A new engineered endo-inulinase with improved activity and thermostability: Application in the production of prebiotic fructo-oligosaccharides from inulin

Production and application of inulinase by new isolates of Aspergillus welwitschiae from fermented peach-palm waste for the production of fructooligosaccharides

Microbial inulinase enzymes have a number of applications in biotechnology. In this study, new strains of Aspergillus welwitschiae were investigated as producers of inulinases and their endo- and exo-inulases were characterized in silico and their protein modeling was performed. The inulinase production by A. welwitschiae employing the Dohelert method to assess the interaction between temperature and cultivation humidity, resulted in a fourfold increase in activity. The optimal temperature and humidity were 25-27 °C and 75-82 %, respectively. The enzyme exhibited optimal activity at a pH of 3.5 and at 60 °C. The hydrolysis of the sisal root yielded 272 mg/g of reducing sugars and oligosaccharides. Our in silico experiments predicted 10 well-validated structures of endo- (5) and exo-inulinases (5) from A. welwitschiae. The notable activity of these inulinases on inulin highlights their potential for the treatment of agro-industrial residues with the objective of producing high-value added products.

Engineering Saccharomyces boulardii for cell surface display of heterologous protein

Saccharomyces boulardii and Saccharomyces cerevisiae share over 99 % genetic similarity yet exhibit distinct metabolic traits. While the cell surface display system of S. cerevisiae is well-documented, the equivalent system in S. boulardii has yet to be fully characterized. This study investigates the cell surface display system of S. boulardii for the expression of a heterologous protein using different anchor proteins. Six strains expressing the enhanced green fluorescent protein (Egfp) and an anchor protein as a fusion protein were constructed to visualize the cell surface display system. Then a heterologous endo-inulinase protein was expressed with selected anchor proteins through fluorescence intensity comparison. Analysis by fluorescence microscopy revealed that the anchor protein Sed1 exhibited the highest fluorescence intensity. Furthermore, expressed selected anchor proteins and heterologous protein, endo-inulinase, the engineered strain could degrade and consume almost inulin in 72 h. Through endo-inulinase expression, we confirmed that not only Egfp but also heterologous protein is well expressed, and we successfully built an S. boulardii cell surface display system.

Insights in inulin binding and inulin oligosaccharide formation by novel multi domain endo-inulinases from Botrytis cinerea

World-wide, pathogenic fungi such as Botrytis cinerea cause tremendous yield losses in terms of food production and post-harvest food decay. Many fungi produce inulin-type oligosaccharides (IOSs) from inulin through endo-inulinases which typically show a two domain structure. B.cinerea lacks a two domain endo-inulinase but contains a three domain structure instead. Genome mining revealed three and four domain (d4) enzymes in the fungal kingdom. Here, three and two domain enzymes were compared in their capacity to produce IOSs from inulin. Hill kinetics were observed in three domain enzymes as compared to Michaelis-Menten kinetics in two domain enzymes, suggesting that the N-terminal extension functions as a carbohydrate binding module. Analysis of the IOS product profiles generated from purified GF6, GF12, GF16 and GF18 inulins and extensive sugar docking approaches led to enhanced insights in the active site functioning, revealing subtle differences between the endo-inulinases from Aspergillus niger and B. cinerea. Improved insights in structure-function relationships in fungal endo-inulinases offer opportunities to develop superior enzymes for the production of specific IOS formulations to improve plant and animal health (priming agents, prebiotics).

Inulinase and fructooligosaccharide production from carob using Aspergillus niger A42 (ATCC 204447) under solid-state fermentation conditions

This study aimed to the production of inulinase and fructooligosaccharides (FOSs) from carob under the solid-state fermentation (SSF) conditions by using Plackett-Burman Design (PBD). Based on the results the maximum inulinase and specific inulinase activities were 249.98 U/mL and 318.29 U/mg protein, respectively. When the fructooligosaccharide (FOS) results were evaluated, the maximum values of 1,1,1-Kestopentaose, 1,1-Kestotetraose, and 1-Kestose were 182.01, 506.16, 132.16 ppm while the lowest and highest total FOS values were 179.35 and 516.66 ppm, respectively. On the other hand, it was observed that the maximum inulinase activity was found at the center points of the design. Therefore, validation fermentations were carried out at center point conditions. Subsequently, the yielded bulk enzyme extracts were partially purified using Spin-X UF membranes with 10, 30, and 50 kDa cut-off values. After purification, the maximum inulinase activity was 247.30 U/mg using a 50 kDa cut-off value. Followed by this process, the purified enzyme was used to produce FOSs and the results indicated that the maximum total FOS amount was 28,712.70 ppm. Consequently, this study successfully demonstrates that Aspergillus niger A42 inulinase produced from carob under the SSF conditions can be used in FOSs production.

Nonconventional Yeasts Engineered Using the CRISPR-Cas System as Emerging Microbial Cell Factories

Because the petroleum-based chemical synthesis of industrial products causes serious environmental and societal issues, biotechnological production using microorganisms is an alternative approach to achieve a more sustainable economy. In particular, the yeast Saccharomyces cerevisiae is widely used as a microbial cell factory to produce biofuels and valuable biomaterials. However, product profiles are often restricted due to the Crabtree-positive nature of S. cerevisiae, and ethanol production from lignocellulose is possibly enhanced by developing alternative stress-resistant microbial platforms. With desirable metabolic pathways and regulation in addition to strong resistance to diverse stress factors, nonconventional yeasts (NCY) may be considered an alternative microbial platform for industrial uses. Irrespective of their high industrial value, the lack of genetic information and useful gene editing tools makes it challenging to develop metabolic engineering-guided scaled-up applications using yeasts. The recently developed clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein (Cas) system is a powerful gene editing tool for NCYs. This review describes the current status of and recent advances in promising NCYs in terms of industrial and biotechnological applications, highlighting CRISPR-Cas9 system-based metabolic engineering strategies. This will serve as a basis for the development of novel yeast applications.

Efficient production of inulo-oligosaccharides from inulin by exo- and endo-inulinase co-immobilized onto a self-assembling protein scaffold

Inulin can be hydrolyzed by inulinases to yield inulo-oligosaccharides (IOSs), which have great application potential in the food and nutraceutical industries. However, conventional enzymatic production of IOSs is limited by long hydrolysis times and poor thermo-stability of inulinases. Here, the self-assembling protein scaffold EutM was engineered to co-immobilize exo-inulinase (EXINU) and endo-inulinase (ENINU) for synergistic hydrolysis of inulin to produce IOSs with 3 to 5 monosaccharide units (DP3-5 IOSs). The immobilization of EXINU/ENINU onto the EutM scaffold resulted in an increase of catalytic efficiency, a 65% increase of the V_max of ENINU, as well as an increase of thermo-stability, with 4.26-fold higher residual activity of EXINU after 22 h-incubation at 50 °C. After optimization, two efficient production protocols were obtained, in which the yield and productivity of DP3-5 IOSs reached 80.38% and 70.86 g·(L·h)^-1, respectively, which were at a high level in similar studies. Overall, this study provides an attractive self-assembling protein platform for the co-immobilization of inulinases, as well as optimized bioprocesses with great promise for the industrial production of DP3-5 IOSs.

Bioprospecting Kluyveromyces marxianus as a Robust Host for Industrial Biotechnology

Kluyveromyces marxianus is an emerging non-conventional food-grade yeast that is generally isolated from diverse habitats, like kefir grain, fermented dairy products, sugar industry sewage, plants, and sisal leaves. A unique set of beneficial traits, such as fastest growth, thermotolerance, and broad substrate spectrum (i.e., hemi-cellulose hydrolysates, xylose, l-arabinose, d-mannose, galactose, maltose, sugar syrup molasses, cellobiose, and dairy industry) makes this yeast a particularly attractive host for applications in a variety of food and biotechnology industries. In contrast to Saccharomyces cerevisiae, most of the K. marxianus strains are apparently Crabtree-negative or having aerobic-respiring characteristics, and unlikely to endure aerobic alcoholic fermentation. This is a desirable phenotype for the large-scale biosynthesis of products associated with biomass formation because the formation of ethanol as an undesirable byproduct can be evaded under aerobic conditions. Herein, we discuss the current insight into the potential applications of K. marxianus as a robust yeast cell factory to produce various industrially pertinent enzymes, bioethanol, cell proteins, probiotic, fructose, and fructo-oligosaccharides, and vaccines, with excellent natural features. Moreover, the biotechnological improvement and development of new biotechnological tools, particularly CRISPR-Cas9-assisted precise genome editing in K. marxianus are delineated. Lastly, the ongoing challenges, concluding remarks, and future prospects for expanding the scope of K. marxianus utilization in modern biotechnology, food, feed, and pharmaceutical industries are also thoroughly vetted. In conclusion, it is critical to apprehend knowledge gaps around genes, metabolic pathways, key enzymes, and regulation for gaining a complete insight into the mechanism for producing relevant metabolites by K. marxianus.

A novel transcriptional activation mechanism of inulinase gene in Kluyveromyces marxianus involving a glycolysis regulator KmGcr1p with unique and functional Q-rich repeats

Kluyveromyces marxianus is the most suitable fungus for inulinase industrial production. However, the underlying transcriptional activation mechanism of the inulinase gene (INU1) is hitherto unclear. Here, we undertook genetic and biochemical analyses to elucidate that a glycolysis regulator KmGcr1p with unique Q-rich repeats is the key transcriptional activator of INU1. We determined that INU1 and glycolytic genes share similar transcriptional activation patterns, and that inulinase activity is induced by fermentable carbon sources including the hydrolysis products of inulin (fructose and glucose), which suggests a novel model of product feedback activation. Furthermore, all four CT-boxes in the INU1 promoter are important for KmGcr1p DNA binding in vitro, but the most downstream CT-box 1 primarily confers upstream activating sequence activity in vivo. More intriguingly, the use of artificial and natural GCR1 mutants suggests that the Q-rich repeats act as a functional module to maintain KmGcr1p transcriptional activity by contributing to its solubility and DNA binding affinity. Altogether, this study uncovers a novel transcriptional activation mechanism for the inulinase gene that is different from the previous understanding for filamentous fungi, but might have universal significance among inulinase-producing yeasts, thereby leading to a better understanding of the regulation mechanism of yeast inulinase genes.

Structural characteristics of Gracilaria lemaneiformis oligosaccharides and their alleviation of dextran sulphate sodium-induced colitis by modulating the gut microbiota and intestinal metabolites in mice

Ulcerative colitis (UC) is a chronic lifetime disorder with a high incidence worldwide. A functional food-based method to prevent UC would be a good option for disease control. G. lemaneiformis oligosaccharides (GLOs) should have potent benefits for the gastrointestinal tract, based on in vitro fermentation assessed in our previous study. This study evaluated the therapeutic potential of GLOs in UC, as well as their possible mechanisms of action. The administration of GLOs was able to reduce the severity of dextran sulphate sodium-induced colitis by protecting mice from weight loss, reductions in colon length, inflammatory infiltration, and colon damage. Gut microbiota composition analysis showed that at the phylum level, GLOs could restore the composition of Bacteroidetes and decrease the level of Firmicutes. Consistently, it increased the contents of beneficial microbial metabolites and short-chain fatty acids in the mouse colitis model. In conclusion, GLOs could comprise a promising functional food strategy to alleviate UC symptoms.

Enhanced hydrolytic efficiency of an engineered CBM11-glucanase enzyme chimera against barley β-d-glucan extracts

The β-d-glucans are abundant cell wall polysaccharides in many cereals and contain both (1,3)- and (1,4)-bonds. The β-1,3-1,4-glucanases (EC 3.2.1.73) hydrolyze β-(1,4)-d-glucosidic linkages in glucans, and have applications in both animal and human food industries. A chimera between the family 11 carbohydrate-binding module from Ruminoclostridium (Clostridium)thermocellumcelH (RtCBM11), with the β-1,3-1,4-glucanase from Bacillus subtilis (BglS) was constructed by end-to-end fusion (RtCBM11-BglS) to evaluate the effects on the catalytic function and its application in barley β-glucan degradation for the brewing industry. The parental and chimeric BglS presented the same optimum pH (6.0) and temperature (50 °C) for maximum activity. The RtCBM11-BglS showed increased thermal stability and 30% higher hydrolytic efficiency against purified barley β-glucan, and the rate of hydrolysis of β-1,3-1,4-glucan in crude barley extracts was significantly increased. The enhanced catalytic performance of the RtCBM11-BglS may be useful for the treatment of crude barley extracts in the brewing industry.

Insight into the effects and biotechnological production of kestoses, the smallest fructooligosaccharides

Kestoses, the smallest fructooligosaccharides, are trisaccharides composed of a fructose molecule and a sucrose molecule linked by either β-(2,1) or β-(2,6) linkage. 1-kestose, 6-kestose and neokestose are the three types of kestoses occurring in nature. As the main kind of fructooligosaccharide, kestoses share similar physiological effects with other fructooligosaccharides, and they have recently been determined to show more notable effects in promoting the growth of probiotics including Faecalibacterium prausnitzii and Bifidobacterium than those of other fructooligosaccharides. Kestoses exist in many plants, but the relatively low content and the isolation and purification are the main barriers limiting their industrial application. The production of kestoses by enzymatic biosynthesis and microbial fermentation has the potential to facilitate its production and industrial use. In this article, the recent advances in the research of kestoses were overviewed, including those studying their functions and production. Kestose-producing enzymes were introduced in detail, and microbial production and fermentation optimization techniques for enhancing the yield of kestoses were addressed. β-Fructofuranosidase is the main one used to produce kestoses because of the extensive range of microbial sources. Therefore, the production of kestoses by microorganisms containing β-fructofuranosidase has also been reviewed. However, few molecular modification studies have attempted to change the production profile of some enzymes and improve the yield of kestoses, which is a topic that should garner more attention. Additionally, the production of kestoses using food-grade microorganisms may be beneficial to their application in the food industry.

Levansucrase from Bacillus amyloliquefaciens KK9 and Its Y237S Variant Producing the High Bioactive Levan-Type Fructooligosaccharides

Levan-typed fructooligosaccharide (LFOS), a β-2,6 linked oligofructose, displays the potential application as a prebiotic and therapeutic dietary supplement. In the present study, LFOS was synthesized using levansucrase from Bacillus amyloliquefaciens KK9 (LsKK9). The wild-type LsKK9 was cloned and expressed in E. coli, and purified by cation exchanger chromatography. Additionally, Y237S variant of LsKK9 was constructed based on sequence alignment and structural analysis to enhance the LFOS production. High-performance anion-exchange chromatography coupled with pulsed amperometric detection (HPAEC-PAD) analysis indicated that Y237S variant efficiently produced a higher amount of short-chain LFOS than wild type. Also, the concentration of enzyme and sucrose in the reactions was optimized. Finally, prebiotic activity assay demonstrated that LFOS produced by Y237S variant had higher prebiotic activity than that of the wild-type enzyme, making the variant enzyme attractive for food biotechnology.

Nondigestible Oligosaccharides with Anti-Obesity Effects

Obesity has an important influence on health conditions, causing a multitude of complications and comorbidities, and drug therapy is considered to be one of the treatment strategies. Nowadays, there is increasing interest in the study of intestinal microbiota regulation of obesity; also, an increasing number of agricultural and sideline products have been found to have anti-obesity potential. In the present review, we summarize an overview of current known and potential anti-obesity oligosaccharides and their molecular structures. We describe their anti-obesity potential activity and the molecular structure associated with this activity, the regulation of intestinal microbiota composition and its mechanism of action, including regulation of the short-chain fatty acid (SCFA) pathway and altering bile acid (BA) pathway. This review will provide new ideas for us to develop new anti-obesity functional foods.