A protease-insensitive feruloyl esterase from China Holstein cow rumen metagenomic library: expression, characterization, and utilization in ferulic acid release from wheat straw

Extracellular Expression of Feruloyl Esterase and Xylanase in Escherichia coli for Ferulic Acid Production from Agricultural Residues

There is still a large amount of ferulic acid (FA), an outstanding antioxidant, present in agricultural residues. Enzymatic hydrolysis has been regarded as the most effective way to release FA. This present study therefore selected feruloyl esterase (FAE) and xylanase (XYN) from the metagenomes of a cow rumen and a camel rumen, respectively, for their recombinant expression in Escherichia coli BL21 and further application in releasing FA. After screening the candidate signal peptides, the optimal one for each enzyme, which were selected as SP1 and SP4, respectively, was integrated into the vectors pET22b(+) and pETDuet-1. Among the generated E. coli strains SP1-F, SP4-X, and SP1-F-SP4-X that could express extracellular enzymes either separately or simultaneously, the latter one performed the best in relation to degrading the biomass and releasing FA. Under the optimized culture and induction conditions, the strain SP1-F-SP4-X released 90% of FA from 10% of de-starched wheat bran and produced 314.1 mg/L FA, which was deemed to be the highest obtained value to the best of our knowledge. This result could pave a way for the re-utilization of agricultural residues and enhancing their add-value.

Enhancing the Hydrolysis and Acyl Transfer Activity of Carboxylesterase DLFae4 by a Combinational Mutagenesis and In-Silico Method

In the present study, a feruloyl esterase DLFae4 identified in our previous research was modified by error-prone PCR and site-directed saturation mutation to enhance the catalytic efficiency and acyltransferase activity further. Five mutants with 6.9–118.9% enhanced catalytic activity toward methyl ferulate (MFA) were characterized under the optimum conditions. Double variant DLFae4-m5 exhibited the highest hydrolytic activity (270.97 U/mg), the Km value decreased by 83.91%, and the Kcat/Km value increased by 6.08-fold toward MFA. Molecular docking indicated that a complex hydrogen bond network in DLFae4-m5 was formed, with four of five bond lengths being shortened compared with DLFae4, which might account for the increase in catalytic activity. Acyl transfer activity assay revealed that the activity of DLFae4 was as high as 1550.796 U/mg and enhanced by 375.49% (5823.172 U/mg) toward 4-nitrophenyl acetate when residue Ala-341 was mutated to glycine (A341G), and the corresponding acyl transfer efficiency was increased by 7.7 times, representing the highest acyltransferase activity to date, and demonstrating that the WGG motif was pivotal for the acyltransferase activity in family VIII carboxylesterases. Further experiments indicated that DLFae4 and variant DLFae4 (A341G) could acylate cyanidin-3-O-glucoside effectively in aqueous solution. Taken together, our study suggested the effectiveness of error-prone PCR and site-directed saturation mutation to increase the specific activity of enzymes and may facilitate the practical application of this critical feruloyl esterase.

Co-Pigmentation Mechanism and Thermal Reaction Kinetics of Mulberry Anthocyanins with Different Phenolic Acids

Applying the intermolecular co-pigmentation to improve the stability of mulberry anthocyanins is an important co-pigment method. Seven co-pigments, ferulic acid (FA), caffeic acid (CA), p-hydroxybenzoic acid (HBA), protocatechuic acid (PA), gallic acid (GA), vanillic acid (VA) and vanillin (VN) were selected to investigate mulberry anthocyanin co-pigmentation thermal reaction kinetics. The strongest co-pigment reactions were observed for FA at a molar ratio of 1:20, pH 3.5 and 20 °C, with the highest hyperchromic effects (52.94%), equilibrium constant (K) values (3.51) and negative values of Gibbs free energy (ΔG°) (-3.06 KJ/mol). Co-pigments that contained more free hydroxyl groups facilitated the co-pigmentation, and methyl contributed more to color enhancement, with respect to the hydrogen group. Ultra Performance Liquid Chromatography-Quadrupole-Time Of Flight-Mass/Mass Spectrometry (UPLC-Q-TOF-MS/MS) results indicated that FA and CA formed different anthocyanin derivatives with mulberry anthocyanin. The Fourier Transform Infrared Spectroscopy (FTIR) and molecular docking confirmed that hydrogen bonding, π-π stacking and hydrophobic interaction were formed between anthocyanins and three prevalent co-pigments (FA, CA and VA). CA and C3G could form four hydrogen bonds and two π-π stackings; this was the most stable system among three phenolic acid-C3G complexes. Due to the functional effect of phenolic acids, the addition of FA and CA not only enhanced the stability and color intensity of mulberry anthocyanins but also the functionality of the processing product.

Esterases as emerging biocatalysts: Mechanistic insights, genomic and metagenomic, immobilization, and biotechnological applications

Esterase enzymes are a family of hydrolases that catalyze the breakdown and formation of ester bonds. Esterases have gained a prominent position in today's world's industrial enzymes market. Due to their unique biocatalytic attributes, esterases contribute to environmentally sustainable design approaches, including biomass degradation, food and feed industry, dairy, clothing, agrochemical (herbicides, insecticides), bioremediation, biosensor development, anticancer, antitumor, gene therapy, and diagnostic purposes. Esterases can be isolated by a diverse range of mammalian tissues, animals, and microorganisms. The isolation of extremophilic esterases increases the interest of researchers in the extraction and utilization of these enzymes at the industrial level. Genomic, metagenomic, and immobilization techniques have opened innovative ways to extract esterases and utilize them for a longer time to take advantage of their beneficial activities. The current study discusses the types of esterases, metagenomic studies for exploring new esterases, and their biomedical applications in different industrial sectors.

Insufficiency in functional genomics studies, data, and applications: A case study of bio-prospecting research in ruminant microbiome

Over the last two decades, biotechnology has advanced at a rapid pace, propelled by the incorporation of bio-products into various aspects of pharmaceuticals, industry, and the environment. These developments have sparked interest in the bioprospecting of microorganisms and their products in a variety of niche environments. Furthermore, the use of omics technologies has greatly aided our analyses of environmental samples by elucidating the microbial ecological framework, biochemical pathways, and bio-products. However, the more often overemphasis on taxonomic identification in most research publications, as well as the data associated with such studies, is detrimental to immediate industrial and commercial applications. This review identifies several factors that contribute to the complexity of sequence data analysis as potential barriers to the pragmatic application of functional genomics, utilizing recent research on ruminants to demonstrate these limitations in the hopes of broadening our horizons and drawing attention to this gap in bioprospecting studies for other niche environments as well. The review also aims to emphasize the importance of routinely incorporating functional genomics into environmental metagenomics analyses in order to improve solutions that drive rapid industrial biocatalysis developments from derived outputs with the aim of achieving potential benefits in energy-use reduction and environmental considerations for current and future applications.

The release and catabolism of ferulic acid in plant cell wall by rumen microbes: A review

Ferulic acid (FA) is one of the most abundant hydroxycinnamic acids in the plant world, especially in the cell wall of grain bran, in comparison with forage and crop residues. Previous studies noted that FA was mainly linked with arabinoxylans and lignin in plant cell walls in ester and ether covalent forms. After forages were ingested by ruminant animals or encountered rumen microbial fermentation in vitro, these cross-linkages form physical and chemical barriers to protect cell-wall carbohydrates from microbial attack and enzymatic hydrolysis. Additionally, increasing studies noted that FA presented some toxic effect on microbial growth in the rumen. In recent decades, many studies have addressed the relationships of ester and/or ether-linked FA with rumen nutrient digestibility, and there is still some controversy whether these linkages could be used as a predicator of forage digestibility in ruminants. The authors in this review summarized the possible relationships between ester and/or ether-linked FA and fiber digestion in ruminants. Rumen microbes, especially bacteria and fungi, were found capable of breaking down the ester linkages within plant cell walls by secreting feruloyl and p-coumaroyl esterase, resulting in the release of free FA and improvement of cell wall digestibility. The increasing evidence noted that these esterases secreted by rumen microbes presented synergistic effects with xylanase and cellulase to effectively hydrolyze forage cell walls. Some released FA were absorbed through the rumen wall directly and entered into blood circulation and presented antioxidant effects on host animals. The others were partially catabolized into volatile fatty acids by rumen microbes, and the possible catabolic pathways discussed. To better understand plant cell wall degradation in the rumen, the metabolic fate of FA along with lignin decomposition mechanisms are needed to be explored via future microbial isolation and incubation studies with aims to maximize dietary fiber intake and enhance fiber digestion in ruminant animals.

Enzyme Production Potential of Penicillium oxalicum M1816 and Its Application in Ferulic Acid Production

The present study focused on isolating an efficient enzyme production microorganism for ferulic acid (FA) production from wheat bran. A wild-type cellulase-, xylanase-, and feruloyl esterase-producing strain was isolated and identified as Penicillium oxalicum M1816. The genome was sequenced and assembled into 30.5 Mb containing 8301 predicted protein-coding genes. In total, 553 genes were associated with carbohydrate metabolism. Genomic CAZymes analysis indicated that P. oxalicum M1816, comprising 39 cellulolytic enzymes and 111 hemicellulases (including 5 feruloyl esterase genes), may play a vital role in wheat bran degradation and FA production. The crude enzyme of strain M1816 could release 1.85 ± 0.08 mg·g-1 FA from de-starched wheat bran (DSWB) at 12 h, which was significantly higher than other commercial enzymes. Meanwhile, when the strain M1816 was cultured in medium supplemented with DSWB, up to 92.89% of the total alkali-extractable FA was released. The process parameters of solid-state fermentation were optimized to enhance enzyme production. The optimized wheat bran Qu of P. oxalicum M1816 was applied to huangjiu fermentation, and the FA content was increased 12.4-fold compared to the control group. These results suggest that P. oxalicum M1816 is a good candidate for the development of fermented foods bio-fortified with FA.

Genomics as a potential tool to unravel the rhizosphere microbiome interactions on plant health

Intense agricultural practices to meet rising food demands have caused ecosystem perturbations. For sustainable crop production, biological agents are gaining attention, but exploring their functional potential on a multi-layered complex ecosystem like the rhizosphere is challenging. This review explains the significance of genomics as a culture-independent molecular tool to understand the diversity and functional significance of the rhizosphere microbiome for sustainable agriculture. It discusses the recent significant studies in the rhizosphere environment carried out using evolving techniques like metagenomics, metatranscriptomics, and metaproteomics, their challenges, constraints infield application, and prospective solutions. The recent advances in techniques such as nanotechnology for the development of bioformulations and visualization techniques contemplating environmental safety were also discussed. The need for development of metagenomic data sets of regionally important crops, their plant microbial interactions and agricultural practices for narrowing down significant data from huge databases have been suggested. The role of taxonomical and functional diversity of soil microbiota in understanding soil suppression and part played by the microbial metabolites in the process have been analyzed and discussed in the context of 'omics' approach. 'Omics' studies have revealed important information about microbial diversity, their responses to various biotic and abiotic stimuli, and the physiology of disease suppression. This can be translated to crop sustainability and combinational approaches with advancing visualization and analysis methodologies fix the existing knowledge gap to a huge extend. With improved data processing and standardization of the methods, details of plant-microbe interactions can be successfully decoded to develop sustainable agricultural practices.

Efficient ferulic acid and xylo-oligosaccharides production by a novel multi-modular bifunctional xylanase/feruloyl esterase using agricultural residues as substrates

Liberating high value-added compounds ferulic acid (FA) and xylo-oligosaccharides (XOSs) from agricultural residues is a promising strategy for the utilization of lignocellulose. In this study, a bifunctional xylanase/feruloyl esterase from bacterial consortium EMSD5 was heterogeneously expressed in Escherichia coli. Depending on the inter-domain synergism of the recombinant enzyme rXyn10A/Fae1A, high yields of FA (2.78, 1.82, 1.15 and 7.31 mg/g substrate, respectively) were obtained from 20 mg in-soluble wheat arabinoxylan, de-starched wheat bran, ultrafine-grinding corn stover and steam-exploded corncob. Meanwhile, 3.210, 1.235, 1.215 and 0.823 mg xylose/XOSs were also released. For cost-saving enzyme production, we firstly constructed a recombinant E. coli, which could secrete the bifunctional xylanase/feruloyl esterase out of cells. When the recombinant E. coli was cultured in medium containing 200 mg de-starched wheat bran, 474 μg FA and 18.2 mg xylose/XOSs were also detected. Hence, rXyn10A/Fae1A and the recombinant strain showed great applied potential for FA and XOSs production.

A Novel VIII Carboxylesterase with High Hydrolytic Activity Against Ampicillin from a Soil Metagenomic Library

A novel carboxylesterase gene, named dlfae4, was discovered and sequenced from a soil metagenomic library. The dlfae4 gene was composed of 1017 base pairs encoding 338 amino acid residues with a predicted molecular mass of 37.2 kDa. DLFae4 exhibited strong hydrolytic activity towards methyl ferulate under optimum pH and temperature conditions (pH 8.6, 50 °C) and displayed remarkable thermostability, with residual activity as high as 50% after incubation for 3 h at 60 °C. A family VIII esterase DLFae4 was found to contain a typical serine residue within the S-X-X-K motif, which serves as a catalytic nucleophile in class C β-lactamases and family VIII esterases. As a consequence of its high sequence similarity with β-lactamases, DLFae4 exhibited significant hydrolytic activity towards ampicillin. In addition, DLFae4 was found to be the first known member of family VIII carboxylesterases with phthalate-degrading ability. Site-directed mutagenesis studies revealed that Ser11, Lys14, and Tyr121 residues play an essential catalytic role in DLFae4. These new findings, which are of great importance for further in-depth research and engineering development of carboxylesterases, should advance the implementation of biotechnological applications.

Molecular cloning, expression and characterization of a novel feruloyl esterase from a soil metagenomic library with phthalate-degrading activity

OBJECTIVES

To discover novel feruloyl esterases (FAEs) by the function-driven screening procedure from soil metagenome.

RESULTS

A novel FAE gene bds4 was isolated from a soil metagenomic library and over-expressed in Escherichia coli. The recombinant enzyme BDS4 was purified to homogeneity with a predicted molecular weight of 38.8 kDa. BDS4 exhibited strong activity (57.05 U/mg) toward methyl ferulate under the optimum pH and temperature of 8.0 and 37°C. Based on its amino acid sequence and model substrates specificity, BDS4 was classified as a type-C FAE. The quantity of the releasing ferulic acid can be enhanced significantly in the presence of xylanase compared with BDS4 alone from de-starched wheat bran. In addition, BDS4 can also hydrolyze several phthalates such as diethyl phthalate, dimethyl phthalate and dibutyl phthalate.

CONCLUSION

The current investigation discovered a novel FAE with phthalate-degrading activity and highlighted the usefulness of metagenomic approaches as a powerful tool for discovery of novel FAEs.

Applications of Microbial Enzymes in Food Industry

The use of enzymes or microorganisms in food preparations is an age-old process. With the advancement of technology, novel enzymes with wide range of applications and specificity have been developed and new application areas are still being explored. Microorganisms such as bacteria, yeast and fungi and their enzymes are widely used in several food preparations for improving the taste and texture and they offer huge economic benefits to industries. Microbial enzymes are the preferred source to plants or animals due to several advantages such as easy, cost-effective and consistent production. The present review discusses the recent advancement in enzyme technology for food industries. A comprehensive list of enzymes used in food processing, the microbial source of these enzymes and the wide range of their application are discussed.

Feruloyl esterases from Schizophyllum commune to treat food industry side-streams

Agro-industrial side-streams are abundant and renewable resources of hydroxycinnamic acids with potential applications as antioxidants and preservatives in the food, health, cosmetic, and pharmaceutical industries. Feruloyl esterases (FAEs) from Schizophyllum commune were functionally expressed in Pichia pastoris with extracellular activities of 6000UL(-1). The recombinant enzymes, ScFaeD1 and ScFaeD2, released ferulic acid from destarched wheat bran and sugar beet pectin. Overnight incubation of coffee pulp released caffeic (>60%), ferulic (>80%) and p-coumaric acid (100%) indicating applicability for the valorization of food processing wastes and enhanced biomass degradation. Based on substrate specificity profiling and the release of diferulates from destarched wheat bran, the recombinant FAEs were characterized as type D FAEs. ScFaeD1 and ScFaeD2 preferably hydrolyzed feruloylated saccharides with ferulic acid esterified to the O-5 position of arabinose residues and showed an unprecedented ability to hydrolyze benzoic acid esters.

Metagenomics for the development of new biocatalysts to advance lignocellulose saccharification for bioeconomic development

The world economy is moving toward the use of renewable and nonedible lignocellulosic biomasses as substitutes for fossil sources in order to decrease the environmental impact of manufacturing processes and overcome the conflict with food production. Enzymatic hydrolysis of the feedstock is a key technology for bio-based chemical production, and the identification of novel, less expensive and more efficient biocatalysts is one of the main challenges. As the genomic era has shown that only a few microorganisms can be cultured under standard laboratory conditions, the extraction and analysis of genetic material directly from environmental samples, termed metagenomics, is a promising way to overcome this bottleneck. Two screening methodologies can be used on metagenomic material: the function-driven approach of expression libraries and sequence-driven analysis based on gene homology. Both techniques have been shown to be useful for the discovery of novel biocatalysts for lignocellulose conversion, and they enabled identification of several (hemi)cellulases and accessory enzymes involved in (hemi)cellulose hydrolysis. This review summarizes the latest progress in metagenomics aimed at discovering new enzymes for lignocellulose saccharification.

Biotechnological applications of functional metagenomics in the food and pharmaceutical industries

Microorganisms are found throughout nature, thriving in a vast range of environmental conditions. The majority of them are unculturable or difficult to culture by traditional methods. Metagenomics enables the study of all microorganisms, regardless of whether they can be cultured or not, through the analysis of genomic data obtained directly from an environmental sample, providing knowledge of the species present, and allowing the extraction of information regarding the functionality of microbial communities in their natural habitat. Function-based screenings, following the cloning and expression of metagenomic DNA in a heterologous host, can be applied to the discovery of novel proteins of industrial interest encoded by the genes of previously inaccessible microorganisms. Functional metagenomics has considerable potential in the food and pharmaceutical industries, where it can, for instance, aid (i) the identification of enzymes with desirable technological properties, capable of catalyzing novel reactions or replacing existing chemically synthesized catalysts which may be difficult or expensive to produce, and able to work under a wide range of environmental conditions encountered in food and pharmaceutical processing cycles including extreme conditions of temperature, pH, osmolarity, etc; (ii) the discovery of novel bioactives including antimicrobials active against microorganisms of concern both in food and medical settings; (iii) the investigation of industrial and societal issues such as antibiotic resistance development. This review article summarizes the state-of-the-art functional metagenomic methods available and discusses the potential of functional metagenomic approaches to mine as yet unexplored environments to discover novel genes with biotechnological application in the food and pharmaceutical industries.

Cloning, expression of a feruloyl esterase from Aspergillus usamii E001 and its applicability in generating ferulic acid from wheat bran

A cDNA gene (AufaeA), which encodes a mature polypeptide of the type-A feruloyl esterase from Aspergillus usamii E001 (abbreviated to AuFaeA), was cloned and heterologously expressed in Pichia pastoris GS115. One transformant, labeled as P. pastoris GSFaeA4-8, expressing the highest recombinant AuFaeA (reAuFaeA) activity of 10.76 U/ml was selected by the flask expression test. The expressed reAuFaeA was purified to homogeneity with an apparent molecular weight of 36.0 kDa by SDS-PAGE analysis, and characterized using the model substrate of methyl ferulate (MFA). The purified reAuFaeA was optimally active at pH 5.0 and 45 °C, and highly stable at pH 4.0–6.5 and 45 °C or below. Its activity was not significantly affected by metal ions tested and EDTA. The K  m and V  max of reAuFaeA towards MFA were 4.64 mM and 115.5 U/mg, respectively. High-performance liquid chromatography analysis showed that only 9.7 % of total alkali-extractable ferulic acid (FA) was released from destarched wheat bran by reAuFaeA alone. The released FA increased to 36.5 % when reAuFaeA was used together with a recombinant Aspergillus usamii GH family 11 xylanase A, indicating a synergistic interaction between them.

Novel xylanase from a holstein cattle rumen metagenomic library and its application in xylooligosaccharide and ferulic Acid production from wheat straw

A novel gene fragment containing a xylanase was identified from a Holstein cattle rumen metagenomic library. The novel xylanase (Xyln-SH1) belonged to the glycoside hydrolase family 10 (GH10) and exhibited a maximum of 44% identity to the glycoside hydrolase from Clostridium thermocellum ATCC 27405. Xyln-SH1 was heterologously expressed, purified, and characterized. A high level of activity was obtained under the optimum conditions of pH 6.5 and 40 °C. A substrate utilization study indicated that Xyln-SH1 was cellulase-free and strictly specific to xylan from softwood. The synergistic effects of Xyln-SH1 and feruloyl esterase (FAE-SH1) were observed for the release of xylooligosaccharides (XOS) and ferulic acid (FA) from wheat straw. In addition, a high dose of Xyln-SH1 alone was observed to improve the release of FA from wheat straw. These features suggest that this enzyme has substantial potential to improve biomass degradation and industrial applications.