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Arabinotriose O-ATR
Product code: O-ATR

50 mg

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Content: 50 mg
Shipping Temperature: Ambient
Storage Temperature: Below -10oC
Physical Form: Liquid
Stability: > 2 years under recommended storage conditions
CAS Number: 89315-59-3
Molecular Formula: C15H26O13
Molecular Weight: 414.4
Purity: > 95%
Substrate For (Enzyme): endo-Arabinanase

High purity Arabinotriose (syrup) for use in research, biochemical enzyme assays and in vitro diagnostic analysis.

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Megazyme publication

Versatile high resolution oligosaccharide microarrays for plant glycobiology and cell wall research.

Pedersen, H. L., Fangel, J. U., McCleary, B., Ruzanski, C., Rydahl, M. G., Ralet, M. C., Farkas, V., Von Schantz, L., Marcus, S. E., Andersen, M.C. F., Field, R., Ohlin, M., Knox, J. P., Clausen, M. H. & Willats, W. G. T. (2012). Journal of Biological Chemistry, 287(47), 39429-39438.

Microarrays are powerful tools for high throughput analysis, and hundreds or thousands of molecular interactions can be assessed simultaneously using very small amounts of analytes. Nucleotide microarrays are well established in plant research, but carbohydrate microarrays are much less established, and one reason for this is a lack of suitable glycans with which to populate arrays. Polysaccharide microarrays are relatively easy to produce because of the ease of immobilizing large polymers noncovalently onto a variety of microarray surfaces, but they lack analytical resolution because polysaccharides often contain multiple distinct carbohydrate substructures. Microarrays of defined oligosaccharides potentially overcome this problem but are harder to produce because oligosaccharides usually require coupling prior to immobilization. We have assembled a library of well characterized plant oligosaccharides produced either by partial hydrolysis from polysaccharides or by de novo chemical synthesis. Once coupled to protein, these neoglycoconjugates are versatile reagents that can be printed as microarrays onto a variety of slide types and membranes. We show that these microarrays are suitable for the high throughput characterization of the recognition capabilities of monoclonal antibodies, carbohydrate-binding modules, and other oligosaccharide-binding proteins of biological significance and also that they have potential for the characterization of carbohydrate-active enzymes.

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Megazyme publication
Developmental complexity of arabinan polysaccharides and their processing in plant cell walls.

Verhertbruggen, Y., Marcus, S. E., Haeger, A., Verhoef, R., Schols, H. A., McCleary, B. V., McKee, L., Gilbert, H. J. & Knox, J. P. (2009). The Plant Journal, 59(3), 413-425.

Plant cell walls are constructed from a diversity of polysaccharide components. Molecular probes directed to structural elements of these polymers are required to assay polysaccharide structures in situ, and to determine polymer roles in the context of cell wall biology. Here, we report on the isolation and the characterization of three rat monoclonal antibodies that are directed to 1,5-linked arabinans and related polymers. LM13, LM16 and LM17, together with LM6, constitute a set of antibodies that can detect differing aspects of arabinan structures within cell walls. Each of these antibodies binds strongly to isolated sugar beet arabinan samples in ELISAs. Competitive-inhibition ELISAs indicate the antibodies bind differentially to arabinans with the binding of LM6 and LM17 being effectively inhibited by short oligoarabinosides. LM13 binds preferentially to longer oligoarabinosides, and its binding is highly sensitive to arabinanase action, indicating the recognition of a longer linearized arabinan epitope. In contrast, the binding of LM16 to branched arabinan and to cell walls is increased by arabinofuranosidase action. The presence of all epitopes can be differentially modulated in vitro using glycoside hydrolase family 43 and family 51 arabinofuranosidases. In addition, the LM16 epitope is sensitive to the action of β-galactosidase. Immunofluorescence microscopy indicates that the antibodies can be used to detect epitopes in cell walls, and that the four antibodies reveal complex patterns of epitope occurrence that vary between organs and species, and relate both to the probable processing of arabinan structural elements and the differing mechanical properties of cell walls.

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Arabinoxylan source and xylanase specificity influence the production of oligosaccharides with prebiotic potential.

Rudjito, R. C., Jiménez-Quero, A., Muñoz, M. D. C. C., Kuil, T., Olsson, L., Stringer, M. A., Krogh, K. B. R. M., Eklof, J. & Vilaplana, F. (2023). Carbohydrate Polymers, 320, 121233.

Cereal arabinoxylans (AXs) are complex polysaccharides in terms of their pattern of arabinose and ferulic acid substitutions, which influence their properties in structural and nutritional applications. We have evaluated the influence of the molecular structure of three AXs from wheat and rye with distinct substitutions on the activity of β-xylanases from different glycosyl hydrolase families (GH 5_34, 8, 10 and 11). The arabinose and ferulic acid substitutions influence the accessibility of the xylanases, resulting in specific profiles of arabinoxylan-oligosaccharides (AXOS). The GH10 xylanase from Aspergillus aculeatus (AcXyn10A) and GH11 from Thermomyces lanuginosus (TlXyn11) showed the highest activity, producing larger amounts of small oligosaccharides in shorter time. The GH8 xylanase from Bacillus sp. (BXyn8) produced linear xylooligosaccharides and was most restricted by arabinose substitution, whereas GH5_34 from Gonapodya prolifera (GpXyn5_34) required arabinose substitution and produced longer (A)XOS substituted on the reducing end. The complementary substrate specificity of BXyn8 and GpXyn5_34 revealed how arabinoses were distributed along the xylan backbones. This study demonstrates that AX source and xylanase specificity influence the production of oligosaccharides with specific structures, which in turn impacts the growth of specific bacteria (Bacteroides ovatus and Bifidobacterium adolescentis) and the production of beneficial metabolites (short-chain fatty acids).

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A combined liquid chromatography–trapped ion mobility–tandem high-resolution mass spectrometry and multivariate analysis approach for the determination of enzymatic reactivity descriptors in biomass hydrolysates.

Ramtanon, I., Berlioz-Barbier, A., Remy, S., Renault, J. H. & Le Masle, A. (2023). Journal of Chromatography A, 1706, 464277.

Intermediate products such as oxygenated compounds may interfere with bioconversion kinetics of lignocellulosic biomass into bioethanol. This work presents a multidimensional approach, based on liquid chromatography (LC), trapped ion mobility spectrometry (TIMS), tandem high-resolution mass spectrometry (HRMS/MS), and multivariate analysis, for the identification of enzymatic reactivity descriptors in 22 industrial biomass samples, called hydrolysates. The first part of the study is dedicated to the improvement of the chemical diversity assessment of the hydrolysates through an original three-dimensional Van Krevelen diagram displaying the double bond equivalent (DBE) as third dimension. In a second part, the evaluation of data by multivariate data analysis allowed the discrimination of sample according to the biomass type and the level of enzymatic reactivity. In the last part, a potential descriptor of low enzymatic reactivity was selected and used in a case study. An in-depth structural analysis was performed on the feature annotated as carbohydrate derivative. Considering the intricate fragmentation spectrum exhibited by the selected feature, trapped ion mobility was employed to enhance separation prior to the HRMS/MS experiments. This final step improved data interpretation and increased the identification confidence level leading to the characterization of xylotriose, 3,5-dimethoxy-4-hydroxybenzaldehyde and 4-hydroxy-3-methoxy-cinnamaldehyde. This is the first study to present an untargeted multidimensional approach for the identification of enzymatic hydrolysis inhibitors in industrial hydrolysate samples.

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Identification of D-arabinan-degrading enzymes in mycobacteria.

Al-Jourani, O., Benedict, S. T., Ross, J., Layton, A. J., van der Peet, P., Marando, V. M., et al. (2023). Nature Communications, 14(1), 2233.

Bacterial cell growth and division require the coordinated action of enzymes that synthesize and degrade cell wall polymers. Here, we identify enzymes that cleave the D-arabinan core of arabinogalactan, an unusual component of the cell wall of Mycobacterium tuberculosis and other mycobacteria. We screened 14 human gut-derived Bacteroidetes for arabinogalactan-degrading activities and identified four families of glycoside hydrolases with activity against the D-arabinan or D-galactan components of arabinogalactan. Using one of these isolates with exo-D-galactofuranosidase activity, we generated enriched D-arabinan and used it to identify a strain of Dysgonomonas gadei as a D-arabinan degrader. This enabled the discovery of endo- and exo-acting enzymes that cleave D-arabinan, including members of the DUF2961 family (GH172) and a family of glycoside hydrolases (DUF4185/GH183) that display endo-D-arabinofuranase activity and are conserved in mycobacteria and other microbes. Mycobacterial genomes encode two conserved endo-D-arabinanases with different preferences for the D-arabinan-containing cell wall components arabinogalactan and lipoarabinomannan, suggesting they are important for cell wall modification and/or degradation. The discovery of these enzymes will support future studies into the structure and function of the mycobacterial cell wall.

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Taxogenomic assessment and genomic characterisation of Weissella cibaria strain 92 able to metabolise oligosaccharides derived from dietary fibres.

Anna, M., Phebe, V., Guðmundsdóttir, E. E., Santesson, S., Nilsson, A., Óli, H. G., Linares-Pasten, J. A. & Nordberg, K. E. (2020). Scientific Reports, 10(1), 5853.

The importance of the gut microbiota in human health has led to an increased interest to study probiotic bacteria. Fermented food is a source of already established probiotics, but it also offers an opportunity to discover new taxa. Four strains of Weissella sp. isolated from Indian fermented food have been genome sequenced and classified into the species W. cibaria based on whole-genome phylogeny. The genome of W. cibaria strain 92, known to utilise xylooligosaccharides and produce lactate and acetate, was analysed to identify genes for oligosaccharide utilisation. Clusters including genes involved in transportation, hydrolysis and metabolism of xylooligosaccharides, arabinooligosaccharides and β-glucosides were identified. Growth on arabinobiose and laminaribiose was detected. A 6-phospho-β-glucosidase clustered with a phosphotransferase system was found upregulated during growth on laminaribiose, indicating a mechanism for laminaribiose utilisation. The genome of W. cibaria strain 92 harbours genes for utilising the phosphoketolase pathway for the production of both acetate and lactate from pentose and hexose sugars but lacks two genes necessary for utilising the pentose phosphate pathway. The ability of W. cibaria strain 92 to utilise several types of oligosaccharides derived from dietary fibres, and produce lactate and acetate makes it interesting as a probiotic candidate for further evaluation.

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A novel neutral and thermophilic endoxylanase from Streptomyces ipomoeae efficiently produced xylobiose from agricultural and forestry residues.

Xian, L., Li, Z., Tang, A. X., Qin, Y. M., Li, Q. Y., Liu, H. B. & Liu, Y. Y. (2019). Bioresource Technology, 285, 121293.

Endoxylanases capable of producing high ratios of xylobiose from agricultural and forestry residues in neutral and high temperature conditions are attractive for the prebiotic and alternative sweetener industries. In this study, a putative glycosyl hydrolase gene from Streptomyces ipomoeae was cloned and expressed in Escherichia coli. The recombinant enzyme, named as SipoEnXyn10A, hydrolyzed beechwood xylan in endo-action mode releasing xylobiose as its main end product. It was most active at pH 6.5 and 75-80°C and showed remarkable stability at 65°C. The xylobiose yield from 10 g corncob and moso bamboo reached 1.123 ± 0.021 and 0.229 ± 0.005 g, respectively, at pH 6.5 and 70°C, which was higher than other reports using the same material. Moreover, high ratios of xylobiose in the xylose-based product of about 85% were obtained from corncob, moso bamboo sawdust, cassava stem and Chinese fir sawdust. These results demonstrated that SipoEnXyn10A has potential for industrial application.

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Heterologous expression and characterization of α-L-arabinofuranosidase 4 from Penicillium purpurogenum and comparison with the other isoenzymes produced by the fungus.

Ravanal, M. C. & Eyzaguirre, J. (2015). Fungal Biology, 119(7), 641-647.

Penicillium purpurogenum secretes at least four arabinofuranosidases. In this work, the gene of α-L-arabinofuranosidase 4 (ABF4) has been sequenced and expressed in Pichia pastoris. The gene is 1521 pb long, has no introns and codes for a protein of 506 amino acid residues including a signal peptide of 26 residues. Mature protein has a calculated molecular mass of 55.4 kDa, shows 77% identity with α-L-arabinofuranosidase 1 from P. purpurogenum and belongs to family 54 of the glycosyl hydrolases. Purified enzyme has a molecular mass near 68 kDa, is active on p-nitrophenyl α-L-arabinofuranoside and p-nitrophenyl-β-D-galactofuranoside, and follows Michaelis-Menten kinetics with KM of 1.58 ± 0.13 mM and 5.3 ± 1.18 mM, respectively. The pH optimum is 4.6 and optimal temperature is 50°C. The enzyme is active on sugar beet arabinan and wheat flour arabinoxylan but does not act on short arabinooligosaccharides or debranched arabinan. It shows synergistic effect on arabinose liberation from wheat arabinoxylan when combined with endoxylanase from P. purpurogenum. The properties of ABF4 have been compared with those of the other arabinofuranosidases produced by the fungus. P. purpurogenum is the first fungus possessing four biochemically characterized arabinofuranosidases. The availability of four different ABFs may be valuable for biotechnological applications.

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Heterologous expression of a Penicillium purpurogenum exo-arabinanase in Pichia pastoris and its biochemical characterization.

Mardones, W., Callegari, E. & Eyzaguirre, J. (2015). Fungal biology, 119(12), 1267-1278.

Arabinan is a component of pectin, which is one of the polysaccharides present in lignocelluose. The enzymes degrading the main chain of arabinan are the endo- (EC and exo-arabinanases (3.2.1.-). Only three exo-arabinanases have been biochemically characterized; they belong to glycosyl hydrolase family 93. In this work, the cDNA of an exo-arabinanase (Arap2) from Penicillium purpurogenum has been heterologously expressed in Pichia pastoris. The gene is 1310 bp long, has three introns and codes for a protein of 380 amino acid residues; the mature protein has a calculated molecular mass of 39 823 Da. The heterologously expressed Arap2 has a molecular mass in the range of 60-80 kDa due to heterogeneous glycosylation. The enzyme is active on debranched arabinan with optimum pH of 4-5.5 and optimal temperature of 40°C, and has an exo-type action mode, releasing arabinobiose from its substrates. The expression profile of arap2 in corncob and sugar beet pulp follows a different pattern and is not related to the presence of arabinan. This is the first exo-arabinanase studied from P. purpurogenum and the first expressed in yeast. The availability of heterologous Arap2 may be useful for biotechnological applications requiring acidic conditions.

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Roasting-induced changes in arabinotriose, a model of coffee arabinogalactan side chains.

Moreira, A. S. P., Coimbra, M. A., Nunes, F. M. & Domingues, M. R. M. (2013). Food Chemistry, 138(4), 2291-2299.

Thermal processing can promote reactions that change the structure of food constituents, often by unknown mechanisms, such as those occurring in arabinose residues of coffee arabinogalactan side chains. Aiming to know more about these modifications, the structurally related α-(1→5)-L-arabinotriose was roasted at 200°C and the products obtained were identified by ESI-MS and MALDI-MS and characterised by ESI-MSn. Depolymerised and polymerised oligosaccharides with up to 16 residues and new types of linkages were formed. Also, products resulting from dehydration, oxidation, and cleavage of a carbon–carbon bond at the reducing end of the corresponding non-modified oligosaccharide were formed, probably promoting the release of formaldehyde, formic acid, glycolaldehyde, glyoxal, acetic acid, glycolic acid, glyceraldehyde, 2-hydroxypropanedialdehyde and lactic acid. As many of these compounds have been reported to occur in roasted coffee beans and/or brews, it can be suggested that the degradation of coffee arabinogalactan side chains can contribute to their formation upon roasting.

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