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|Stability:||> 2 years under recommended storage conditions|
|Main Chain Glycosidic Linkage:||β-1,4|
|Substrate For (Enzyme):||Acetylxylan esterase|
High purity Xylan (Birchwood, partially acetylated) for use in research, biochemical enzyme assays and in vitro diagnostic analysis.
Arabinoxylan-based substrate preferences and predicted metabolic properties of Bifidobacterium longum subspecies as a basis to design differential media.
Calvete-Torre, I., Sabater, C., Delgado, S., Ruas-Madiedo, P., Rupérez-García, A., Montilla, A., Moreno. F. J., Margolles, A. & Ruiz, L. (2023). Food Research International, 167, 112711.
Arabinoxylan (AX) and arabinoxylo-oligosaccharides (AXOS) derived therefrom are emergent prebiotics with promising health promoting properties, likely linked to its capacity to foster beneficial species in the human gut. Bifidobacteria appear to be one taxa that is frequently promoted following AX or AXOS consumption, and that is known to establish metabolic cross-feeding networks with other beneficial commensal species. Therefore, probiotic bifidobacteria with the capability to metabolize AX-derived prebiotics represent interesting candidates to develop novel probiotic and synbiotic combinations with AX-based prebiotics. In this work we have deepen into the metabolic capabilities of bifidobacteria related to AX and AXOS metabolization through a combination of in silico an in vitro tools. Both approaches revealed that Bifidobacterium longum and, particularly, B. longum subsp. longum, appears as the better equipped to metabolize complex AX substrates, although other related subspecies such as B. longum subsp. infantis, also hold some machinery related to AXOS metabolization. This correlates to the growth profiles exhibited by representative strains of both subspecies in AX or AXOS enriched media. Based on these results, we formulated a differential carbohydrate free medium (CFM) supplemented with a combination of AX and AXOS that enabled to recover a wide diversity of Bifidobacterium species from complex fecal samples, while allowing easy discrimination of AX metabolising strains by the appearance of a precipitation halo. This new media represent an appealing alternative to isolate novel probiotic bifidobacteria, rapidly discriminating their capacity to metabolize structurally complex AX-derived prebiotics. This can be convenient to assist formulation of novel functional foods and supplements, including bifidobacterial species with capacity to metabolize AX-derived prebiotic ingredients.Hide Abstract
Insight into CAZymes of Alicyclobacillus mali FL18: Characterization of a New Multifunctional GH9 Enzyme.
Carbonaro, M., Aulitto, M., Gallo, G., Contursi, P., Limauro, D. & Fiorentino, G. (2023). International Journal of Molecular Sciences, 24(1), 243.
In the bio-based era, cellulolytic and hemicellulolytic enzymes are biocatalysts used in many industrial processes, playing a key role in the conversion of recalcitrant lignocellulosic waste biomasses. In this context, many thermophilic microorganisms are considered as convenient sources of carbohydrate-active enzymes (CAZymes). In this work, a functional genomic annotation of Alicyclobacillus mali FL18, a recently discovered thermo-acidophilic microorganism, showed a wide reservoir of putative CAZymes. Among them, a novel enzyme belonging to the family 9 of glycosyl hydrolases (GHs), named AmCel9, was identified; in-depth in silico analyses highlighted that AmCel9 shares general features with other GH9 members. The synthetic gene was expressed in Escherichia coli and the recombinant protein was purified and characterized. The monomeric enzyme has an optimal catalytic activity at pH 6.0 and has comparable activity at temperatures ranging from 40°C to 70°C. It also has a broad substrate specificity, a typical behavior of multifunctional cellulases; the best activity is displayed on β-1,4 linked glucans. Very interestingly, AmCel9 also hydrolyses filter paper and microcrystalline cellulose. This work gives new insights into the properties of a new thermophilic multifunctional GH9 enzyme, that looks a promising biocatalyst for the deconstruction of lignocellulose.Hide Abstract
Improving cellulases hydrolytic action: An expanded role for electron donors of lytic polysaccharide monooxygenases in cellulose saccharification.
Xin, D., Blossom, B. M., Lu, X. & Felby, C. (2022). Bioresource Technology, 346, 126662.
Ascorbic acid (AscA) and gallic acid (GalA) are common electron donors and their boosting effect on lytic polysaccharide monooxygenases (LPMO) has been studied extensively. However, their influence on cellulase hydrolytic action has been ignored. In this work, the effect of AscA and GalA on cellulases hydrolytic action was evaluated. It was found that AscA could increase the hydrolysis of cellulose by cellulases, while GalA showed no effect on cellulases' hydrolytic action. The effect of AscA differed for the monocomponent cellulases: it showed a special boosting effect on cellobiohydrolase, rather than endoglucanase and β-glucosidase. This promoting effect could be another mechanism behind the boosting effect of the AscA-driven LPMO system on cellulose saccharification. These findings thus advance the understanding of the role of electron donors on cellulose saccharification and offer important clues on how to evaluate the feasibility of electron donors from a new perspective.Hide Abstract
Structural and Biochemical Characterization of a Nonbinding SusD-Like Protein Involved in Xylooligosaccharide Utilization by an Uncultured Human Gut Bacteroides Strain.
Tauzin, A. S., Wang, Z., Cioci, G., Li, X., Labourel, A., Machado, B., Lippens, G. & Potocki-Veronese, G. (2022). Msphere, 7(5), e00244-22.
In the human gut microbiota, Bacteroidetes break down dietary and endogenous glycosides through highly specific polysaccharide utilization loci (PULs). PULs encode a variety of sensor regulators, binding proteins, transporters, and carbohydrate-active enzymes (CAZymes). Surface glycan-binding proteins (SGBPs) are essential for the efficient capture of the glycosides present on the cell surface, providing Bacteroidetes with a competitive advantage in colonizing their habitats. Here, we present the functional and structural characterization of a SusD-like protein encoded by a xylooligosaccharide (XOS) PUL from an uncultured human gut Bacteroides strain. This locus is also conserved in Bacteroides vulgatus, thereby providing new mechanistic insights into the role of SGBPs in the metabolism of dietary fiber of importance for gut health. Various in vitro analyses, including saturation transfer difference nuclear magnetic resonance (STD-NMR) spectroscopy, revealed that the SusD-like protein cannot bind to the cognate substrate of the XOS PUL, although its presence is essential for the PUL to function. Analysis of the crystal structure of the SusD-like protein reveals an unfolded binding surface and the absence or inappropriate orientation of several key residues compared with other known SusD-like structures. These results highlight the critical role of the SusD-like protein in the transport of oligosaccharides and provide fundamental knowledge about the structure-function of SusC/D-like transporters, revealing that the binding specificity of SusD-like SGBPs does not necessarily reflect the uptake specificity of the transporter.Hide Abstract
Isolation and Characterization of a Novel Cold-Active, Halotolerant Endoxylanase from Echinicola rosea Sp. Nov. JL3085T.
He, J., Liu, L., Liu, X. & Tang, K. (2020). Marine Drugs, 18(5), 245.
We cloned a xylanase gene (xynT) from marine bacterium Echinicola rosea sp. nov. JL3085T and recombinantly expressed it in Escherichia coli BL21. This gene encoded a polypeptide with 379 amino acid residues and a molecular weight of ~43 kDa. Its amino acid sequence shared 45.3% similarity with an endoxylanase from Cellvibrio mixtus that belongs to glycoside hydrolases family 10 (GH10). The XynT showed maximum activity at 40°C and pH 7.0, and a maximum velocity of 62 μmoL min−1 mg−1. The XynT retained its maximum activity by more than 69%, 51%, and 26% at 10°C, 5°C, and 0°C, respectively. It also exhibited the highest activity of 135% in the presence of 4 M NaCl and retained 76% of its activity after 24 h incubation with 4 M NaCl. This novel xylanase, XynT, is a cold-active and halotolerant enzyme that may have promising applications in drug, food, feed, and bioremediation industries.Hide Abstract
Quantification of morphochemical changes during in situ enzymatic hydrolysis of individual biomass particles based on autofluorescence imaging.
Kapsokalyvas, D., Loos, J., Boogers, I. A. L. A., Appeldoorn, M. M., Kabel, M. A. & Zandvoort, M. V. (2019). Biopolymers, 111(3), e23347.
Enzymatic hydrolysis of biomass is an established method for producing biofuels. Lignocellulosic biomass such as corn stover is very inhomogeneous material with big variation on conversion rates between individual particles therefore leading to variable recalcitrance results. In this study, we used noninvasive optical microscopy techniques, such as two‐photon microscopy and fluorescence lifetime imaging microscopy, to visualize and analyze morphological and chemical changes of individual corn stover particles pretreated with sulfuric acid during hydrolysis. Morphochemical changes were interpreted based on the fluorescence properties of isolated building blocks of plant cell wall, such as cellulose, hemicellulose, and lignin. Enzymatic hydrolysis resulted in particle size reduction, side wall collapse, decrease of second harmonic signal from cellulose, redshifting of autofluorescence emission, and lifetime decrease attributed to the relative increase of lignin. Based on these observations, tracking compositional change after hydrolysis of individual particles was accomplished. The methodologies developed offer a paradigm for imaging and analyzing enzymatic hydrolysis in vitro and in situ, which could be used for screening enzymes cocktails targeting specific recalcitrant structures or investigating locally enzyme anti‐inhibitory agents.Hide Abstract
Highly Efficient Degradation of Xylan into Xylose by a Single Enzyme.
Basit, A., Miao, T., Liu, J., Wen, J., Song, L., Zheng, F., Lou, H. & Jiang, W. (2019). ACS Sustainable Chemistry & Engineering, 7(13), 11360-11368.
Here, we report highly efficient degradation of xylan into xylose by a single multifunctional xylanolytic enzyme from the filamentous fungus Thermothelomyces thermophila (termed Ttxy43). Ttxy43 shows three different enzyme activities toward carbohydrates, β-xylosidase (80.8 U/mg), endoxylanase (105.42 U/mg), and α-l-arabinofuranosidase enzyme activities (15.81 U/mg). Analysis of the catalytic mode of action of Ttxy43 for birchwood-xylan (BWX) reveals that endoxylanase initially degrades xylan to unbranched xylooligosaccharides (XOSs) (xylobiose, xylotriose, xylotetraose) as intermediates, which are then quickly hydrolyzed into single xylose by β-xylosidase. Site-directed mutagenesis studies indicate that Ttxy43 residues Asp134 and Glu228 are essential catalytic sites, while Glu176, Asp38, and Asp85 play an accessory role. More importantly, Ttxy43 displays higher degradation efficiency in comparison with a commercial β-xylosidase and endoxylanase “cocktail”. These findings elucidate an efficient integrated degradation mechanism of xylan under industrial reaction conditions, which provides a novel strategy to design techniques for biomass energy production.Hide Abstract
Structural and functional characterization of a bifunctional GH30-7 xylanase B from the filamentous fungus Talaromyces cellulolyticus.
Nakamichi, Y., Fouquet, T., Ito, S., Watanabe, M., Matsushika, A. & Inoue, H. (2019). Journal of Biological Chemistry, 294(11), 4065-4078.
Glucuronoxylanases are endo-xylanases and members of the glycoside hydrolase family 30 subfamilies 7 (GH30-7) and 8 (GH30-8). Unlike for the well-studied GH30-8 enzymes, the structural and functional characteristics of GH30-7 enzymes remain poorly understood. Here, we report the catalytic properties and three-dimensional structure of GH30-7 xylanase B (Xyn30B) identified from the cellulolytic fungus Talaromyces cellulolyticus. Xyn30B efficiently degraded glucuronoxylan to acidic xylooligosaccharides (XOSs), including an α-1,2-linked 4-O-methyl-D-glucuronosyl substituent (MeGlcA). Rapid analysis with negative-mode electrospray-ionization multistage MS (ESI(−)-MSn) revealed that the structures of the acidic XOS products are the same as those of the hydrolysates (MeGlcA2Xyln, n > 2) obtained with typical glucuronoxylanases. Acidic XOS products were further degraded by Xyn30B, releasing first xylobiose and then xylotetraose and xylohexaose as transglycosylation products. This hydrolase reaction was unique to Xyn30B, and the substrate was cleaved at the xylobiose unit from its nonreducing end, indicating that Xyn30B is a bifunctional enzyme possessing both endo-glucuronoxylanase and exo-xylobiohydrolase activities. The crystal structure of Xyn30B was determined as the first structure of a GH30-7 xylanase at 2.25 Å resolution, revealing that Xyn30B is composed of a pseudo-(α/β)8-catalytic domain, lacking an α6 helix, and a small β-rich domain. This structure and site-directed mutagenesis clarified that Arg46, conserved in GH30-7 glucuronoxylanases, is a critical residue for MeGlcA appendage-dependent xylan degradation. The structural comparison between Xyn30B and the GH30-8 enzymes suggests that Asn93 in the β2-α2 loop is involved in xylobiohydrolase activity. In summary, our findings indicate that Xyn30B is a bifunctional endo- and exo-xylanase.Hide Abstract
Structural and biochemical characterization of the Cutibacterium acnes exo-β-1,4-mannosidase that targets the N-glycan core of host glycoproteins.
Reichenbach, T., Kalyani, D., Gandini, R., Svartström, O., Aspeborg, H. & Divne, C. (2018). PloS One, 13(9), e0204703.
Commensal and pathogenic bacteria have evolved efficient enzymatic pathways to feed on host carbohydrates, including protein-linked glycans. Most proteins of the human innate and adaptive immune system are glycoproteins where the glycan is critical for structural and functional integrity. Besides enabling nutrition, the degradation of host N-glycans serves as a means for bacteria to modulate the host’s immune system by for instance removing N-glycans on immunoglobulin G. The commensal bacterium Cutibacterium acnes is a gram-positive natural bacterial species of the human skin microbiota. Under certain circumstances, C. acnes can cause pathogenic conditions, acne vulgaris, which typically affects 80% of adolescents, and can become critical for immunosuppressed transplant patients. Others have shown that C. acnes can degrade certain host O-glycans, however, no degradation pathway for host N-glycans has been proposed. To investigate this, we scanned the C. acnes genome and were able to identify a set of gene candidates consistent with a cytoplasmic N-glycan-degradation pathway of the canonical eukaryotic N-glycan core. We also found additional gene sequences containing secretion signals that are possible candidates for initial trimming on the extracellular side. Furthermore, one of the identified gene products of the cytoplasmic pathway, AEE72695, was produced and characterized, and found to be a functional, dimeric exo-β-1,4-mannosidase with activity on the β-1,4 glycosidic bond between the second N-acetylglucosamine and the first mannose residue in the canonical eukaryotic N-glycan core. These findings corroborate our model of the cytoplasmic part of a C. acnes N-glycan degradation pathway.Hide Abstract