Enhanced expression of endoinulinase from Aspergillus niger by codon optimization in Pichia pastoris and its application in inulooligosaccharide production

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.

Recent trends in the biotechnology of functional non-digestible oligosaccharides with prebiotic potential

Prebiotics as a part of dietary nutrition can play a crucial role in structuring the composition and metabolic function of intestinal microbiota and can thus help in managing a clinical scenario by preventing diseases and/or improving health. Among the different prebiotics, non-digestible carbohydrates are molecules that selectively enrich a typical class of bacteria with probiotic potential. This review summarizes the current knowledge about the different aspects of prebiotics, such as its production, characterization and purification by various techniques, and its link to novel product development at an industrial scale for wide-scale use in diverse range of health management applications. Furthermore, the path to effective valorization of agricultural residues in prebiotic production has been elucidated. This review also discusses the recent developments in application of genomic tools in the area of prebiotics for providing new insights into the taxonomic characterization of gut microorganisms, and exploring their functional metabolic pathways for enzyme synthesis. However, the information regarding the cumulative effect of prebiotics with beneficial bacteria, their colonization and its direct influence through altered metabolic profile is still getting established. The future of this area lies in the designing of clinical condition specific functional foods taking into consideration the host genotypes, thus facilitating the creation of balanced and required metabolome and enabling to maintain the healthy status of the host.

Oligosaccharides production from coprophilous fungi: An emerging functional food with potential health-promoting properties

Functional foods are essential food products that possess health-promoting properties for the treatment of infectious diseases. In addition, they provide energy and nutrients, which are required for growth and survival. They occur as prebiotics or dietary supplements, including oligosaccharides, processed foods, and herbal products. However, oligosaccharides are more efficiently recognized and utilized, as they play a fundamental role as functional ingredients with great potential to improve health in comparison to other dietary supplements. They are low molecular weight carbohydrates with a low degree of polymerization. They occur as fructooligosaccharide (FOS), inulooligosaccharadie (IOS), and xylooligosaccahride (XOS), depending on their monosaccharide units. Oligosaccharides are produced by acid or chemical hydrolysis. However, this technique is liable to several drawbacks, including inulin precipitation, high processing temperature, low yields, and high production costs. As a consequence, the application of microbial enzymes for oligosaccharide production is recognized as a promising strategy. Microbial enzymatic production of FOS and IOS occurs by submerged or solid-state fermentation in the presence of suitable substrates (sucrose, inulin) and catalyzed by fructosyltransferases and inulinases. Incorporation of FOS and IOS enriches the rheological and physiological characteristics of foods. They are used as low cariogenic sugar substitutes, suitable for diabetics, and as prebiotics, probiotics and nutraceutical compounds. In addition, these oligosaccharides are employed as anticancer, antioxidant agents and aid in mineral absorption, lipid metabolism, immune regulation etc. This review, therefore, focuses on the occurrence, physico-chemical characteristics, and microbial enzymatic synthesis of FOS and IOS from coprophilous fungi. In addition, the potential health benefits of these oligosaccharides were discussed in detail.

A Novel Inulin-Mediated Ethanol Precipitation Method for Separating Endo-Inulinase From Inulinases for Inulooligosaccharides Production From Inulin

Inulin is a kind of polysaccharide that can be obtained various biomass. Inulooligosaccharides (IOS), a kind of oligosaccharides that can be obtained from inulin by enzymatic hydrolysis using inulinases, have been regarded as the functional food ingredients. Commercially available inulinases produced by natural Aspergillus niger contained both endo- and exo-inulinase activities. For IOS production from inulin, it is desirable to use only endo-inulinase as exo-inulinase would produce mainly the monosacchairde fructose from inulin. In the present study, a simple inulin-mediated ethanol precipitation method was developed to separate endo- and exo-inulinases present in natural inulinases. IOS production from inulin using the enriched endo-inulinase was then optimized in process conditions including pH and temperature, achieving a high yield of ∼94%. The resultant IOS products had a degree of polymerization ranging from 2 to 7. The study demonstrated a novel method for obtaining partially purified or enriched endo-inulinase for IOS production from inulin in an efficient process.

An effective combination of codon optimization, gene dosage, and process optimization for high-level production of fibrinolytic enzyme in Komagataella phaffii (Pichia pastoris)

BACKGROUND

As a main drug for diseased thrombus, some clinically used thrombolytic agents have various disadvantages, safer novel thrombolytic agents are of great demand. This study aimed to achieve high and efficient production of a fibrinolytic enzyme with superior enzymatic properties, by a combination strategy of codon optimization, gene dosage and process optimization in Komagataella phaffii (K. phaffii).

RESULTS

After codon optimization, the fibase from a marine Bacillus subtilis was expressed and secreted in K. phaffii GS115. Recombinant strains harboring different copies of the fib gene (fib-nc) were successfully obtained via Geneticin (0.25-4 mg/ml) screening on minimal dextrose selection plates and assessment via real-time quantitative PCR. The respective levels of fibase produced by strains expressing fib-5.4c, fib-6c, fib-8c, fib-9c, and fib-12c were 4428, 5781, 7323, 7930, and 2472 U/ml. Levels increased as the copy number increased from 4 to 9, but decreased dramatically at copy number 12. After high cell density fermentation optimization, the highest fibase activity of the strain expressing fib-9c was 7930 U/ml in a shake flask and increased to 12,690 U/ml after 3 days of continuous culture in a 5-L fermenter, which is one of the highest levels of production reported. The recombinant fibase was maximally active at pH 9.0 and 45 °C, and was remarkably stable at pH levels ranging from 5 to 10 and temperatures up to 50 °C. As a metal-dependent serine protease, fibase did not cause hemolysis in vitro and preferentially degraded fibrin directly.

CONCLUSIONS

The combination of codon optimization, gene dosage, and process optimization described herein could be used for the expression of other therapeutic proteins difficult to express. The characteristics of the recombinant fibase suggest that it has potential applications for thrombosis prevention and therapy.

Understanding the interactive influence of hydrolytic conditions on biocatalytic production of fructooligosaccharides from inulin

Statistical optimization of hydrolytic conditions for the production of fructooligosaccharides (FOSs) from pure inulin using Aspergillus tritici endoinulinase was carried out in a batch system. FOSs yield 99.19% was obtained under the optimized hydrolytic conditions i.e. inulin concentration (7.3%), enzyme load (65 IU), hydrolysis time (13 h) and agitation (100 rpm). The closeness of value of co-efficient of determination (R²) to 1, good agreement between model's predicted and experimental values, low percentage error (<5%), high adequate precision (>4%) and F value (11,634.32), and low Lack of fit (0.60) of the designed model authenticates its fitness. High substrate concentration, low enzyme load and short hydrolysis span justifies efficiency of developed process for the preparation of FOSs from inulin using fungal endoinulinase. TLC chromatographic and densitometry studies confirmed the synthesis of short-chain length FOSs. FOSs preparation contained 33.85% GF2 (ketose), 24.50% GF3 (nystose), 7.26% GF4 (fructofuranosylnystose) and 33.58% FOSs of DP5-9.

Investigating the effect of different inulin-rich substrate preparations from Jerusalem artichoke (Helianthus tuberosus L.) tubers on efficient inulooligosaccharides production

Commercial production of inulooligosaccharides (IOS) relies largely on chicory roots. However, Jerusalem artichoke (JA) tubers provide a suitable alternative due to their high inulin content and low cultivation requirements. In this study, three inulin-rich substrate preparations from JA were investigated to maximize IOS production, namely powder from dried JA tuber slices (Substrate 1), solid residues after extracting protein from the JA powder (Substrate 2) and an inulin-rich fraction extracted from protein extraction residues (Substrate 3). The preferred temperature, pH and inulin substrate concentration were determined after which enzyme dosage and extraction time were optimized to maximize IOS extraction from the three substrates, using pure chicory inulin as benchmark. Under the optimal conditions, Substrate 3 resulted in the highest IOS yield of 82.3% (w/w_inulin). However, IOS production from the Substrate 1 proved more efficient since it renders the highest overall IOS yield (mass of IOS per mass of the starting biomass). In the case of co-production of protein and IOS from the JA tuber in a biorefinery concept, IOS production from the Substrate 2 is preferred since it reduces the inulin losses incurred during substrate preparation. For all the inulin-rich substrates studied, an enzyme dosage of 14.8 U/g_inulin was found to be optimal at reaction time less than 6 h. JA tuber exhibited excellent potential for commercial production of IOS with improved yield and the possible advantage of a reduced biomass cost.

Production of Short Chain Fructo-oligosaccharides from Inulin of Chicory Root Using Fungal Endoinulinase

Short chain fructo-oligosaccharides (SC-FOS) are the potential prebiotics possessing diverse applications in both food and feed industries. The present study was aimed to extract inulin from chicory roots followed by its conversion into SC-FOS applying endoinulinase from Aspergillus fumigatus. The inulin was extracted from chicory roots through boiling in hot water, followed by precipitation with ethanol at room temperature or freezing condition. Maximum yield (42%) of inulin was obtained with three volumes of chilled absolute ethanol at room temperature. HPLC analysis of enzymatic hydrolysate detected kestose (GF2), nystose (GF3), and other FOS having higher degree of polymerization (DP). Maximum GF2 (5.79 mg/ml) was detected at temperature 50 °C, pH 5.5 with 2 U of enzyme dose after 6 h of hydrolysis; while maximum GF3 (4.33 mg/ml) was recorded at 60 °C, 5.5 pH with 0.5 U enzyme dose after 2 h of hydrolysis. Nevertheless, complete hydrolysis of inulin was noticed with 99% total oligosaccharide yield at 55 °C, 5.5 pH with 0.5 U enzyme dose after 4 h of hydrolysis with negligible amount of mono- and di-saccharides. The present finding demonstrated the process for higher yield of inulin from chicory roots followed by its conversion into SC-FOS applying fungal endoinulinase.

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

To construct a high-performance engineered endo-inulinase for fructo-oligosaccharides (FOS) production from inulin, an inulin binding module (IBM) was fused into either N- or C-terminal of an endo-inulinase. After heterologous expression, purification and characterization, the C-terminal fusion one (Eninu-IBM) with better activity, thermostability and inulin binding ability was employed for high-temperature in situ inulin hydrolysis in a 10-L fermentor. During this process, Eninu-IBM was first efficiently produced by the yeast cells at 28 °C for 96 h, and subsequently 1600 g unsterilized inulin per liter fermentation liquor was directly supplemented into the bioreactor for FOS production at 60 °C for 2 h. Finally, high purity of FOS (91.4%) were obtained with FOS titer, yield and productivity of 717.3 g/L, 0.912 g_FOS/g_Inulin and 358.6 g/L/h, respectively. The in vitro prebiotic assay indicated that the final FOS products with main polymerization degrees of 3-5 were preferably fermented by beneficial bifidobacteria and lactobacilli.

Production of Universal Group O Red Blood Cells by Alpha-N-Acetylgalactosaminidase Enzyme Expressed in Pichia pastoris

Enzymatic removal of blood groups antigens A and B is an efficient method for production of universal red blood cells. In this research, an α-N-acetylgalactosaminidase (NAGA) enzyme was expressed in Pichia pastoris for digestion of the A blood antigen. DNA sequence of the gene NAGA, originally expressed in Elizabethkingia meningosepticum (NAGA-EM), was ordered for optimization and synthesis. It was then expressed in P. pastoris (KM71H and GS115 strains). Expression of the recombinant NAGA was evaluated by dot blot, SDS-PAGE, and Western blotting. The activity of the enzyme was measured using a synthetic substrate in addition to the conversion of group A red blood cells to the O cells. Expression of NAGA-EM with an apparent molecular mass of 55 kDa was verified by dot blot, SDS-PAGE and Western blot analysis. The maximum enzyme activity in the supernatant of KM71H was higher than that in the GS115 (250 vs. 200 U/ml). Treated group A RBCs did not react with the anti-A antiserum or with the sera from individuals with blood groups B and O. The results of this study indicated that NAGA-EM is an efficient enzyme for production of universal O blood cells.

Engineering strategies for enhanced production of protein and bio-products in Pichia pastoris: A review

Pichia pastoris has been recognized as one of the most industrially important hosts for heterologous protein production. Despite its high protein productivity, the optimization of P. pastoris cultivation is still imperative due to strain- and product-specific challenges such as promoter strength, methanol utilization type and oxygen demand. To address the issues, strategies involving genetic and process engineering have been employed. Optimization of codon usage and gene dosage, as well as engineering of promoters, protein secretion pathways and methanol metabolic pathways have proved beneficial to innate protein expression levels. Large-scale production of proteins via high cell density fermentation additionally relies on the optimization of process parameters including methanol feed rate, induction temperature and specific growth rate. Recent progress related to the enhanced production of proteins in P. pastoris via various genetic engineering and cultivation strategies are reviewed. Insight into the regulation of the P. pastoris alcohol oxidase 1 (AOX1) promoter and the development of methanol-free systems are highlighted. Novel cultivation strategies such as mixed substrate feeding are discussed. Recent advances regarding substrate and product monitoring techniques are also summarized. Application of P. pastoris to the production of biodiesel and other value-added products via metabolic engineering are also reviewed. P. pastoris is becoming an indispensable platform through the use of these combined engineering strategies.

Efficient Conversion of Inulin to Inulooligosaccharides through Endoinulinase from Aspergillus niger

Inulooligosaccharides (IOS) represent an important class of oligosaccharides at industrial scale. An efficient conversion of inulin to IOS through endoinulinase from Aspergillus niger is presented. A 1482 bp codon optimized gene fragment encoding endoinulinase from A. niger DSM 2466 was cloned into pPIC9K vector and was transformed into Pichia pastoris KM71. Maximum activity of the recombinant endoinulinase, 858 U/mL, was obtained at 120 h of the high cell density fermentation process. The optimal conditions for inulin hydrolysis using the recombinant endoinulinase were investigated. IOS were harvested with a high concentration of 365.1 g/L and high yield up to 91.3%. IOS with different degrees of polymerization (DP, mainly DP 3-6) were distributed in the final reaction products.

Efficient Secretory Overexpression of Endoinulinase in Escherichia coli and the Production of Inulooligosaccharides

Endoinulinase production was achieved by heteroexpression of endoinulinase-encoding gene from Aspergillus ficuum which is an eukaryotic organism in Escherichia coli BL21 (DE3). Further analysis demonstrated that the native signal peptide existed in inu2 gene lowered the enzyme expression level. To realize extracellular accumulation of target protein and improve its expression level, native signal peptide was substituted with pelB, ompC, and pelB fusing with the native signal peptides; then, the effects on endoinulinase production were investigated. As a result, E. coli A606-3, with replacement of pelB as its signal peptide, showed the highest endoinulinase enzyme activity (75.22 U/mg). Also, it suggested that eukaryotic signal peptides have an inhibition on enzyme expression in prokaryotic organism. Moreover, the condition for inulooligosaccharide (IOS) production from inulin was optimized, and an IOS yield of 94.41 % was achieved under the condition of 15 % (w/v) inulin, purified endoinulinase dosage of 5 U/g inulin, 55 °C, and pH 4.6 for 24 h. The major products of hydrolysis of inulin were identified as DP3 to DP7.

Multi-omics data driven analysis establishes reference codon biases for synthetic gene design in microbial and mammalian cells

In this study, we analyzed multi-omics data and subsets thereof to establish reference codon usage biases for codon optimization in synthetic gene design. Specifically, publicly available genomic, transcriptomic, proteomic and translatomic data for microbial and mammalian expression hosts, Escherichia coli, Saccharomyces cerevisiae, Pichia pastoris and Chinese hamster ovary (CHO) cells, were compiled to derive their individual codon and codon pair frequencies. Then, host dependent and -omics specific codon biases were generated and compared by principal component analysis and hierarchical clustering. Interestingly, our results indicated the similar codon bias patterns of the highly expressed transcripts, highly abundant proteins, and efficiently translated mRNA in microbial cells, despite the general lack of correlation between mRNA and protein expression levels. However, for CHO cells, the codon bias patterns among various -omics subsets are not distinguishable, forming one cluster. Thus, we further investigated the effect of different input codon biases on codon optimized sequences using the codon context (CC) and individual codon usage (ICU) design parameters, via in silico case study on the expression of human IFNγ sequence in CHO cells. The results supported that CC is more robust design parameter than ICU for improved heterologous gene design.

Genetic Modification of the Marine-Isolated Yeast Aureobasidium melanogenum P16 for Efficient Pullulan Production from Inulin

In this study, in order to directly and efficiently convert inulin into pullulan, the INU1 gene from Kluyveromyces maximum KM was integrated into the genomic DNA and actively expressed in the high pullulan producer Aureobasidium melanogenum P16 isolated from the mangrove ecosystem. After the ability to produce pullulan from inulin by different transformants was examined, it was found that the recombinant strain EI36, one of the transformants, produced 40.92 U/ml of inulinase activity while its wild-type strain P16 only yielded 7.57 U/ml of inulinase activity. Most (99.27 %) of the inulinase produced by the recombinant strain EI36 was secreted into the culture. During the 10-l fermentation, 70.57 ± 1.3 g/l of pullulan in the fermented medium was attained from inulin (138.0 g/l) within 108 h, high inulinase activity (42.03 U/ml) was produced within 60 h, the added inulin was actively hydrolyzed by the secreted inulinase, and most of the reducing sugars were used by the recombinant strain EI36. This confirmed that the genetically engineered yeast of A. melanogenum strain P16 was suitable for direct pullulan production from inulin.

High-level extracellular expression of inulin fructotransferase in Pichia pastoris for DFA III production

BACKGROUND

Inulin fructotransferase (IFTase) catalyzes inulin conversion to difructose anhydride (DFA III), which is a natural low-calorie sweetener. Although heterologous expression of IFTase was achieved in Escherichia coli, the extracellular enzyme activity was very low, which limited the commercialization of IFTase.

RESULTS

Active IFTase of about 43 kDa molecular mass of subunit was extracellularly expressed by Pichia pastoris and was greatly regulated by the IFTase gene copy number integrated into the P. pastoris genome and by the methanol concentration in the induction phase. Under optimized culture conditions, multicopy P. pastoris exhibited a maximum extracellular IFTase activity of 105.4 U mL(-1) in a 5 L fermenter, which was 8.9-fold the activity in shake flasks and 5.3-fold that obtained from wild-type strain.

CONCLUSION

IFTase was expressed in a eukaryotic P. pastoris system for the first time and achieved high-level extracellular expression using a high-cell-density fed-batch cultivation strategy. This demonstrated that P. pastoris was a good candidate for potential DFA III production as a novel IFTase expression system.

Microbial enzymatic production and applications of short-chain fructooligosaccharides and inulooligosaccharides: recent advances and current perspectives

The industrial production of short-chain fructooligosaccharides (FOS) and inulooligosaccharides is expanding rapidly due to the pharmaceutical importance of these compounds. These compounds, concisely termed prebiotics, have biofunctional properties and hence health benefits if consumed in recommended dosages. Prebiotics can be produced enzymatically from sucrose elongation or via enzymatic hydrolysis of inulin by exoinulinases and endoinulinases acting alone or synergistically. Exoinulinases cleave the non-reducing β-(2, 1) end of inulin-releasing fructose while endoinulinases act on the internal linkages randomly to release inulotrioses (F3), inulotetraoses (F4) and inulopentaoses (F5) as major products. Fructosyltransferases act by cleaving a sucrose molecule and then transferring the liberated fructose molecule to an acceptor molecule such as sucrose or another oligosaccharide to elongate the short-chain fructooligosaccharide. The FOS produced by the action of fructosyltransferases are 1-kestose (GF2), nystose (GF3) and fructofuranosyl nystose (GF4). The production of high yields of oligosaccharides of specific chain length from simple raw materials such as inulin and sucrose is a technical challenge. This paper critically explores recent research trends in the production and application of short-chain oligosaccharides. Inulin and enzyme sources for the production of prebiotics are discussed. The mechanism of FOS chain elongation and also the health benefits associated with prebiotics consumption are discussed in detail.