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Molecules (Basel, Switzerland) Jul 2021This study describes the catalytic properties of a GH30_7 xylanase produced by the fungus . The enzyme is an ando-β-1,4-xylanase, showing similar specific activity...
This study describes the catalytic properties of a GH30_7 xylanase produced by the fungus . 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 MeGlcAXyl. Due to the significant non-specific endoxylanase activity of the enzyme, these acidic products are further attacked in the unbranched regions, finally yielding MeGlcAXyl. 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.
Topics: Amino Acid Sequence; Arabinose; Carbohydrate Sequence; Endo-1,4-beta Xylanases; Fungal Proteins; Gene Expression; Glucuronates; Hydrolysis; Oligosaccharides; Sequence Alignment; Sequence Homology, Amino Acid; Substrate Specificity; Talaromyces; Xylans
PubMed: 34361767
DOI: 10.3390/molecules26154614 -
Enzyme and Microbial Technology May 2023Xylose isomerase catalyzes the isomerization of D-xylose to D-xylulose with promiscuous activity for other saccharides including D-glucose, D-allose, and L-arabinose....
Xylose isomerase catalyzes the isomerization of D-xylose to D-xylulose with promiscuous activity for other saccharides including D-glucose, D-allose, and L-arabinose. The xylose isomerase from the fungus Piromyces sp. E2 (PirE2_XI) is used to engineer xylose usage by the fermenting yeast Saccharomyces cerevisiae, but its biochemical characterization is poorly understood with divergent catalytic parameters reported. We have measured the kinetic parameters of the PirE2_XI and analyzed its thermostability and pH-dependence towards different substrates. The PirE2_XI shows promiscuous activity towards D-xylose, D-glucose, D-ribose and L-arabinose with variable effects depending on different divalent ions and epimerizes D-xylose at C3 to produce D-ribulose in a substrate/product dependent ratio. The enzyme follows Michaelis-Menten kinetics for the substrates used and although K values for D-xylose are comparable at 30 and 60 °C, the k/K is three-fold greater at 60 °C. The purified PirE2_XI shows maximal activity at 65 °C in the pH range of 6.5-7.5 and is a thermostable enzyme, maintaining full activity over 48 h at 30 °C or 12 h at 60 °C. This is the first report demonstrating epimerase activity of the PirE2_XI and its ability to isomerize D-ribose and L-arabinose, and provides a comprehensive in vitro study of substrate specificity, effect of metal ions and temperature on enzyme activity and these findings advance the knowledge of the mechanism of action of this enzyme.
Topics: Piromyces; Racemases and Epimerases; Xylose; Arabinose; Ribose; Glucose; Aldose-Ketose Isomerases
PubMed: 36966679
DOI: 10.1016/j.enzmictec.2023.110230 -
Carbohydrate Research Nov 2019From the leaves of Silybum marianum L. were isolated arabinogalactan with molecular weight 38 kDa and pectic substances. The monosaccharide composition of...
From the leaves of Silybum marianum L. were isolated arabinogalactan with molecular weight 38 kDa and pectic substances. The monosaccharide composition of arabinogalactan was represented by β-galactose and α-arabinose in a ratio of 2.6:1.0 and β-galacturonic acid as a minor component. By chemical methods and GC, GC-MS, 1D and 2D NMR spectroscopy was established that the arabinogalactan consists of d-galactopyranose residues linked by β-1,6-glycosidic bonds as a main chain, and the side chain was represented by α-arabinose, β-galactose and 4-O-methylglucuronic acid. Pectic substance was found in small amounts. According to NMR data it contains also a branched rhamnogalacturonan.
Topics: Asteraceae; Carbohydrate Sequence; Galactans; Pectins
PubMed: 31494303
DOI: 10.1016/j.carres.2019.107797 -
World Journal of Microbiology &... Nov 2019This review examines the recent models describing the mode of action of various xylanolytic enzymes and how these enzymes can be applied (sequentially or simultaneously)... (Review)
Review
This review examines the recent models describing the mode of action of various xylanolytic enzymes and how these enzymes can be applied (sequentially or simultaneously) with their distinctive roles in mind to achieve efficient xylan degradation. With respect to homeosynergy, synergism appears to be as a result of β-xylanase and/or oligosaccharide reducing-end β-xylanase liberating xylo-oligomers (XOS) that are preferred substrates of the processive β-xylosidase. With regards to hetero-synergism, two cross relationships appear to exist and seem to be the reason for synergism between the enzymes during xylan degradation. These cross relations are the debranching enzymes such as α-glucuronidase or side-chain cleaving enzymes such as carbohydrate esterases (CE) removing decorations that would have hindered back-bone-cleaving enzymes, while backbone-cleaving-enzymes liberate XOS that are preferred substrates of the debranching and side-chain-cleaving enzymes. This interaction is demonstrated by high yields in co-production of xylan substituents such as arabinose, glucuronic acid and ferulic acid, and XOS. Finally, lytic polysaccharide monooxygenases (LPMO) have also been implicated in boosting whole lignocellulosic biomass or insoluble xylan degradation by glycoside hydrolases (GH) by possibly disrupting entangled xylan residues. Since it has been observed that the same enzyme (same Enzyme Commission, EC, classification) from different GH or CE and/or AA families can display different synergistic interactions with other enzymes due to different substrate specificities and properties, in this review, we propose an approach of enzyme selection (and mode of application thereof) during xylan degradation, as this can improve the economic viability of the degradation of xylan for producing precursors of value added products.
Topics: Arabinose; Biodegradation, Environmental; Coumaric Acids; Endo-1,4-beta Xylanases; Esterases; Glucuronic Acid; Glycoside Hydrolases; Oligosaccharides; Polysaccharides; Substrate Specificity; Xylans; Xylosidases
PubMed: 31728656
DOI: 10.1007/s11274-019-2765-z -
Journal of Agricultural and Food... Dec 2019l-Arabinose is a monosaccharide extracted from plants or fibers, which is known to have a variety of functional properties. In this study, we aim to investigate whether...
l-Arabinose is a monosaccharide extracted from plants or fibers, which is known to have a variety of functional properties. In this study, we aim to investigate whether l-arabinose could inhibit colitis by modulating gut microbiota. l-Arabinose was administered in mice daily in a dextran sodium sulfate (DSS)-induced colitis model. The histological analysis, disease index, and the expression of inflammatory genes were measured. 16S-rRNA sequence analysis was performed to investigate gut microbiota. Intriguingly, we found that l-arabinose could repress DSS-induced colitis and inhibit p38-/p65-dependent inflammation activation. Besides that, our data revealed that l-arabinose-modulated DSS-induced gut microbiota were disturbed. Additionally, the perturbed gut microbiota was responsible for the suppressive effects of l-arabinose on DSS-induced colitis treated with antibiotics. Lastly, Caco-2 cells were used to confirm the protective effects of l-arabinose in colitis or inflammatory bowel disease. As expected, the protein expression levels in Caco-2 cells of pro-inflammatory genes, which were treated with l-arabinose and incubated with or without tumor necrosis factor alpha. Our work suggested that l-arabinose exerts anti-inflammation effects in DSS-induced colitis. These beneficial effects have correlations with the composition, diversity, and abundance of the gut microbiota regulated by l-arabinose. l-Arabinose could be a remarkable candidate as a functional food or novel therapeutic strategy for intestinal health.
Topics: Animals; Arabinose; Colitis; Cytokines; Dextran Sulfate; Female; Gastrointestinal Microbiome; Humans; Male; Mice; Mice, Inbred C57BL; Transcription Factor RelA; p38 Mitogen-Activated Protein Kinases
PubMed: 31674784
DOI: 10.1021/acs.jafc.9b05829 -
International Journal of Molecular... Dec 2023A microbial fungicide developed from NCD-2 has been registered for suppressing verticillium wilt in crops in China. Spores are the main ingredient of this fungicide and...
A microbial fungicide developed from NCD-2 has been registered for suppressing verticillium wilt in crops in China. Spores are the main ingredient of this fungicide and play a crucial role in suppressing plant disease. Therefore, increasing the number of spores of strain NCD-2 during fermentation is important for reducing the cost of the fungicide. In this study, five kinds of carbon sources were found to promote the metabolism of strain NCD-2 revealed via Biolog Phenotype MicroArray (PM) technology. L-arabinose showed the strongest ability to promote the growth and sporulation of strain NCD-2. L-arabinose increased the bacterial concentration and the sporulation efficiency of strain NCD-2 by 2.04 times and 1.99 times compared with D-glucose, respectively. Moreover, L-arabinose significantly decreased the autolysis of strain NCD-2. Genes associated with arabinose metabolism, sporulation, spore resistance to heat, and spore coat formation were significantly up-regulated, and genes associated with sporulation-delaying protein were significantly down-regulated under L-arabinose treatment. The deletion of , which is involved in arabinose transport in the genus, decreased growth and sporulation by 53.71% and 86.46% compared with wild-type strain NCD-2, respectively. Complementing the mutant strain by importing an intact gene restored the strain's growth and sporulation.
Topics: Humans; Arabinose; Bacillus subtilis; Fungicides, Industrial; Noncommunicable Diseases; Fermentation
PubMed: 38139303
DOI: 10.3390/ijms242417472 -
Carbohydrate Polymers Aug 2021The polysaccharide (AP1-b) of molecular weight 6.59 × 10 Da was isolated from lignified okra (Abelmoschus esculentus (L.) Moench) by hot-water extraction, 40 %...
The polysaccharide (AP1-b) of molecular weight 6.59 × 10 Da was isolated from lignified okra (Abelmoschus esculentus (L.) Moench) by hot-water extraction, 40 % ethanol precipitation and purified by DEAE Cellulose chromatography, respectively. The structure and anti-inflammatory activity of AP1-b were investigated. AP1-b was composed of galactose, rhamnose, gluctose, arabinose and galacturonic acid in a molar ratio of 1.98:1.00:0.15:0.32:0.29. The structural features showed that the AP1-b consisted of →2)-α-d-Rhap-(1→, →4)-β-d-Galp-(1→, →4)-α-d-GalpA-(1→, →6)-β-d-Galp-(1→, β-d-Glcp-(1→ and α-l-Araf-(1→. AP1-b could observably improve the inflammatory injury of LPS-induced RAW 264.7 cells by inhibiting the secretion of NO and decreasing the levels of pro-inflammatory factors (IL-1β, iNOS and TNF-α). AP1-b also inhibited the phosphorylation levels of IκB and p65 proteins, manifesting the anti-inflammatory activity of AP1-b may associated with inhibition of NF-κB signaling pathway. Therefore, AP1-b had potential value in treating inflammatory injury.
Topics: Abelmoschus; Animals; Anti-Inflammatory Agents; Arabinose; Cell Survival; Cytokines; Galactose; Hexuronic Acids; Magnetic Resonance Spectroscopy; Mice; Molecular Weight; NF-kappa B; Nitric Oxide; Polysaccharides; RAW 264.7 Cells; Rhamnose
PubMed: 33966845
DOI: 10.1016/j.carbpol.2021.118081 -
Nutrition (Burbank, Los Angeles County,... Jul 2023The global prevalence of obesity, a chronically trophic metabolic disease, has garnered significant attention. The aim of this study was to investigate L-arabinose, a...
OBJECTIVES
The global prevalence of obesity, a chronically trophic metabolic disease, has garnered significant attention. The aim of this study was to investigate L-arabinose, a unique functional sugar that improves insulin resistance and intestinal environment while promoting probiotic proliferation, for its potential in preventing obesity induced by a high-fat and high-sugar (HFHS) diet in mice.
METHODS
The L-arabinose group was intragastrically administered with 0.4 mL 60 mg/(kg body weight) L-arabinose for 8 wk. The metformin group was intragastrically administered at 0.4 mL 300 mg/(kg body weight), as a positive control group.
RESULTS
Treatment with L-arabinose resulted in a reduction of various obesity symptoms, such as prevented weight gain, increased liver-to-body ratio, decreased insulin, homeostasis model assessment for insulin resistance (HOMA-IR) index, and lipopolysaccharide (LPS) levels, as well as improved insulin resistance, reduced fat volume, inhibited hepatic steatosis, and repaired the pancreas. The L-arabinose treatment also improved lipid metabolism and inflammatory response, decreased the Firmicutes-to-Bacteroidetes ratio at the phylum level, and increased the relative abundance of Parabacteroides gordonii and Akkermansia muciniphila at the species level.
CONCLUSION
Based on these results, L-arabinose could be a promising candidate for combating obesity and obesity-related diseases by regulating insulin resistance and gut microbiota.
Topics: Mice; Animals; Insulin Resistance; Arabinose; Mice, Obese; Gastrointestinal Microbiome; Diet, High-Fat; Obesity; Mice, Inbred C57BL
PubMed: 37207566
DOI: 10.1016/j.nut.2023.112041 -
Journal of Bacteriology Jan 2020The species and were found to grow on d-ribose, d-xylose, and l-arabinose. Here, we report the discovery of a novel promiscuous oxidative pathway of pentose...
The species and were found to grow on d-ribose, d-xylose, and l-arabinose. Here, we report the discovery of a novel promiscuous oxidative pathway of pentose degradation based on genome analysis, identification and characterization of enzymes, transcriptional analysis, and growth experiments with knockout mutants. Together, the data indicate that in spp., d-ribose, d-xylose, and l-arabinose were degraded to α-ketoglutarate involving the following enzymes: (i) a promiscuous pentose dehydrogenase that catalyzed the oxidation of d-ribose, d-xylose, and l-arabinose; (ii) a promiscuous pentonolactonase that was involved in the hydrolysis of ribonolactone, xylonolactone, and arabinolactone; (iii) a highly specific dehydratase, ribonate dehydratase, which catalyzed the dehydration of ribonate, and a second enzyme, a promiscuous xylonate/gluconate dehydratase, which was involved in the conversion of xylonate, arabinonate, and gluconate. Phylogenetic analysis indicated that the highly specific ribonate dehydratase constitutes a novel sugar acid dehydratase family within the enolase superfamily; and (iv) finally, 2-keto-3-deoxypentanonate dehydratase and α-ketoglutarate semialdehyde dehydrogenase catalyzed the conversion of 2-keto-3-deoxypentanonate to α-ketoglutarate via α-ketoglutarate semialdehyde. We conclude that the expanded substrate specificities of the pentose dehydrogenase and pentonolactonase toward d-ribose and ribonolactone, respectively, and the presence of a highly specific ribonate dehydratase are prerequisites of the oxidative degradation of d-ribose in spp. This is the first characterization of an oxidative degradation pathway of d-ribose to α-ketoglutarate in archaea. The utilization and degradation of d-ribose in archaea, the third domain of life, have not been analyzed so far. We show that species utilize d-ribose, which is degraded to α-ketoglutarate via a novel oxidative pathway. Evidence is presented that the oxidative degradation of d-ribose involves novel promiscuous enzymes, pentose dehydrogenase and pentonolactonase, and a novel sugar acid dehydratase highly specific for ribonate. This is the first report of an oxidative degradation pathway of d-ribose in archaea, which differs from the canonical nonoxidative pathway of d-ribose degradation reported for most bacteria. The data contribute to our understanding of the unusual sugar degradation pathways and enzymes in archaea.
Topics: Arabinose; Archaea; Haloarcula; Oxidation-Reduction; Ribose; Xylose
PubMed: 31712277
DOI: 10.1128/JB.00608-19 -
Nature Chemical Biology Jul 2021The L-arabinose-responsive AraC and its cognate P promoter underlie one of the most often used chemically inducible prokaryotic gene expression systems in microbiology...
The L-arabinose-responsive AraC and its cognate P promoter underlie one of the most often used chemically inducible prokaryotic gene expression systems in microbiology and synthetic biology. Here, we change the sensing capability of AraC from L-arabinose to blue light, making its dimerization and the resulting P activation light-inducible. We engineer an entire family of blue light-inducible AraC dimers in Escherichia coli (BLADE) to control gene expression in space and time. We show that BLADE can be used with pre-existing L-arabinose-responsive plasmids and strains, enabling optogenetic experiments without the need to clone. Furthermore, we apply BLADE to control, with light, the catabolism of L-arabinose, thus externally steering bacterial growth with a simple transformation step. Our work establishes BLADE as a highly practical and effective optogenetic tool with plug-and-play functionality-features that we hope will accelerate the broader adoption of optogenetics and the realization of its vast potential in microbiology, synthetic biology and biotechnology.
Topics: AraC Transcription Factor; Arabinose; Escherichia coli; Escherichia coli Proteins; Genetic Engineering; Light
PubMed: 33903769
DOI: 10.1038/s41589-021-00787-6