Enzymatic synthesis of galacto-oligosaccharides in an organic-aqueous biphasic system by a novel β-galactosidase from a metagenomic library

Novel Viral DNA Polymerases From Metagenomes Suggest Genomic Sources of Strand-Displacing Biochemical Phenotypes

Viruses are the most abundant and diverse biological entities on the planet and constitute a significant proportion of Earth's genetic diversity. Most of this diversity is not represented by isolated viral-host systems and has only been observed through sequencing of viral metagenomes (viromes) from environmental samples. Viromes provide snapshots of viral genetic potential, and a wealth of information on viral community ecology. These data also provide opportunities for exploring the biochemistry of novel viral enzymes. The in vitro biochemical characteristics of novel viral DNA polymerases were explored, testing hypothesized differences in polymerase biochemistry according to protein sequence phylogeny. Forty-eight viral DNA Polymerase I (PolA) proteins from estuarine viromes, hot spring metagenomes, and reference viruses, encompassing a broad representation of currently known diversity, were synthesized, expressed, and purified. Novel functionality was shown in multiple PolAs. Intriguingly, some of the estuarine viral polymerases demonstrated moderate to strong innate DNA strand displacement activity at high enzyme concentration. Strand-displacing polymerases have important technological applications where isothermal reactions are desirable. Bioinformatic investigation of genes neighboring these strand displacing polymerases found associations with SNF2 helicase-associated proteins. The specific function of SNF2 family enzymes is unknown for prokaryotes and viruses. In eukaryotes, SNF2 enzymes have chromatin remodeling functions but do not separate nucleic acid strands. This suggests the strand separation function may be fulfilled by the DNA polymerase for viruses carrying SNF2 helicase-associated proteins. Biochemical data elucidated from this study expands understanding of the biology and ecological behavior of unknown viruses. Moreover, given the numerous biotechnological applications of viral DNA polymerases, novel viral polymerases discovered within viromes may be a rich source of biological material for further in vitro DNA amplification advancements.

Membrane separation processes for enrichment of bovine and caprine milk oligosaccharides from dairy byproducts

Breast milk is an ideal source of human milk oligosaccharides (HMOs) for isolation and purification. However, breast milk is not for sale and at most is distributed to neonatal intensive care units as donor milk. To overcome this limitation, isolating HMOs analogs including bovine milk oligosaccharides (BMOs) and caprine milk oligosaccharides (CMOs) from other sources is timely and significant. Advances in the development of equipment and analytical methods have revealed that dairy processing byproducts are good sources of BMOs and CMOs. Enrichment of these oligosaccharides from dairy byproducts, such as whey, permeate, and mother liquor, is of increasing academic and economic value. The commonly employed approach for oligosaccharides purification is chromatographic technique, but it is only used at lab scale. In the dairy industry, chromatographic methods (large-scale ion exchange, 10,000 L size) are currently routinely used for the isolation/purification of milk proteins (e.g., lactoferrin). In contrast, membrane technology has been proven to be a suitable approach for the isolation and purification of BMOs and CMOs from dairy byproducts. Therefore, this review simply introduces BMOs and CMOs in dairy processing byproducts. This review also summarizes membrane separation processes for isolating and purifying BMOs and CMOs from different dairy byproducts. Finally, the technological challenges and solutions of each processing strategy are discussed in detail.

Effect of Concentrated Salts Solutions on the Stability of Immobilized Enzymes: Influence of Inactivation Conditions and Immobilization Protocol

This paper aims to investigate the effects of some salts (NaCl, (NH₄)₂SO₄ and Na₂SO₄) at pH 5.0, 7.0 and 9.0 on the stability of 13 different immobilized enzymes: five lipases, three proteases, two glycosidases, and one laccase, penicillin G acylase and catalase. The enzymes were immobilized to prevent their aggregation. Lipases were immobilized via interfacial activation on octyl agarose or on glutaraldehyde-amino agarose beads, proteases on glyoxyl agarose or glutaraldehyde-amino agarose beads. The use of high concentrations of salts usually has some effects on enzyme stability, but the intensity and nature of these effects depends on the inactivation pH, nature and concentration of the salt, enzyme and immobilization protocol. The same salt can be a stabilizing or a destabilizing agent for a specific enzyme depending on its concentration, inactivation pH and immobilization protocol. Using lipases, (NH₄)₂SO₄ generally permits the highest stabilities (although this is not a universal rule), but using the other enzymes this salt is in many instances a destabilizing agent. At pH 9.0, it is more likely to find a salt destabilizing effect than at pH 7.0. Results confirm the difficulty of foreseeing the effect of high concentrations of salts in a specific immobilized enzyme.

Efficient Synthesis of Theaflavin 3-Gallate by a Tyrosinase-Catalyzed Reaction with (-)-Epicatechin and (-)-Epigallocatechin Gallate in a 1-Octanol/Buffer Biphasic System

Theaflavins, the orange-red pigments contained in black tea, have attracted attention as a result of their health-promoting effects. However, their synthetic preparation, in which the enzymatic oxidation of catechol-type catechin is followed by the quinone-induced oxidative dimerization of selectively combined catechol- and pyrogallol-type catechins, provides only a low yield. In the present study, we found that a 1-octanol/buffer biphasic system improved the yield of theaflavin 3-gallate in a tyrosinase-catalyzed synthetic reaction with (-)-epicatechin and (-)-epigallocatechin gallate. When the enzymatic reaction proceeded in a buffer solution, oxidized (-)-epigallocatechin gallate was preferentially used for self-dimerization. However, self-dimerization was suppressed in the octanol phase, allowing oxidized (-)-epigallocatechin gallate to participate in coupling with (-)-epicatechin quinone, leading to effective production of theaflavin 3-gallate. Furthermore, the preferential localization of theaflavin 3-gallate in the octanol phase prevented (-)-epicatechin-quinone-induced degradation.

Metagenome Analysis: a Powerful Tool for Enzyme Bioprospecting

Microorganisms are found throughout every corner of nature, and vast number of microorganisms is difficult to cultivate by classical microbiological techniques. The advent of metagenomics has revolutionized the field of microbial biotechnology. Metagenomics allow the recovery of genetic material directly from environmental niches without any cultivation techniques. Currently, metagenomic tools are widely employed as powerful tools to isolate and identify enzymes with novel biocatalytic activities from the uncultivable component of microbial communities. The employment of next-generation sequencing techniques for metagenomics resulted in the generation of large sequence data sets derived from various environments, such as soil, the human body and ocean water. This review article describes the state-of-the-art techniques and tools in metagenomics and discusses the potential of metagenomic approaches for the bioprospecting of industrial enzymes from various environmental samples. We also describe the unusual novel enzymes discovered via metagenomic approaches and discuss the future prospects for metagenome technologies.

Extremozymes from metagenome: Potential applications in food processing

The long-established use of enzymes for food processing and product formulation has resulted in an increased enzyme market compounding to 7.0% annual growth rate. Advancements in molecular biology and recognition that enzymes with specific properties have application for industrial production of infant, baby and functional foods boosted research toward sourcing the genes of microorganisms for enzymes with distinctive properties. In this regard, functional metagenomics for extremozymes has gained attention on the premise that such enzymes can catalyze specific reactions. Hence, metagenomics that can isolate functional genes of unculturable extremophilic microorganisms has expanded attention as a promising tool. Developments in this field of research in relation to food sector are reviewed.

Improved synthesis of isomaltooligosaccharides using immobilized α-glucosidase in organic-aqueous media

α-Glucosidase was immobilized onto an epoxy-activated resin (Eupergit C) to catalyze maltose into isomaltooligosaccharides (IMO), and then the effects of organic-aqueous media on the enzymatic properties of immobilized α-glucosidase were examined. An immobilization efficiency of 79.61% was obtained under the condition of pH 6.0, ionic strength of 2.0 M, and 30 mg of protein/g of resin. The butyl acetate-aqueous biphasic system was found to significantly improve the catalytic activity of the immobilized enzyme and the yield of IMO. The highest yield of IMO (50.83%, w/w) was obtained at pH 4.5 and 55 °C in a butyl acetate/buffer system (25:75, v/v). In addition, the immobilized enzyme particles were distributed into the organic phase after the completion of transglycosylation, which facilitates the separation and recycling use of the immobilized enzyme. Immobilized α-glucosidase retains a robust reusability in this continuous operation model. The present findings are of potential in improving the IMO manufacturing process.

Recyclable Strategy for the Production of High-Purity Galacto-oligosaccharides by Kluyveromyces lactis

A recyclable strategy for the production of high-purity (>95%) galacto-oligosaccharides (GOS) was developed using Kluyveromyces lactis in both the synthesis and purification steps. For the synthesis of GOS, ethanol-permeabilized cells (p-cells) of K. lactis were used because the enhanced permeability facilitated the mass transfer of the substrate and the release of oligosaccharide products. For the purification of GOS, non-permeabilized K. lactis cells (np-cells) were preferred as a result of their intrinsic cell membrane barrier toward GOS, which led to the selective consumption of carbohydrate. In this way, undesired glucose, galactose, and lactose in the raw GOS solution can be completely removed. This strategy is recyclable not only because of the high stability and reusability of p-cells and np-cells but also because the ethanol, which is simultaneously generated during the purification, can be reused for the preparation of p-cells. The strategy proposed in this study is a promising candidate for the efficient production of high-purity GOS.

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.

Immobilization of thermostable β-galactosidase on epoxy support and its use for lactose hydrolysis and galactooligosaccharides biosynthesis

Thermoresistant, recombinant β-galactosidase from Thermotoga maritima was purified and immobilized on the surface of epoxy-coated magnetic beads. The enzyme, which has hexameric quaternary structure as shown by gel filtration chromatography, attaches to the resin through multiple covalent linkages that involve different subunits. The bound enzyme shows higher stability than the free form. The immobilized enzyme showed to be efficient for the hydrolysis of lactose and the biosynthesis of galactooligosaccharides (GOS). The chemical structure of synthesized GOS has been determined by NMR revealing that the main product was β-3′-galactosyl lactose. Although β-galactosidases from different sources have been used for the same purposes, the distinct advantage of the methodology described in this communication is that the enzyme can be easily produced, purified and immobilized in large quantities.

Continuous synthesis of lactulose in an enzymatic membrane reactor reduces lactulose secondary hydrolysis

Newly developed parallel small-scale enzymatic membrane reactors (EMRs) were used to enhance the synthesis of lactulose using β-galactosidase. Under batch operation, the productivity of lactulose decreased abruptly from 2.72 down to 0.04 mg lactulose/(Uenzymeh) over 35 h of reaction. This was presumably caused by the action of β-galactosidase which performed secondary hydrolysis upon the produced lactulose. The continuous operations of an EMR system led to continuous removal of lactulose in the reactors restricting lactulose degradation caused by secondary hydrolysis. Therefore, continuous lactulose syntheses in the EMRs yielded significantly higher specific productivities under "steady state" conditions. Approximately 0.70 and 0.50 mg lactulose/(U enzyme h) for hydraulic residence times of 5 and 7h were reached, respectively. Continuous lactulose synthesis performed in an EMR system conclusively can circumvent the drawbacks (e.g., secondary hydrolysis) of lactulose synthesis encountered in batch operation. It is, therefore, beneficial in terms of enhanced lactulose productivity and reduced enzyme consumption.

Production and secretion of Lactobacillus crispatus β-galactosidase in Pichia pastoris

Lactobacillus β-galactosidases are mostly heterodimeric proteins, which are encoded by the two overlapping genes, lacL and lacM, and produced in recombinant prokaryotic systems for higher yield. This is the first report on the expression of a heterodimeric β-galactosidase from Lactobacillus crispatus B470 in Pichia pastoris. The overlapping consecutive genes, lacL and lacM, that shared 17 nucleotides were cloned from the genomic DNA of L. crispatus. A recombinant plasmid harboring both expression cassettes of lacL and lacM was constructed and transformed into P. pastoris GS115 competent cells. Two recombinant P. pastoris strains (GSLac01 and GSLac02) showed the highest β-galactosidase activities of 24.5 and 31.0 U/ml in the culture supernatants, respectively. The recombinant β-galactosidase (LcLacLM) from GSLac02 was purified to electrphoretic homogeneity by ion-exchange chromatography and molecular sieve chromatography. Similar to most Lactobacillus β-galactosidases that operate at moderately thermophilic and weak acid to neutral conditions, LcLacLM showed optimal activity at 50°C and pH 5.5-6.5. It's the first report on functional and secretory expression of LacLM-type β-galactosidase in eukaryotic system. This strategy might be applied to the expression of other overlapping genes.