Inactivated enzymes as probes of the structure of arabinoxylans as observed by atomic force microscopy

Conformational Behavior, Topographical Features, and Antioxidant Activity of Partly De-Esterified Arabinoxylans

This study aimed to investigate the effect of arabinoxylans (AX) partial de-esterification with feruloyl esterase on the polysaccharide conformational behavior, topographical features, and antioxidant activity. After enzyme treatment, the ferulic acid (FA) content in AX was reduced from 7.30 to 5.48 µg FA/mg polysaccharide, and the molecule registered a small reduction in radius of gyration (RG), hydrodynamic radius (Rh), characteristic ratio (C∞), and persistence length (q). A slight decrease in α and a small increase in K constants in the Mark-Houwink-Sakurada equation for partially de-esterified AX (FAX) suggested a reduction in molecule structural rigidity and a more expanded coil conformation, respectively, in relation to AX. Fourier transform infrared spectroscopy spectra of AX and FAX presented a pattern characteristic for this polysaccharide. Atomic force microscopy topographic analysis of FAX showed a more regular surface without larger hollows in relation to AX. The antioxidant activity of FAX, compared to AX, was reduced by 30 and 41% using both 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid) (ABTS+) and 1,1-diphenyl-2-picryl-hydrazyl (DPPH) methods, respectively. These results suggest that feruloyl esterase treatment of AX could offer a strategy to tailor AX chains conformation, morphological features, and antioxidant activity, impacting the development of advanced biomaterials for biomedical and pharmaceutical applications.

Impact of arabinoxylan on characteristics, stability and lipid oxidation of oil-in-water emulsions: Arabinoxylan from wheat bran, corn bran, rice bran, and rye bran

To investigate the impact of arabinoxylan (AX) on the physical and oxidative stability of oil-in-water emulsions, AX from wheat bran, corn bran, rice bran, or rye bran was incorporated into the production of whey protein isolate-stabilised emulsions. Decreased interfacial charge and increased mean particle diameters were recorded in all fresh emulsions with 0.1%-0.5% AX, as recorded by the ζ-potential and particle size measurement, indicating the adsorption of AX onto the oil droplets. No phase separation was observed in all emulsions with ≤0.3% AX after 14-day storage in dark. Spectrophotometric analysis demonstrated that all AX lowered the peroxide value and thiobarbituric acid reactive substance concentration in emulsions, with AX from rice bran being slightly more effective. Consequently, AX has the potential to be used as a natural interfacial antioxidant in emulsions, and the antioxidant capacity of AX varies with its source.

An enzymatic toolkit for selective proteolysis, detection, and visualization of mucin-domain glycoproteins

Densely O-glycosylated mucin domains are found in a broad range of cell surface and secreted proteins, where they play key physiological roles. In addition, alterations in mucin expression and glycosylation are common in a variety of human diseases, such as cancer, cystic fibrosis, and inflammatory bowel diseases. These correlations have been challenging to uncover and establish because tools that specifically probe mucin domains are lacking. Here, we present a panel of bacterial proteases that cleave mucin domains via distinct peptide- and glycan-based motifs, generating a diverse enzymatic toolkit for mucin-selective proteolysis. By mutating catalytic residues of two such enzymes, we engineered mucin-selective binding agents with retained glycoform preferences. StcE^E447D is a pan-mucin stain derived from enterohemorrhagic Escherichia coli that is tolerant to a wide range of glycoforms. BT4244^E575A derived from Bacteroides thetaiotaomicron is selective for truncated, asialylated core 1 structures commonly associated with malignant and premalignant tissues. We demonstrated that these catalytically inactive point mutants enable robust detection and visualization of mucin-domain glycoproteins by flow cytometry, Western blot, and immunohistochemistry. Application of our enzymatic toolkit to ascites fluid and tissue slices from patients with ovarian cancer facilitated characterization of patients based on differences in mucin cleavage and expression patterns.

A Glycoside Hydrolase Family 62 A-L-Arabinofuranosidase from Trichoderma Reesei and Its Applicable Potential during Mashing

Arabinoxylan is the second most abundant component in the endosperm cell wall of barley and it has been shown to have negative effects on the viscosity and filtration rate of wort and beer. In this study, a glycoside hydrolase (GH) family 62 α-L-arabinofuranosidase (AFase), termed as TrAbf62A, was purified from the culture filtrate of Trichoderma reesei CICC 41495 by a combined chromatographic method. The preferred substrates of the purified TrAbf62A were soluble, highly substituted arabinoxylan oligosaccharides and polymers, similar to the type found in barley grain. TrAbf62A exhibited activity towards oligomeric and polymeric arabinoxylans, as well as colorimetric arabinose-based substrates, thus meeting the criteria to be classified as a type B AFase. TrAbf62A released mainly arabinose and xylose from soluble wheat arabinoxylan, thus indicating a dual lytic enzyme activity. Supplementation of TrAbf62A during mashing, with a loading of 12 mU/g malt, resulted in a 36.3% decrease in arabinoxylan polymer content, a 5.6% reduction in viscosity, and finally, a 22.1% increase in filtration rate. These results revealed that TrAbf62A has a high potential value in improving lautering performance during mashing.

Enzymatic cross-linking of ferulated arabinoxylan: effect of laccase or peroxidase catalysis on the gel characteristics

Arabinoxylans (AX) gels at 4% (w/v) were prepared using laccase (LAX gels) or peroxidase (PAX gels), and their cross-linking, rheological, structural, and spectroscopic characteristics were investigated. LAX gels presented lower amount of 5,5'-diferulic acid (11%), smaller mesh size (128 nm), and higher hardness (37 N) and elasticity (430 Pa) than the PAX gels (28%, 197 nm, 7 N, and 120 Pa, respectively). Microscopy of the LAX gels showed linked strands, while the system was less connected in the PAX gels. The Raman band at 2895 cm-1 of the LAX and PAX gels was less intense, indicating enhanced hydrogen bonding compared to that of AX. This decrease was less dramatic for the PAX gels. The greater content of 5,5'-diferulic acid in PAX gels could favor intrachain bonds, affecting their rheological, structural, and spectroscopic characteristics. Laccase may be a better option than peroxidase for AX gelation intended for food and biotechnological applications.

Dietary fiber sources and human benefits: The case study of cereal and pseudocereals

Dietary fiber (DF) includes the remnants of the edible part of plants and analogous carbohydrates that are resistant to digestion and absorption in the human small intestine with complete or partial fermentation in the human large intestine. DF can be classified into two main groups according to its solubility, namely insoluble dietary fiber (IDF) that mainly consists on cell wall components, including cellulose, some hemicelluloses, lignin and resistant starch, and soluble dietary fiber (SDF) that consists of non-cellulosic polysaccharides as non-digestible oligosaccharides, arabinoxylans (AX), β-glucans, some hemicelluloses, pectins, gums, mucilages and inulin. The intake of DF is associated with health benefits. IDF can contribute to the normal function of the intestinal tract and it has an important role in the prevention of colonic diverticulosis and constipation. SDF is extensively fermented by gut microbiota and it is associated with carbohydrate and lipid metabolism, with important health benefits due to its hypocholesterolemic properties. Due to these nutritional and health properties, DF is widely used as functional ingredients in food industry, being whole grain cereals, pulses, fruits and vegetables the main sources of DF. Also some synthetic sources are employed, namely polydextrose, hydroxypropyl methylcellulose or cyclodextrins. The DF content of cereals varies depending on cultivars, their botanical components (pericarp, emdosperm and germ) and the processing conditions they have undergone (baking, extrusion, etc.). In cereal grains, AX are the predominant non-cellulose DF polysaccharides followed by cellulose and β-glucans, while in pseudocereals, pectins are quantitatively predominant.

Getting the feel of food structure with atomic force microscopy

This article describes the progress in the development of the atomic force microscope as an imaging tool and a force transducer, with particular reference to applications in food science. Use as an imaging tool has matured and emphasis is placed on the novel insights gained from the use of the technique to study food macromolecules and food colloids, and the subsequent applications of this new knowledge in food science. Use as a force transducer is still emerging and greater emphasis is given on the methodology and analysis. Where available, applications of force measurements between molecules or between larger colloidal particles are discussed, where they have led to new insights or solved problems related to food science. The future prospects of the technique in imaging or through force measurements are discussed.

Rheology and microstructure of gels based on wheat arabinoxylans enzymatically modified in arabinose to xylose ratio

BACKGROUND

Arabinoxylans (AX) are polysaccharides consisting of a backbone of xyloses with arabinose substituents ester-linked to ferulic acid (FA). The arabinose to xylose ratio (A/X) in AX may vary from 0.3 to 1.1. AX form covalent gels by cross-linking of FA but physical interactions between AX chains also contribute to the network formation. The present study aimed to investigate the rheological and microstructural characteristics of gels based on AX enzymatically modified in A/X.

RESULTS

Tailored AX presented A/X ranging from 0.68 to 0.51 and formed covalent gels. Dimers of FA content and elasticity (G') increased from 0.31 to 0.39 g kg^-1 AX and from 106 to 164 Pa when the A/X in the polysaccharide decreased from 0.68 to 0.51. Atomic force microscopy images of AX gels showed a sponge-like microstructure at A/X = 0.68, whereas, at lower values, gels presented a more compact microstructure. Scanning electron microscopy analysis of AX gels show an arrangement of different morphology, passing from an imperfect honeycomb (A/X = 0.68) to a flake-like microstructure (A/X = 0.51).

CONCLUSION

Lower A/X values favor the aggregation of AX chains resulting in an increase in di-FA content, which improves the rheological and microstructural characteristics of the gel formed. © 2017 Society of Chemical Industry.

Polysaccharide degradation systems of the saprophytic bacterium Cellvibrio japonicus

Study of recalcitrant polysaccharide degradation by bacterial systems is critical for understanding biological processes such as global carbon cycling, nutritional contributions of the human gut microbiome, and the production of renewable fuels and chemicals. One bacterium that has a robust ability to degrade polysaccharides is the Gram-negative saprophyte Cellvibrio japonicus. A bacterium with a circuitous history, C. japonicus underwent several taxonomy changes from an initially described Pseudomonas sp. Most of the enzymes described in the pre-genomics era have also been renamed. This review aims to consolidate the biochemical, structural, and genetic data published on C. japonicus and its remarkable ability to degrade cellulose, xylan, and pectin substrates. Initially, C. japonicus carbohydrate-active enzymes were studied biochemically and structurally for their novel polysaccharide binding and degradation characteristics, while more recent systems biology approaches have begun to unravel the complex regulation required for lignocellulose degradation in an environmental context. Also included is a discussion for the future of C. japonicus as a model system, with emphasis on current areas unexplored in terms of polysaccharide degradation and emerging directions for C. japonicus in both environmental and biotechnological applications.

Mining the "glycocode"--exploring the spatial distribution of glycans in gastrointestinal mucin using force spectroscopy

Mucins are the main components of the gastrointestinal mucus layer. Mucin glycosylation is critical to most intermolecular and intercellular interactions. However, due to the highly complex and heterogeneous mucin glycan structures, the encoded biological information remains largely encrypted. Here we have developed a methodology based on force spectroscopy to identify biologically accessible glycoepitopes in purified porcine gastric mucin (pPGM) and purified porcine jejunal mucin (pPJM). The binding specificity of lectins Ricinus communis agglutinin I (RCA), peanut (Arachis hypogaea) agglutinin (PNA), Maackia amurensis lectin II (MALII), and Ulex europaeus agglutinin I (UEA) was utilized in force spectroscopy measurements to quantify the affinity and spatial distribution of their cognate sugars at the molecular scale. Binding energy of 4, 1.6, and 26 aJ was determined on pPGM for RCA, PNA, and UEA. Binding was abolished by competition with free ligands, demonstrating the validity of the affinity data. The distributions of the nearest binding site separations estimated the number of binding sites in a 200-nm mucin segment to be 4 for RCA, PNA, and UEA, and 1.8 for MALII. Binding site separations were affected by partial defucosylation of pPGM. Furthermore, we showed that this new approach can resolve differences between gastric and jejunum mucins.

GH11 xylanases: Structure/function/properties relationships and applications

For technical, environmental and economical reasons, industrial demands for process-fitted enzymes have evolved drastically in the last decade. Therefore, continuous efforts are made in order to get insights into enzyme structure/function relationships to create improved biocatalysts. Xylanases are hemicellulolytic enzymes, which are responsible for the degradation of the heteroxylans constituting the lignocellulosic plant cell wall. Due to their variety, xylanases have been classified in glycoside hydrolase families GH5, GH8, GH10, GH11, GH30 and GH43 in the CAZy database. In this review, we focus on GH11 family, which is one of the best characterized GH families with bacterial and fungal members considered as true xylanases compared to the other families because of their high substrate specificity. Based on an exhaustive analysis of the sequences and 3D structures available so far, in relation with biochemical properties, we assess biochemical aspects of GH11 xylanases: structure, catalytic machinery, focus on their "thumb" loop of major importance in catalytic efficiency and substrate selectivity, inhibition, stability to pH and temperature. GH11 xylanases have for a long time been used as biotechnological tools in various industrial applications and represent in addition promising candidates for future other uses.

Catalytically active monomer of glutathione S-transferase pi and key residues involved in the electrostatic interaction between subunits

Human glutathione transferase pi (GST pi) has been crystallized as a homodimer, with a subunit molecular mass of approximately 23 kDa; however, in solution the average molecular mass depends on protein concentration, approaching that of monomer at <0.03 mg/ml, concentrations typically used to measure catalytic activity of the enzyme. Electrostatic interaction at the subunit interface greatly influences the dimer-monomer equilibrium of the enzyme and is an important force for holding subunits together. Arg-70, Arg-74, Asp-90, Asp-94, and Thr-67 were selected as target sites for mutagenesis, because they are at the subunit interface. R70Q, R74Q, D90N, D94N, and T67A mutant enzymes were constructed, expressed in Escherichia coli, and purified. The construct of N-terminal His tag enzyme facilitates the purification of GST pi, resulting in a high yield of enzyme, but does not alter the kinetic parameters or secondary structure of the enzyme. Our results indicate that these mutant enzymes show no appreciable changes in K(m) for 1-chloro-2,4-dinitrobenzene and have similar CD spectra to that of wild-type enzyme. However, elimination of the charges of either Arg-70, Arg-74, Asp-90, or Asp-94 shifts the dimer-monomer equilibrium toward monomer. In addition, replacement of Asp-94 or Arg-70 causes a large increase in the K(m)(GSH), whereas substitution for Asp-90 or Arg-74 primarily results in a marked decrease in V(max). The GST pi retains substantial catalytic activity as a monomer probably because the glutathione and electrophilic substrate sites (such as for 1-chloro-2,4-dinitrobenzene) are predominantly located within each subunit.

Versatile derivatives of carbohydrate-binding modules for imaging of complex carbohydrates approaching the molecular level of resolution

The innate binding specificity of different carbohydrate-binding modules (CBMs) offers a versatile approach for mapping the chemistry and structure of surfaces that contain complex carbohydrates. We have employed the distinct recognition properties of a double His-tagged recombinant CBM tagged with semiconductor quantum dots for direct imaging of crystalline cellulose at the molecular level of resolution, using transmission and scanning transmission electron microscopy. In addition, three different types of CBMs from families 3, 6, and 20 that exhibit different carbohydrate specificities were each fused with either green fluorescent protein (GFP) or red fluorescent protein (RFP) and employed for double-labeling fluorescence microscopy studies of primary cell walls and various mixtures of complex carbohydrate target molecules. CBM probes can be used for characterizing both native complex carbohydrates and engineered biomaterials.

Alpha-L-arabinofuranosidases: the potential applications in biotechnology

Recently, alpha-L-arabinofuranosidases (EC3.2.1.55) have received increased attention primarily due to their role in the degradation of lignocelluloses as well as their positive effect on the activity of other enzymes acting on lignocelluloses. As a result, these enzymes are used in many biotechnological applications including wine industry, clarification of fruit juices, digestion enhancement of animal feedstuffs and as a natural improver for bread. Moreover, these enzymes could be used to improve existing technologies and to develop new technologies. The production, mechanisms of action, classification, synergistic role, biochemical properties, substrate specificities, molecular biology and biotechnological applications of these enzymes have been reviewed in this article.

Probing the cell wall heterogeneity of micro-dissected wheat caryopsis using both active and inactive forms of a GH11 xylanase

The external envelope of wheat grain (Triticum aestivum L. cv. Isengrain) is a natural composite whose tissular and cellular heterogeneity constitute a significant barrier for enzymatic cell wall disassembly. To better understand the way in which the cell wall network and tissular organization hamper enzyme penetration, we have devised a strategy based on in situ visualization of an active and an inactive form of a xylanase in whole-wheat bran and in three micro-dissected layers (the outer bran, the inner bran and the aleurone layer). The main aims of this study were to (1) evaluate the role of cuticular layers as obstacles to enzyme diffusion, (2) assess the impact of the cell wall network on xylanase penetration, (3) highlight wall heterogeneity. To conduct this study, we created by in vitro mutagenesis a hydrolytically inactive xylanase that displayed full substrate binding ability, as demonstrated by the calculation of dissociation constants (K(d)) using fluorescence titration. To examine enzyme penetration and action, immunocytochemical localization of the xylanases and of feebly substituted arabinoxylans (AXs) was performed following incubation of the bran layers, or whole bran with active and inactive isoforms of the enzyme for different time periods. The data obtained showed that the micro-dissected layers provided an increased accessible surface for the xylanase and that the enzyme-targeted cell walls were penetrated more quickly than those in intact bran. Examination of immunolabelling of xylanase indicated that the cuticle layers constitute a barrier for enzyme penetration in bran. Moreover, our data indicated that the cell wall network by itself physically restricts enzyme penetration. Inactive xylanase penetration was much lower than that of the active form, whose penetration was facilitated by the concomitant depletion of AXs in enzyme-sensitive cell walls.

AFM studies of water-soluble wheat arabinoxylans—effects of esterase treatment

The degradation products of water-soluble wheat arabinoxylans treated with Aspergillus niger ferulic acid esterase (FAEA-able to cleave 5,5'- and 8-O-4'-ferulic acid dimers) have been characterised by atomic force microscopy (AFM) and size exclusion chromatography. The AFM images of arabinoxylans confirmed that a small proportion ( approximately 15%) of the population of arabinoxylan molecules contain xylan-based branches attached to the xylan-based backbone. Treatment with FAEA reduced the contour length of the molecules suggesting that certain dimeric ferulic acid linkages may play a previously unconfirmed role in the elongation of arabinoxylans. Overnight treatment with FAEA led to a reduction in the density of branches suggesting that they may also be linked to the backbone through phenolic linkages.