Progress in cyclodextrins as important molecules regulating catalytic processes of glycoside hydrolases

Cyclodextrins (CDs) are important starch derivatives and commonly comprise α-, β-, and γ-CDs. Their hydrophilic surface and hydrophobic inner cavity enable regulation of enzyme catalysis through direct or indirect interactions. Clarifying interactions between CDs and enzyme is of great value for enzyme screening, mechanism exploration, regulation of catalysis, and applications. We summarize the interactions between CDs and glycoside hydrolases (GHs) according to two aspects: 1) CD as products, substrates, inhibitors and activators of enzymes, directly affecting the reaction process; 2) CDs indirectly affecting the enzymatic reaction by solubilizing substrates, relieving substrate/product inhibition, increasing recombinant enzyme production and storage stability, isolating and purifying enzymes, and serving as ligands in crystal structure to identify functional amino acid residues. Additionally, CD enzyme mimetics are developed and used as catalysts in traditional artificial enzymes as well as nanozymes, making the application of CDs no longer limited to GHs. This review concerns the regulation of GHs catalysis by CDs, and gives insights into research on interactions between enzymes and ligands.

Degree of hydrolysis is a poor predictor of the sensitizing capacity of whey- and casein-based hydrolysates in a Brown Norway rat model of cow's milk allergy

The use of infant formulas (IFs) based on hydrolyzed cow's milk proteins to prevent cow's milk allergy (CMA) is highly debated. The risk of sensitization to milk proteins induced by IFs may be affected by the degree of hydrolysis (DH) as well as other physicochemical properties of the cow's milk-based protein hydrolysates within the IFs. The immunogenicity (specific IgG1 induction) and sensitizing capacity (specific IgE induction) of 30 whey- or casein-based hydrolysates with different physicochemical characteristics were compared using an intraperitoneal model of CMA in Brown Norway rats. In general, the whey-based hydrolysates demonstrated higher immunogenicity than casein-based hydrolysates, inducing higher levels of hydrolysate-specific and intact-specific IgG1. The immunogenicity of the hydrolysates was influenced by DH, peptide size distribution profile, peptide aggregation, nano-sized particle formation, and surface hydrophobicity. Yet, only the surface hydrophobicity was found to affect the sensitizing capacity of hydrolysates, as high hydrophobicity was associated with higher levels of specific IgE. The whey- and casein-based hydrolysates exhibited distinct immunological properties with highly diverse molecular composition and physicochemical properties which are not accounted for by measuring DH, which was a poor predictor of sensitizing capacity. Thus, future studies should consider and account for physicochemical characteristics when assessing the sensitizing capacity of cow's milk-based protein hydrolysates.

N1019D Mutant of Limosilactobacillus reuteri 121 4,6-α-Glucanotransferase GtfB Significantly Improved Catalytic Activity

Limosilactobacillus reuteri 121 4,6-α-glucanotransferase GtfB (Lr 121 GtfB), belonging to glycoside hydrolase family 70 (GH70), synthesizes linear isomalto/malto polysaccharides having (α1→6) linkages attached to the nonreducing ends of (α1→4) linked maltose oligosaccharide segments using starch or maltodextrin as a substrate. Since Lr 121 GtfB has low catalytic activity and efficiency, it leads to substrate regeneration and reduced substrate utilization. In this study, we superimposed the crystal structure of Lr 121 GtfB-ΔNΔV with that of L. reuteri NCC 2613 GtfB-ΔNΔV (Lr 2613 GtfB-ΔNΔV) to identify the acceptor binding subsites +1 to +3 and constructed five single-residue mutants and a random mutagenesis of N1019. Compared with the wild-type, N1019D Lr 121 GtfB-ΔN did not alter the product specificity, increased the catalytic activity and efficiency by 420 and 590%, respectively, and maintained >80% relative activity in the pH 3.5-6.5 interval. The findings will contribute to the industrial application of Lr 121 GtfB and provide new solutions for starch synthesis of higher value derivatives.

Bioinformatics and functional selection of GH77 4-α-glucanotransferases for potato starch modification

4-α-glucanotransferases (4αGTs, EC 2.4.1.25) from glycoside hydrolase family 77 (GH77) catalyze chain elongation of starch amylopectin chains and can be utilized to structurally modify starch to tailor its gelation properties. The potential relationship between the structural design of 4αGTs and functional starch modification is unknown. Here, family GH77 was mined in silico for enzyme candidates based on sub-grouping guided by Conserved Unique Peptide Patterns (CUPP) bioinformatics categorization. From + 12,000 protein sequences a representative set of 27 4αGTs, representing four different domain architectures, different bacterial origins and diverse CUPP groups, was selected for heterologous expression and further study. Most of the enzymes catalyzed starch modification, but their efficacies varied substantially. Five of the 4αGTs were characterized in detail, and their action was compared to that of the industrial benchmark enzyme, Tt4αGT (CUPP 77_1.2), from Thermus thermophilus. Reaction optima of the five 4αGTs ranged from ∼40-60 °C and pH 7.3-9.0. Several were stable for a minimum 4 h at 70 °C. Domain architecture type A proteins, consisting only of a catalytic domain, had high thermal stability and high starch modification ability. All five novel 4αGTs (and Tt4αGT) induced enhanced gelling of potato starch. One, At4αGT from Azospirillum thermophilum (CUPP 77_2.4), displayed distinct starch modifying abilities, whereas T24αGT from Thermus sp. 2.9 (CUPP 77_1.2) modified the starch similarly to Tt4αGT, but slightly more effectively. T24αGT and At4αGT are thus interesting candidates for industrial starch modification. A model is proposed to explain the link between the 4αGT induced molecular modifications and macroscopic starch gelation.

Insights into the Structure-Function Relationship of GH70 GtfB α-Glucanotransferases from the Crystal Structure and Molecular Dynamic Simulation of a Newly Characterized Limosilactobacillus reuteri N1 GtfB Enzyme

α-Glucanotransferases of the CAZy family GH70 convert starch-derived donors to industrially important α-glucans. Here, we describe characteristics of a novel GtfB-type 4,6-α-glucanotransferase of high enzyme activity (60.8 U mg-1) from Limosilactobacillus reuteri N1 (LrN1 GtfB), which produces surprisingly large quantities of soluble protein in heterologous expression (173 mg pure protein per L of culture) and synthesizes the reuteran-like α-glucan with (α1 → 6) linkages in linear chains and branch points. Protein structural analysis of LrN1 GtfB revealed the potential crucial residues at subsites -2∼+2, particularly H265, Y214, and R302, in the active center as well as previously unidentified surface binding sites. Furthermore, molecular dynamic simulations have provided unprecedented insights into linkage specificity hallmarks of the enzyme. Therefore, LrN1 GtfB represents a potent enzymatic tool for starch conversion, and this study promotes our knowledge on the structure-function relationship of GH70 GtfB α-glucanotransferases, which might facilitate the production of tailored α-glucans by enzyme engineering in future.

Flagellar interference with plasmid uptake in biofilms: a joint experimental and modeling study

Plasmid conjugation is a key facilitator of horizontal gene transfer (HGT), and plasmids encoding antibiotic resistance drive the increasing prevalence of antibiotic resistance. In natural, engineered, and clinical environments, bacteria often grow in protective biofilms. Therefore, a better understanding of plasmid transfer in biofilms is needed. Our aim was to investigate plasmid transfer in a biofilm-adapted wrinkly colony mutant of Xanthomonas retroflexus (XRw) with enhanced matrix production and reduced motility. We found that XRw biofilms had an increased uptake of the broad host-range IncP-1ϵ plasmid pKJK5 compared to the wild type (WT). Proteomics revealed fewer flagellar-associated proteins in XRw, suggesting that flagella were responsible for reducing plasmid uptake. This was confirmed by the higher plasmid uptake of non-flagellated fliM mutants of the X. retroflexus wrinkly mutant as well as the wild type. Moreover, testing several flagellar mutants of Pseudomonas putida suggested that the flagellar effect was more general. We identified seven mechanisms with the potential to explain the flagellar effect and simulated them in an individual-based model. Two mechanisms could thus be eliminated (increased distances between cells and increased lag times due to flagella). Another mechanism identified as viable in the modeling was eliminated by further experiments. The possibility of steric hindrance of pilus movement and binding by flagella, reducing the frequency of contact and thus plasmid uptake, proved viable, and the three other viable mechanisms had a reduced probability of plasmid transfer in common. Our findings highlight the important yet complex effects of flagella during bacterial conjugation in biofilms.IMPORTANCEBiofilms are the dominant form of microbial life and bacteria living in biofilms are markedly different from their planktonic counterparts, yet the impact of the biofilm lifestyle on horizontal gene transfer (HGT) is still poorly understood. Horizontal gene transfer by conjugative plasmids is a major driver in bacterial evolution and adaptation, as exemplified by the troubling spread of antibiotic resistance. To either limit or promote plasmid prevalence and dissemination, we need a better understanding of plasmid transfer between bacterial cells, especially in biofilms. Here, we identified a new factor impacting the transfer of plasmids, flagella, which are required for many types of bacterial motility. We show that their absence or altered activity can lead to enhanced plasmid uptake in two bacterial species, Xanthomonas retroflexus and Pseudomonas putida. Moreover, we demonstrate the utility of mathematical modeling to eliminate hypothetical mechanisms.

Sequential starch modification by branching enzyme and 4-α-glucanotransferase improves retention of curcumin in starch-alginate beads

A new super-branched amylopectin with longer exterior chains was produced from normal maize starch by modification with branching enzyme followed by 4-α-glucanotransferase, and applied for co-entrapment of a curcumin-loaded emulsion in alginate beads. The network structure of the gel beads was obtained with Ca2+-cross-linked alginate and a modest load of retrograded starch. The dual enzyme modified starch contained more and longer α-1,6-linked branch chains than single enzyme modified and unmodified starches and showed superior resistance to digestive enzymes. Alginate beads with or without starch were of similar size (1.69-1.74 mm), but curcumin retention was improved 1.4-2.8-fold in the presence of different starches. Thus, subjecting the curcumin-loaded beads to in vitro simulated gastrointestinal digestion resulted in retention of 70, 43 and 22 % of the curcumin entrapped in the presence of modified, unmodified, or no starch, respectively. Molecular docking provided support for curcumin interacting with starch via hydrogen bonding, hydrophobic contacts and π-π stacking. The study highlights the potential of utilizing low concentration of dual-enzyme modified starch with alginate to create a versatile vehicle for controlled release and targeted delivery of bioactive compounds.

Functional Roles of N-Terminal Domains in Pullulanase from Human Gut Lactobacillus acidophilus

Pullulanases are multidomain α-glucan debranching enzymes with one or more N-terminal domains (NTDs) including carbohydrate-binding modules (CBMs) and domains of unknown function (DUFs). To elucidate the roles of NTDs in Lactobacillus acidophilus NCFM pullulanase (LaPul), two truncated variants, Δ41-LaPul (lacking CBM41) and Δ(41+DUFs)-LaPul (lacking CBM41 and two DUFs), were produced recombinantly. LaPul recognized 1.3- and 2.2-fold more enzyme attack-sites on starch granules compared to Δ41-LaPul and Δ(41+DUFs)-LaPul, respectively, as measured by interfacial kinetics. Δ41-LaPul displayed markedly lower affinity for starch granules and β-cyclodextrin (10- and >21-fold, respectively) in comparison to LaPul, showing substrate binding mainly stems from CBM41. Δ(41+DUFs)-LaPul exhibited a 12 °C lower melting temperature than LaPul and Δ41-LaPul, indicating that the DUFs are critical for LaPul stability. Notably, Δ41-LaPul exhibited a 14-fold higher turnover number (kcat) and 9-fold higher Michaelis constant (KM) compared to LaPul, while Δ(41+DUFs)-LaPul's values were close to those of LaPul, possibly due to the exposure of aromatic by truncation.

Three alginate lyases provide a new gut Bacteroides ovatus isolate with the ability to grow on alginate

Humans consume alginate in the form of seaweed, food hydrocolloids, and encapsulations, making the digestion of this mannuronic acid (M) and guluronic acid (G) polymer of key interest for human health. To increase knowledge on alginate degradation in the gut, a gene catalog from human feces was mined for potential alginate lyases (ALs). The predicted ALs were present in nine species of the Bacteroidetes phylum, of which two required supplementation of an endo-acting AL, expected to mimic cross-feeding in the gut. However, only a new isolate grew on alginate. Whole-genome sequencing of this alginate-utilizing isolate suggested that it is a new Bacteroides ovatus strain harboring a polysaccharide utilization locus (PUL) containing three ALs of families: PL6, PL17, and PL38. The BoPL6 degraded polyG to oligosaccharides of DP 1-3, and BoPL17 released 4,5-unsaturated monouronate from polyM. BoPL38 degraded both alginates, polyM, polyG, and polyMG, in endo-mode; hence, it was assumed to deliver oligosaccharide substrates for BoPL6 and BoPL17, corresponding well with synergistic action on alginate. BoPL17 and BoPL38 crystal structures, determined at 1.61 and 2.11 Å, respectively, showed (α/α)6-barrel + anti-parallel β-sheet and (α/α)7-barrel folds, distinctive for these PL families. BoPL17 had a more open active site than the two homologous structures. BoPL38 was very similar to the structure of an uncharacterized PL38, albeit with a different triad of residues possibly interacting with substrate in the presumed active site tunnel. Altogether, the study provides unique functional and structural insights into alginate-degrading lyases of a PUL in a human gut bacterium.IMPORTANCEHuman ingestion of sustainable biopolymers calls for insight into their utilization in our gut. Seaweed is one such resource with alginate, a major cell wall component, used as a food hydrocolloid and for encapsulation of pharmaceuticals and probiotics. Knowledge is sparse on the molecular basis for alginate utilization in the gut. We identified a new Bacteroides ovatus strain from human feces that grew on alginate and encoded three alginate lyases in a gene cluster. BoPL6 and BoPL17 show complementary specificity toward guluronate (G) and mannuronate (M) residues, releasing unsaturated oligosaccharides and monouronic acids. BoPL38 produces oligosaccharides degraded by BoPL6 and BoPL17 from both alginates, G-, M-, and MG-substrates. Enzymatic and structural characterization discloses the mode of action and synergistic degradation of alginate by these alginate lyases. Other bacteria were cross-feeding on alginate oligosaccharides produced by an endo-acting alginate lyase. Hence, there is an interdependent community in our guts that can utilize alginate.

The Engineered Hexosaminidase TtOGA-D120N Is an Efficient O-/N-/S-Glycoligase That Also Catalyzes Formation and Release of Oxazoline Donors for Cascade Syntheses with Glycosynthases or Transglycosylases

Engineering glycoside hydrolases is a major route to obtaining catalysts forming glycosidic bonds. Glycosynthases, thioglycoligases, and transglycosylases represent the main strategies, each having advantages and drawbacks. Here, we show that an engineered enzyme from the GH84 family, the acid-base mutant TtOGA-D120N, is an efficient O-, N-, and S-glycoligase, able to use Ssp3, Osp3, Nsp2, and Nsp nucleophiles. Moreover, TtOGA-D120N catalyzes the formation and release of N-acetyl-d-glucosamine 1,2-oxazoline, the intermediate of hexosaminidases displaying substrate-assisted catalysis. This release of an activated intermediate allows cascade synthesis by combination with transglycosylases or glycosynthases, here exemplified by synthesis of the human milk oligosaccharide lacto-N-triose II.

A serologically assessed neo-epitope biomarker of cellular fibronectin degradation is related to pulmonary fibrosis

BACKGROUND

Idiopathic pulmonary fibrosis (IPF) is characterized by excessive extracellular matrix (ECM) remodeling, herein ECM degradation. Fibronectin (FN) is an important component of the ECM that is produced by multiple cell types, including fibroblasts. Extra domain B (EDB) is specific for a cellular FN isoform which is found in the ECM. We sought to develop a non-invasive test to investigate whether matrix metalloproteinase 8 (MMP-8) degradation of EDB in cellular FN results in a specific protein fragment that can be assessed serologically and if levels relate to pulmonary fibrosis.

METHOD

Cellular FN was cleaved in vitro by MMP-8 and a protein fragment was identified by mass spectrometry. A monoclonal antibody (mAb) was generated, targeting a neo-epitope originating from EDB in cellular FN. Utilizing this mAb, a neo-epitope specific enzyme-linked immunosorbent assay (FN-EDB) was developed and technically validated. Serum FN-EDB was assessed in an IPF cohort (n=98), registered at clinicaltrials.gov (NCT02818712), and in healthy controls (n=35).

RESULTS

The FN-EDB assay had high specificity for the MMP-8 degraded neo-epitope and was technically robust. FN-EDB serum levels were not influenced by age, sex, ethnicity, or BMI. Moreover, FN-EDB serum levels were significantly higher in IPF patients (median 31.38 [IQR 25.79-46.84] ng/mL) as compared to healthy controls (median 28.05 [IQR 21.58-33.88] ng/mL, p=0.023).

CONCLUSION

We developed the neo-epitope specific FN-EDB assay, a competitive ELISA, as a tool for serological assessment of MMP-8 mediated degradation of EDB in cellular FN. This study indicates that degradation of EDB in cellular FN is elevated in IPF and warrants further investigation.

Cost-effective and controllable synthesis of isomalto/malto-polysaccharides from β-cyclodextrin by combined action of cyclodextrinase and 4,6-α-glucanotransferase GtfB

Isomalto/malto-polysaccharides (IMMPs) derived from malto-oligosaccharides such as maltoheptaose (G7) are elongated non-branched gluco-oligosaccharides produced by 4,6-α-glucanotransferase (GtfB). However, G7 is expensive and cumbersome to produce commercially. In this study, a cost-effective enzymatic process for IMMPs synthesis is developed that utilizes the combined action of cyclodextrinase from Palaeococcus pacificus (PpCD) and GtfB-ΔN from Limosilactobacillus reuteri 121 to convert β-cyclodextrin into IMMPs with a maximum yield (16.19 %, w/w). The purified IMMPs synthesized by simultaneous or sequential treatments, designated as IMMP-Sim and IMMP-Seq, possess relatively high contents of α-(1 → 6) glucosidic linkages. By controlling the release of G7 and smaller malto-oligosaccharides by PpCD, IMMP-Seq was obtained of DP varying from 12.9 to 29.5. Enzymatic fingerprinting revealed different linkage-type distribution of α-(1 → 6) linked segments with α-(1 → 4) segments embedded at the reducing end and middle part. The proportion of α-(1 → 6) segments containing the non-reducing end was 56.76 % for IMMP-Sim but 28.98 % for IMMP-Seq. Addition of G3 or G4 as specific acceptors resulted in IMMPs exhibiting low polydispersity. This procedure can be applied as a novel bioprocess that does not require costy high-purity malto-oligosaccharides and with control of the average DP of IMMPs by adjusting the substrate composition.

Improved Hydrolysis of Granular Starches by a Psychrophilic α-Amylase Starch Binding Domain-Fusion

Degradation of starch granules by a psychrophilic α-amylase, AHA, from the Antarctic bacterium Pseudoalteromonas haloplanktis TAB23 was facilitated by C-terminal fusion to a starch-binding domain (SBD) from either Aspergillus niger glucoamylase (SBD_GA) or Arabidopsis thaliana glucan, water dikinase 3 (SBD_GWD3) via a decapeptide linker. Depending on the waxy, normal or high-amylose starch type and the botanical source, the AHA-SBD fusion enzymes showed up to 3 times higher activity than AHA wild-type. The SBD-fusion thus increased the density of enzyme attack-sites and binding-sites on the starch granules by up to 5- and 7-fold, respectively, as measured using an interfacial catalysis approach that combined conventional Michaelis-Menten kinetics, with the substrate in excess, and inverse kinetics, having enzyme in excess, with enzyme-starch granule adsorption isotherms. Higher substrate affinity of the SBD_GA compared to SBD_GWD3 was accompanied by the superior activity of AHA-SBD_GA in agreement with the Sabatier principle of adsorption limited heterogenous catalysis.

Exploration of the Transglycosylation Activity of Barley Limit Dextrinase for Production of Novel Glycoconjugates

A few α-glucan debranching enzymes (DBEs) of the large glycoside hydrolase family 13 (GH13), also known as the α-amylase family, have been shown to catalyze transglycosylation as well as hydrolysis. However, little is known about their acceptor and donor preferences. Here, a DBE from barley, limit dextrinase (HvLD), is used as a case study. Its transglycosylation activity is studied using two approaches; (i) natural substrates as donors and different p-nitrophenyl (pNP) sugars as well as different small glycosides as acceptors, and (ii) α-maltosyl and α-maltotriosyl fluorides as donors with linear maltooligosaccharides, cyclodextrins, and GH inhibitors as acceptors. HvLD showed a clear preference for pNP maltoside both as acceptor/donor and acceptor with the natural substrate pullulan or a pullulan fragment as donor. Maltose was the best acceptor with α-maltosyl fluoride as donor. The findings highlight the importance of the subsite +2 of HvLD for activity and selectivity when maltooligosaccharides function as acceptors. However, remarkably, HvLD is not very selective when it comes to aglycone moiety; different aromatic ring-containing molecules besides pNP could function as acceptors. The transglycosylation activity of HvLD can provide glycoconjugate compounds with novel glycosylation patterns from natural donors such as pullulan, although the reaction would benefit from optimization.

Interfacial Catalysis during Amylolytic Degradation of Starch Granules: Current Understanding and Kinetic Approaches

Enzymatic hydrolysis of starch granules forms the fundamental basis of how nature degrades starch in plant cells, how starch is utilized as an energy resource in foods, and develops efficient, low-cost saccharification of starch, such as bioethanol and sweeteners. However, most investigations on starch hydrolysis have focused on its rates of degradation, either in its gelatinized or soluble state. These systems are inherently more well-defined, and kinetic parameters can be readily derived for different hydrolytic enzymes and starch molecular structures. Conversely, hydrolysis is notably slower for solid substrates, such as starch granules, and the kinetics are more complex. The main problems include that the surface of the substrate is multifaceted, its chemical and physical properties are ill-defined, and it also continuously changes as the hydrolysis proceeds. Hence, methods need to be developed for analyzing such heterogeneous catalytic systems. Most data on starch granule degradation are obtained on a long-term enzyme-action basis from which initial rates cannot be derived. In this review, we discuss these various aspects and future possibilities for developing experimental procedures to describe and understand interfacial enzyme hydrolysis of native starch granules more accurately.

Increasing Protein Content of Rice Flour with Maintained Processability by Using Granular Starch Hydrolyzing Enzyme

Rice flour (RF) has become a promising food material. In the present study, RF with higher protein content was prepared using a granular starch hydrolyzing enzyme (GSHE). Particle size, morphology, crystallinity, and molecular structures of RF and rice starch (RS) were characterized to establish a hydrolytic mechanism; thermal, pasting, and rheological properties were determined to evaluate processability using differential scanning calorimetry (DSC), rapid viscosity analysis (RVA), and rheometer, respectively. The GSHE treatment resulted in pinholes, pits, and surface erosion through sequential hydrolysis of crystalline and amorphous areas on the starch granule surface. The amylose content decreased with hydrolysis time, while the very short chains (DP < 6) increased rapidly at 3 h but decreased slightly later. After hydrolysis for 24 h, the protein content in RF increased from 8.52% to 13.17%. However, the processability of RF was properly maintained. Specifically, the data from DSC showed that the conclusion temperature and endothermic enthalpy of RS barely changed. The result of rapid RVA and rheological measurement indicated that RF paste viscosity and viscoelastic properties dropped rapidly after 1 h hydrolysis and thereafter recovered slightly. This study provided a new RF raw material useful for improving and developing RF-based foods.

Designing starch derivatives with desired structures and functional properties via rearrangements of glycosidic linkages by starch-active transglycosylases

Modification of starch by transglycosylases from glycoside hydrolase families has attracted much attention recently; these enzymes can produce starch derivatives with novel properties, i.e. processability and functionality, employing highly efficient and safe methods. Starch-active transglycosylases cleave starches and transfer linear fragments to acceptors introducing α-1,4 and/or linear/branched α-1,6 glucosidic linkages, resulting in starch derivatives with excellent properties such as complexing and resistance to digestion characteristics, and also may be endowed with new properties such as thermo-reversible gel formation. This review summarizes the effects of variations in glycosidic linkage composition on structure and properties of modified starches. Starch-active transglycosylases are classified into 4 groups that form compounds: (1) in cyclic with α-1,4 glucosidic linkages, (2) with linear chains of α-1,4 glucosidic linkages, (3) with branched α-1,6 glucosidic linkages, and (4) with linear chains of α-1,6 glucosidic linkages. We discuss potential processability and functionality of starch derivatives with different linkage combinations and structures. The changes in properties caused by rearrangements of glycosidic linkages provide guidance for design of starch derivatives with desired structures and properties, which promotes the development of new starch products and starch processing for the food industry.

Gut bacterial alginate degrading enzymes

Alginates are abundant marine anionic polysaccharides consumed by humans. Thus, over the years some understanding has emerged about alginate utilization by human gut microbiota (HGM). However, insights have been obtained only recently at the molecular level with regard to structure and function of alginate degrading and metabolizing enzymes from HGM. Still, numerous studies report on effects of alginates on bacterial communities from digestive tracts of various, predominantly marine organisms feeding on alginate and some of the involved alginate lyases have been characterized. Other studies describe the beneficial impact on gut microbiota elicited by alginates in animal models, for example, high-fat-diet-fed mice addressing obesity or as feed supplements for livestock. Alginates are depolymerized by a β-elimination reaction catalyzed by polysaccharide lyases (PLs) referred to as alginate lyases (ALs). The ALs are found in 15 of the 42 PL families categorized in the CAZy database. While genome mining has led to prediction of ALs encoded by bacteria of the HGM; currently, only four enzymes from this niche have been characterized biochemically and two crystal structures are reported. Alginates are composed of mannuronate (M) and guluronate (G) residues organized in M-, G-, and MG-blocks, which calls for ALs of complementary specificity to effectively depolymerize alginate to alginate oligosaccharides (AOSs) and monosaccharides. Typically, ALs of different PL families are encoded by genes arranged in clusters denoted as polysaccharide utilization loci. Currently, biochemical and structural analyses of marine bacterial ALs contribute to depicting the mode of action of predicted enzymes from bacteria of the HGM.

A practical approach to producing the single-arm linear dextrin, a chimeric glucosaccharide containing an (α-1 → 4) linked portion at the nonreducing end of an (α-1 → 6) glucochain

How to improve the solubility of linear dextrins (LD) and retain their characteristic helix amphiphilic cavities with flexible embedding capability, is a question worth exploring without adding new chemical groups. The strategy presented in this study is to attach a highly flexible (α-1 → 6) glucochain at the reducing end of LD by preparing a new type of dextrin, referred to as single-arm linear dextrin (SLD). In the actual synthesis, an (α-1 → 6) linked oligosaccharide of DP¯ 10.7 (PDI = 1.28) was formed by extension of glucose units onto sucrose (2 M) by using L940W mutant of the glucansucrase GTF180-ΔN firstly. Next using γ-CD as glucosylation donor γ-CGTase extended this (α-1 → 6) glucochain with (α-1 → 4) bonds. SLD is a chimeric glucosaccharide comprising an (α-1 → 4) linked part (DP¯ 10.5) attached to the nonreducing end of an (α-1 → 6) glucochain as verified by enzyme fingerprinting and ¹H NMR. Furthermore, SLD was validated to show greatly improved solubility and dispersibility of resveratrol in water, as indicated by a 3.12-fold enhancement over the solubility in the presence of 0.014 M SLD. This study provided a new strategy for solving the solubility problem of LD and opens possibilities for new design of the fine structure of starch-like materials.

Importance of Inactivation Methodology in Enzymatic Processing of Raw Potato Starch: NaOCl as Efficient α-Amylase Inactivation Agent

Efficient inactivation of microbial α-amylases (EC 3.2.1.1) can be a challenge in starch systems as the presence of starch has been shown to enhance the stability of the enzymes. In this study, commonly used inactivation methods, including multistep washing and pH adjustment, were assessed for their efficiency in inactivating different α-amylases in presence of raw potato starch. Furthermore, an effective approach for irreversible α-amylase inactivation using sodium hypochlorite (NaOCl) is demonstrated. Regarding inactivation by extreme pH, the activity of five different α-amylases was either eliminated or significantly reduced at pH 1.5 and 12. However, treatment at extreme pH for 5 min, followed by incubation at pH 6.5, resulted in hydrolysis yields of 42–816% relative to controls that had not been subjected to extreme pH. “Inactivation” by multistep washing with water, ethanol, and acetone followed by gelatinization as preparation for analysis gave significant starch hydrolysis compared to samples inactivated with NaOCl before the wash. This indicates that the further starch degradation observed in samples subjected to washing only took place during the subsequent gelatinization. The current study demonstrates the importance of inactivation methodology in α-amylase-mediated raw starch depolymerization and provides a method for efficient α-amylase inactivation in starch systems.

Tuning alginate β-lactoglobulin complex coacervation by modulating pH and temperature

The use of biomolecules in food matrices and encapsulation systems is, as in other areas, moving towards greener solutions and a center piece here is the complex coacervation between natural anionic polysaccharides and proteins. Both alginate and β-lactoglobulin (β-Lg) are used in different sectors and have been shown to coacervate at pH < 5.2. Albeit with increased interest, complex coacervation has almost exclusively been studied from a macromolecular perspective, and described as an interaction based on charge-charge attraction. Here, we show that through changes in pH and temperature, alginate β-Lg complex coacervation can be tuned to purpose. By detailed biophysical and chemical characterization of coacervation and coacervate particles, insights into the molecular interaction and effect of external factors are obtained. We find that carboxylate resonance stabilization causes a release of protons at pH < pK_a,alginate and an uptake of protons at pH > pK_a,alginate upon coacervation. Proton release and uptake were quantified at pH 2.65 and 4.00 by isothermal titration calorimetry to be 4 and 2 protons per β-Lg molecule, respectively. By increasing the temperature to 65 °C, we discovered a secondary β-Lg concentration dependent coacervation step, where the formed particles change into large assemblies driven by entropy. These findings bring new insights to complex coacervation and its applicability in microencapsulation and drug delivery.

Molecular insights into alginate β-lactoglobulin A multivalencies-The foundation for their amorphous aggregates and coacervation

For improved control of biomaterial property design, a better understanding of complex coacervation involving anionic polysaccharides and proteins is needed. Here, we address the initial steps in condensate formation of β-lactoglobulin A (β-LgA) with nine defined alginate oligosaccharides (AOSs) and describe their multivalent interactions in structural detail. Binding of AOSs containing four, five, or six uronic acid residues (UARs), either all mannuronate (M), all guluronate (G), or alternating M and G embodying the block structural components of alginates, was characterized by isothermal titration calorimetry, nuclear magnetic resonance spectroscopy (NMR), and molecular docking. β-LgA was highly multivalent exhibiting binding stoichiometries decreasing from five to two AOSs with increasing degree of polymerization (DP) and similar affinities in the mid micromolar range. The different AOS binding sites on β-LgA were identified by NMR chemical shift perturbation analyses and showed diverse compositions of charged, polar and hydrophobic residues. Distinct sites for the shorter AOSs merged to accommodate longer AOSs. The AOSs bound dynamically to β-LgA, as concluded from saturation transfer difference and ¹ H-ligand-targeted NMR analyses. Molecular docking using Glide within the Schrödinger suite 2016-1 revealed the orientation of AOSs to only vary slightly at the preferred β-LgA binding site resulting in similar XP glide scores. The multivalency coupled with highly dynamic AOS binding with lack of confined conformations in the β-LgA complexes may help explain the first steps toward disordered β-LgA alginate coacervate structures.

Impact of Starch Binding Domain Fusion on Activities and Starch Product Structure of 4-α-Glucanotransferase

A broad range of enzymes are used to modify starch for various applications. Here, a thermophilic 4-α-glucanotransferase from Thermoproteus uzoniensis (TuαGT) is engineered by N-terminal fusion of the starch binding domains (SBDs) of carbohydrate binding module family 20 (CBM20) to enhance its affinity for granular starch. The SBDs are N-terminal tandem domains (SBD_St1 and SBD_St2) from Solanum tuberosum disproportionating enzyme 2 (StDPE2) and the C-terminal domain (SBD_GA) of glucoamylase from Aspergillus niger (AnGA). In silico analysis of CBM20s revealed that SBD_GA and copies one and two of GH77 DPE2s belong to well separated clusters in the evolutionary tree; the second copies being more closely related to non-CAZyme CBM20s. The activity of SBD-TuαGT fusions increased 1.2-2.4-fold on amylose and decreased 3-9 fold on maltotriose compared with TuαGT. The fusions showed similar disproportionation activity on gelatinised normal maize starch (NMS). Notably, hydrolytic activity was 1.3-1.7-fold elevated for the fusions leading to a reduced molecule weight and higher α-1,6/α-1,4-linkage ratio of the modified starch. Notably, SBD_GA-TuαGT and-SBD_St2-TuαGT showed K_d of 0.7 and 1.5 mg/mL for waxy maize starch (WMS) granules, whereas TuαGT and SBD_St1-TuαGT had 3-5-fold lower affinity. SBD_St2 contributed more than SBD_St1 to activity, substrate binding, and the stability of TuαGT fusions.

Affinity Electrophoresis for Analysis of Catalytic Module-Carbohydrate Interactions

Affinity electrophoresis has long been used to study the interaction between proteins and large soluble ligands. The technique has been found to have great utility for the examination of polysaccharide binding by proteins, particularly carbohydrate-binding modules (CBMs). In recent years carbohydrate surface binding sites of proteins, mostly enzymes, have also been investigated by this method. Here we describe a protocol for identifying binding interactions between enzyme catalytic modules and a variety of carbohydrate ligands.

Enzymatic preparation and potential applications of agar oligosaccharides: a review

Oligosaccharides derived from agar, that is, agarooligosaccharides and neoagarooligosaccharides, have demonstrated various kinds of bioactivities which have been utilized in a variety of fields. Enzymatic hydrolysis is a feasible approach that principally allows for obtaining specific agar oligosaccharides in a sustainable way at an industrial scale. This review summarizes recent technologies employed to improve the properties of agarase. Additionally, the relationship between the degree of polymerization, bioactivities, and potential applications of agar-derived oligosaccharides for pharmaceutical, food, cosmetic, and agricultural industries are discussed. Engineered agarase exhibited general improvement of enzymatic performance, which is mostly achieved by truncation. Rational and semi-rational design assisted by computational methods present the latest strategy for agarase improvement with greatest potential to satisfy future industrial needs. Agarase immobilized on magnetic Fe3O4 nanoparticles via covalent bond formation showed characteristics well suited for industry. Additionally, albeit with the relationship between the degree of polymerization and versatile bioactivities like anti-oxidants, anti-inflammatory, anti-microbial agents, prebiotics and in skin care of agar-derived oligosaccharides are discussed here, further researches are still needed to unravel the complicated relationship between bioactivity and structure of the different oligosaccharides.

Unaided efficient transglutaminase cross-linking of whey proteins strongly impacts the formation and structure of protein alginate particles

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Microbial transglutaminase (MTG) cross-linked >70% β-lactoglobulin (β-Lg) at pH 8.5.

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Initial MTG catalyzed isopeptide bond formation caused partial unfolding of β-Lg.

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>75% of whey protein cross-linked, forming hetero-polymers containing β-Lg.

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50% less alginate is needed to form particles with cross-linked than with native β-Lg.

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Cross-linked β-Lg and alginate formed suspendable hydrophobically driven particles.

There is a dogma within whey protein modification, which dictates the necessity of pretreatment to enzymatic cross-linking of β-lactoglobulin (β-Lg). Here microbial transglutaminase (MTG) cross-linked whey proteins and β-Lg effectively in 50 mM NaHCO₃, pH 8.5, without pretreatment. Cross-linked β-Lg spanned 18 to >240 kDa, where 6 of 9 glutamines reacted with 8 of 15 lysines. The initial isopeptide bond formation caused loss of β-Lg native structure with t_1/2 = 3 h, while the polymerization occurred with t_1/2 = 10 h. Further, cross-linking effects on protein carbohydrate interaction have been overlooked, leaving a gap in understanding of these complex food matrices. Complexation with alginate showed that β-Lg cross-linking decreased onset of particle formation, hydrodynamic diameter, stoichiometry (β-Lg/alginate) and dissociation constant. The complexation was favored at higher temperatures (40 °C), suggesting that hydrophobic interactions were important. Thus, β-Lg was cross-linked without pretreatment and the resulting polymers gave rise to altered complexation with alginate.

1H, 13C, 15N resonance assignment of the enzyme KdgF from Bacteroides eggerthii

To fully utilize carbohydrates from seaweed biomass, the degradation of the family of polysaccharides known as alginates must be understood. A step in the degradation of alginate is the conversion of 4,5-unsaturated monouronates to 4-deoxy-L-erythro-5-hexoseulose catalysed by the enzyme KdgF. In this study BeKdgF from Bacteroides eggerthii from the human gut microbiota has been produced isotopically labelled in Escherichia coli. Here the ¹H, ¹³C, and ¹⁵N NMR chemical shift assignment for BeKdgF is reported.

Simulated gastrointestinal digestion of protein alginate complexes: effects of whey protein cross-linking and the composition and degradation of alginate

Alginate and whey protein are common additives in food production improving storage stability, texture and nutritional value. Alginate forms complexes with whey protein and inhibits proteolysis by pepsin and trypsin, but the influence of alginate protein complexation on digestion is poorly understood. This study shows that whey protein cross-linking by microbial transglutaminase dramatically decreased particle size (2-fold) and viscosity of alginate protein complexes. The INFOGEST in vitro simulated gastrointestinal digestion of whey protein was increased by cross-linking (16%) and suppressed by alginate, most pronounced with high mannuronic acid and least with high guluronic acid content. Sizes of alginate whey protein particles increased during gastric digestion, whereas for cross-linked whey protein complexes the size initially increased, but returned to their initial size at the end of gastric digestion. While alginate is not degraded by human enzymes, a few gut bacteria were recently found to encode lyases and other enzymes metabolizing alginate. Alginate lyase added to the intestinal phase enhanced digestion (9%) as controlled by alginate composition and enzyme specificity. Thus we provide evidence that use of hydrocolloids and processing of protein strongly influence digestion and should be considered when using food additives.

Effect of Starch Primers on the Fine Structure of Enzymatically Synthesized Glycogen-like Glucan

Glycogen-like glucan (GnG) is a unique hyperbranched polysaccharide nanoparticle which is drawing increasing attention due to its biodegradability and abundant short branches that can be functionalized. Because starch and GnG are both composed of glucose residues and have similar glucosidic bonds, GnG could be fabricated by sucrose phosphorylase, α-glucan phosphorylase, and branching enzymes from starch primers and sucrose. In this study, high-amylose starch, normal starch, and waxy corn starch were used as primers to synthesize GnG, and their impact on the fine structure of GnG was investigated. Structural analysis indicated that with increasing content of amylopectin in the starch primer, the proportion of short chains in GnG decreased, and the degree of β-amylolysis and α-amylolysis was enhanced. Amylose in the primer contributed to a compact and homogeneous structure of GnG, while amylopectin triggered the formation of branch points with a more open distribution. These findings provide a new strategy for regulating the fine structure of GnG.

Metabolic Profiling of Interspecies Interactions During Sessile Bacterial Cultivation Reveals Growth and Sporulation Induction in Paenibacillus amylolyticus in Response to Xanthomonas retroflexus

The toolbox available for microbiologists to study interspecies interactions is rapidly growing, and with continuously more advanced instruments, we are able to expand our knowledge on establishment and function of microbial communities. However, unravelling molecular interspecies interactions in complex biological systems remains a challenge, and interactions are therefore often studied in simplified communities. Here we perform an in-depth characterization of an observed interspecies interaction between two co-isolated bacteria, Xanthomonas retroflexus and Paenibacillus amylolyticus. Using microsensor measurements for mapping the chemical environment, we show how X. retroflexus promoted an alkalization of its local environment through degradation of amino acids and release of ammonia. When the two species were grown in proximity, the modified local environment induced a morphological change and growth of P. amylolyticus followed by sporulation. 2D spatial metabolomics enabled visualization and mapping of the degradation of oligopeptide structures by X. retroflexus and morphological changes of P. amylolyticus through e.g. the release of membrane-associated metabolites. Proteome analysis and microscopy were used to validate the shift from vegetative growth towards sporulation. In summary, we demonstrate how environmental profiling by combined application of microsensor, microscopy, metabolomics and proteomics approaches can reveal growth and sporulation promoting effects resulting from interspecies interactions.

Enhancing gel strength of Thermoproteus uzoniensis 4-α-glucanotransferase modified starch by amylosucrase treatment

4-α-glucanotransferase is used to produce thermoreversible starch gels to alleviate limitations to use of starch gels in repetitively heat-processed foods. However, the gel strength was weakened after this enzyme modification. In the present study, treatment by amylosucrase (NpAS) of corn starch and sucrose was applied to retain the gel thermoreversibility and eliminate the shortcoming caused by 4-α-glucanotransferase (TuαGT). Changes in molecular structure, rheological and retrogradation properties of modified starch were investigated after NpAS and TuαGT sequential and one-pot treatment, respectively. The apparent amylose content was reduced and increased by sequential and one-pot treatments, respectively, compared to single TuαGT modification. Chain length profiles showed higher proportion of degree of polymerization (DP) ≥ 13 by sequential treatment, whereas DP 6-12 was higher after one-pot treatment. All modified starches had reduced molecular weight. G' and G" increased by dual enzyme compared to single TuαGT treatment having little effect on retrogradation. Interestingly, starch subjected to 3 h one-pot treatment caused G' and G" temperature curves to cross-over, improving thermoreversible properties. The results indicate that NpAS treatment compensated for loss of starch gel strength caused by TuαGT and offered possibility to provide a wider range of thermoreversible starches.

Structure, Function and Protein Engineering of Cereal-Type Inhibitors Acting on Amylolytic Enzymes

Numerous plants, including cereals, contain seed proteins able to inhibit amylolytic enzymes. Some of these inhibitors, the CM-proteins (soluble in chloroform:methanol mixtures)—also referred to as cereal-type inhibitors (CTIs)—are the topic of this review. CM-proteins were first reported 75 years ago. They are small sulfur-rich proteins of the prolamine superfamily embracing bifunctional α-amylase/trypsin inhibitors (ATIs), α-amylase inhibitors (AIs), limit dextrinase inhibitors (LDIs), and serine protease inhibitors. Phylogenetically CM-proteins are predicted across poaceae genomes and many isoforms are identified in seed proteomes. Their allergenicity and hence adverse effect on humans were recognized early on, as were their roles in plant defense. Generally, CTIs target exogenous digestive enzymes from insects and mammals. Notably, by contrast LDI regulates activity of the endogenous starch debranching enzyme, limit dextrinase, during cereal seed germination. CM-proteins are four-helix bundle proteins and form enzyme complexes adopting extraordinarily versatile binding modes involving the N-terminal and different loop regions. A number of these inhibitors have been characterized in detail and here focus will be on target enzyme specificity, molecular recognition, forces and mechanisms of binding as well as on three-dimensional structures of CM-protein–enzyme complexes. Lastly, prospects for CM-protein exploitation, rational engineering and biotechnological applications will be discussed.

Structure, function and enzymatic synthesis of glucosaccharides assembled mainly by α1 → 6 linkages - A review

A variety of glucosaccharides composed of glucosyl residues can be classified into α- and β-type and have wide application in food and medicine areas. Among these glucosaccharides, β-type, such as cellulose and α-type, such as starch and starch derivatives, both contain 1 → 4 linkages and are well studied. Notably, in past decades also α1 → 6 glucosaccharides obtained increasing attention for unique physiochemical and biological properties. Especially in recent years, α1 → 6 glucosaccharides of different molecular weight distribution have been created and proved to be functional. However, compared to β- type and α1 → 4 glucosaccharides, only few articles provide a systematic overview of α1 → 6 glucosaccharides. This motivated, the present first comprehensive review on structure, function and synthesis of these α1 → 6 glucosaccharides, aiming both at improving understanding of traditional α1 → 6 glucosaccharides, such as isomaltose, isomaltooligosaccharides and dextrans, and to draw the attention to newly explored α1 → 6 glucosaccharides and their derivatives, such as cycloisomaltooligosaccharides, isomaltomegalosaccharides, and isomalto/malto-polysaccharides.

Controlling the Fine Structure of Glycogen-like Glucan by Rational Enzymatic Synthesis

Glycogen-like glucan (GnG), a hyperbranched glucose polymer, has been receiving increasing attention to generate synthetic polymers and nanoparticles. Importantly, different branching patterns strongly influence the functionality of GnG. To uncover ways of obtaining different GnG branching patterns, a series of GnG with radius from 22.03 to 27.06 nm were synthesized using sucrose phosphorylase, α-glucan phosphorylase (GP), and branching enzyme (BE). Adjusting the relative activity ratio of GP and BE (GP/BE) made the molecular weight (MW) distribution of intermediate GnG products follow two different paths. At a low GP/BE, the GnG developed from "small to large" during the synthetic process, with the MW increasing from 6.15 × 10⁶ to 1.21 × 10⁷ g/mol, and possessed a compact structure. By contrast, a high GP/BE caused the "large to small" model, with the MW reduction of GnG from 1.62 × 10⁷ to 1.21 × 10⁷ g/mol, and created a loose external structure. The higher GP activity promoted the elongation of external chains and restrained chain transfer by the BE to the inner zone of GnG, which would modulate the loose-tight structure of GnG. These findings provide new useful insights into the construction of structurally well-defined nanoparticles.

Exceptionally rich keratinolytic enzyme profile found in the rare actinomycetes Amycolatopsis keratiniphila D2T

The non-spore forming Gram-positive actinomycetes Amycolatopsis keratiniphila subsp. keratiniphila D2^T (DSM 44,409) has a high potential for keratin valorization as demonstrated by a novel biotechnological microbial conversion process consisting of a bacterial growth phase and a keratinolytic phase, respectively. Compared to the most gifted keratinolytic Bacillus species, a very large number of 621 putative proteases are encoded by the genome of Amycolatopsis keratiniphila subsp. keratiniphila D2^T, as predicted by using Peptide Pattern Recognition (PPR) analysis. Proteome analysis by using LC-MS/MS on aliquots of the supernatant of A. keratiniphila subsp. keratiniphila D2^T culture on slaughterhouse pig bristle meal, removed at 24, 48, 96 and 120 h of growth, identified 43 proteases. This was supplemented by proteome analysis of specific fractions after enrichment of the supernatant by anion exchange chromatography leading to identification of 50 proteases. Overall 57 different proteases were identified corresponding to 30% of the 186 proteins identified from the culture supernatant and distributed as 17 metalloproteases from 11 families, including an M36 protease, 38 serine proteases from 4 families, and 13 proteolytic enzymes from other families. Notably, M36 keratinolytic proteases are prominent in fungi, but seem not to have been discovered in bacteria previously. Two S01 family peptidases, named T- and C-like proteases, prominent in the culture supernatant, were purified and shown to possess a high azo-keratin/azo-casein hydrolytic activity ratio. The C-like protease revealed excellent thermostability, giving promise for successful applications in biorefinery processes. Notably, the bacterium seems not to secrete enzymes for cleavage of disulfides in the keratinous substrates. KEY POINTS: • A. keratiniphila subsp. keratiniphila D2^T is predicted to encode 621 proteases. • This actinomycete efficiently converts bristle meal to a protein hydrolysate. • Proteome analysis identified 57 proteases in its secretome.

Pain in rheumatoid arthritis: a seven-year follow-up study of pain distribution and factors associated with transition from and to chronic widespread pain

Objective: To study transitions from and to chronic widespread pain (CWP) over 7 years in patients with rheumatoid arthritis (RA).Method: Two postal questionnaires were sent to patients included in the BARFOT (Better Anti-Rheumatic Pharmacotherapy) study, the first in 2010 and the second in 2017. The questionnaires assessed pain, number of tender and swollen joints, functional disability, health-related quality of life (HRQoL), pharmacological treatment, lifestyle factors, and patient-reported body mass index (BMI). The responders to both questionnaires were divided into three groups according to the reported pain duration and distribution: patients having no chronic pain (NCP), chronic regional pain (CRP), and CWP.Results: In all, 953 patients answered the questionnaires at both time-points. One-third (324) of the patients reported CWP in 2010, and 140 (43%) of the patients had transition to NCP or CRP in 2017. In multivariate logistic regression models, adjusting for age, gender, and disease duration, transition from CWP was associated with normal BMI, fewer tender joints, less pain, less fatigue, fewer pain regions, less disability, better HRQoL, and biologic treatment. In 2010, 628 patients reported NCP or CRP, whereas 114 of them reported CWP in 2017. Transition to CWP was associated with female gender, obesity, more tender and swollen joints, higher pain-related variables, worse disability, and worse HRQoL.Conclusion: There are modifiable factors associated with transitions from and to CWP that could be identified. Paying attention to these factors could improve pain treatment in the management of RA.

Rational Enzyme Design without Structural Knowledge: A Sequence-Based Approach for Efficient Generation of Transglycosylases

Glycobiology is dogged by the relative scarcity of synthetic, defined oligosaccharides. Enzyme-catalysed glycosylation using glycoside hydrolases is feasible but is hampered by the innate hydrolytic activity of these enzymes. Protein engineering is useful to remedy this, but it usually requires prior structural knowledge of the target enzyme, and/or relies on extensive, time-consuming screening and analysis. Here, a straightforward strategy that involves rational rapid in silico analysis of protein sequences is described. The method pinpoints 6-12 single-mutant candidates to improve transglycosylation yields. Requiring very little prior knowledge of the target enzyme other than its sequence, the method is generic and procures catalysts for the formation of glycosidic bonds involving various d/l-, α/β-pyranosides or furanosides, and exo or endo action. Moreover, mutations validated in one enzyme can be transposed to others, even distantly related enzymes.

Wheat ATIs: Characteristics and Role in Human Disease

Amylase/trypsin-inhibitors (ATIs) comprise about 2–4% of the total wheat grain proteins and may contribute to natural defense against pests and pathogens. However, they are currently among the most widely studied wheat components because of their proposed role in adverse reactions to wheat consumption in humans. ATIs have long been known to contribute to IgE-mediated allergy (notably Bakers' asthma), but interest has increased since 2012 when they were shown to be able to trigger the innate immune system, with attention focused on their role in coeliac disease which affects about 1% of the population and, more recently, in non-coeliac wheat sensitivity which may affect up to 10% of the population. This has led to studies of their structure, inhibitory properties, genetics, control of expression, behavior during processing, effects on human adverse reactions to wheat and, most recently, strategies to modify their expression in the plant using gene editing. We therefore present an integrated account of this range of research, identifying inconsistencies, and gaps in our knowledge and identifying future research needs.

Note 

This paper is the outcome of an invited international ATI expert meeting held in Amsterdam, February 3-5 2020

Quantitative Label-Free Comparison of the Metabolic Protein Fraction in Old and Modern Italian Wheat Genotypes by a Shotgun Approach

Wheat represents one of the most important cereals for mankind. However, since wheat proteins are also the causative agent of several adverse reactions, during the last decades, consumers have shown an increasing interest in the old wheat genotypes, which are generally perceived as more "natural" and healthier than the modern ones. Comparison of nutritional value for modern and old wheat genotypes is still controversial, and to evaluate the real impact of these foods on human health comparative experiments involving old and modern genotypes are desirable. The nutritional quality of grain is correlated with its proteomic composition that depends on the interplay between the genetic characteristics of the plant and external factors related to the environment. We report here the label-free shotgun quantitative comparison of the metabolic protein fractions of two old Sicilian landraces (Russello and Timilia) and the modern variety Simeto, from the 2010-2011 and 2011-2012 growing seasons. The overall results show that Timilia presents the major differences with respect to the other two genotypes investigated. These differences may be related to different defense mechanisms and some other peculiar properties of these genotypes. On the other hand, our results confirm previous results leading to the conclusion that with respect to a nutritional value evaluation, there is a substantial equivalence between old and modern wheat genotypes. Data are available via ProteomeXchange with identifier <PXD024204>.

Functional diversity of three tandem C-terminal carbohydrate-binding modules of a β-mannanase

Carbohydrate active enzymes, such as those involved in plant cell wall and storage polysaccharide biosynthesis and deconstruction, often contain repeating noncatalytic carbohydrate-binding modules (CBMs) to compensate for low-affinity binding typical of protein–carbohydrate interactions. The bacterium Saccharophagus degradans produces an endo-β-mannanase of glycoside hydrolase family 5 subfamily 8 with three phylogenetically distinct family 10 CBMs located C-terminally from the catalytic domain (SdGH5_8-CBM10x3). However, the functional roles and cooperativity of these CBM domains in polysaccharide binding are not clear. To learn more, we studied the full-length enzyme, three stepwise CBM family 10 (CBM10) truncations, and GFP fusions of the individual CBM10s and all three domains together by pull-down assays, affinity gel electrophoresis, and activity assays. Only the C-terminal CBM10-3 was found to bind strongly to microcrystalline cellulose (dissociation constant, K_d = 1.48 μM). CBM10-3 and CBM10-2 bound galactomannan with similar affinity (K_d = 0.2–0.4 mg/ml), but CBM10-1 had 20-fold lower affinity for this substrate. CBM10 truncations barely affected specific activity on carob galactomannan and konjac glucomannan. Full-length SdGH5_8-CBM10x3 was twofold more active on the highly galactose-decorated viscous guar gum galactomannan and crystalline ivory nut mannan at high enzyme concentrations, but the specific activity was fourfold to ninefold reduced at low enzyme and substrate concentrations compared with the enzyme lacking CBM10-2 and CBM10-3. Comparison of activity and binding data for the different enzyme forms indicates unproductive and productive polysaccharide binding to occur. We conclude that the C-terminal-most CBM10-3 secures firm binding, with contribution from CBM10-2, which with CBM10-1 also provides spatial flexibility.

Binding Sites for Oligosaccharide Repeats from Lactic Acid Bacteria Exopolysaccharides on Bovine β-Lactoglobulin Identified by NMR Spectroscopy

Lactic acid bacterial exopolysaccharides (EPS) are used in the food industry to improve the stability and rheological properties of fermented dairy products. β-Lactoglobulin (BLG), the dominant whey protein in bovine milk, is well known to bind small molecules such as fatty acids, vitamins, and flavors, and to interact with neutral and anionic polysaccharides used in food and pharmaceuticals. While sparse data are available on the affinity of EPS-milk protein interactions, structural information on BLG-EPS complexes, including the EPS binding sites, is completely lacking. Here, binding sites on BLG variant A (BLGA), for oligosaccharides prepared by mild acid hydrolysis of two EPS produced by Streptococcus thermophilus LY03 and Lactobacillus delbrueckii ssp. bulgaricus CNRZ 1187, respectively, are identified by NMR spectroscopy and supplemented by isothermal titration calorimetry (ITC) and molecular docking of complexes. Evidence of two binding sites (site 1 and site 2) on the surface of BLGA is achieved for both oligosaccharides (LY03-OS and 1187-OS) through NMR chemical shift perturbations, revealing multivalency of BLGA for EPS. The affinities of LY03-OS and 1187-OS for BLGA gave K D values in the mM range obtained by both NMR (pH 2.65) and ITC (pH 4.0). Molecular docking suggested that the BLGA and EPS complexes depend on hydrogen bonds and hydrophobic interactions. The findings provide insights into how BLGA engages structurally different EPS-derived oligosaccharides, which may facilitate the design of BLG-EPS complexation, of relevance for formulation of dairy products and improve understanding of BLGA coacervation.