but also highlights applicable value of OsCSLD4 and the large-scale screening system in developing SSAS-tolerant rice. Full article

This study explores the production of prebiotic xylooligosaccharide (XOS) from cassava pulp waste and its effectiveness for the growth of Lactobacillus acidophilus (L. acidophilus). We successfully produced and characterized XOS from cassava pulp xylan using a Bacillus sp. endo-β-1,4-D-xylanase. The XOS was added to modify the MRS medium (MRSm) in various concentrations (0, 1, 3 and 5%) in which the L. acidophilus was inoculated. The growth of L. acidophilus was observed every 12 h for 2 days, and the fermentation products were analyzed for pH, sugar content, and short-chain fatty acids (SCFA) in terms of types and amount. The study showed that L. acidophilus grew well in MRSm. The optimum XOS concentration in MRSm was 5%, indicated by the highest growth of L. acidophilus (8.61 log CFU mL⁻¹). The profile of SCFA products is 14.42 mM acetic acid, 0.25 mM propionic acid, 0.13 mM isobutyric acid, 0.41 mM n-butyric acid, 0.02 mM n-valeric acid, 0.25 mM isovaleric acid, and 25.08 mM lactic acid. Full article

Acetyl xylan esterases (AXEs) are enzymes capable of hydrolysing the acetyl bonds in acetylated xylan, allowing for enhanced activity of backbone-depolymerizing enzymes. Bioprospecting novel AXE is essential in designing enzyme cocktails with desired characteristics targeting the complete breakdown of lignocellulose. In this article, we report the characterisation of a novel AXE identified as Gene_id_40363 in the metagenomic library analysed from the gut microbiota of the common black slug. The conserved domain description was identified with an NCBI BLASTp search using the translated nucleotide sequence as a query. The activity of the recombinant enzyme was tested on various synthetic substrates and acetylated substrates. The protein sequence matched the conserved domain described as putative hydrolase and aligned closely to an uncharacterized esterase from Buttiauxella agrestis, hence the designation as BaAXE. BaAXE showed low sequence similarity among characterized CE family proteins with an available 3D structure. BaAXE was active on 4-nitrophenyl acetate, reporting a specific activity of 78.12 U/mg and a Km value of 0.43 mM. The enzyme showed optimal activity at 40 °C and pH 8 and showed high thermal stability, retaining over 40% activity after 2 h of incubation from 40 °C to 100 °C. BaAXE hydrolysed acetyl bonds, releasing acetic acid from acetylated xylan and β-D-glucose pentaacetate. BaAXE has great potential for biotechnological applications harnessing its unique characteristics. In addition, this proves the possibility of bioprospecting novel enzymes from understudied environments. Full article

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. Full article