Interspecific evolutionary relationships of alpha-glucuronidase in the genus Aspergillus

The increased availability and production of lignocellulosic agroindustrial wastes has originated proposals for their use as raw material to obtain biofuels (ethanol and biodiesel) or derived products. However, for biomass generated from lignocellulosic residues to be successfully degraded, in most cases it requires a physical (thermal), chemical, or enzymatic pretreatment before the application of microbial or enzymatic fermentation technologies (biocatalysis). In the context of enzymatic technologies, fungi have demonstrated to produce enzymes capable of degrading polysaccharides like cellulose, hemicelluloses and pectin. Because of this ability for degrading lignocellulosic material, researchers are making efforts to isolate and identify fungal enzymes that could have a better activity for the degradation of plant cell walls and agroindustrial biomass. We performed an in silico analysis of alpha-glucoronidase in 82 accessions of the genus Aspergillus. The constructed dendrograms of amino acid sequences defined the formation of 6 groups (I, II, III, IV, V, and VI), which demonstrates the high diversity of the enzyme. Despite this ample divergence between enzyme groups, our 3D structure modeling showed both conservation and differences in amino acid residues participating in enzyme–substrate binding, which indicates the possibility that some enzymes are functionally specialized for the specific degradation of a substrate depending on the genetics of each species in the genus and the condition of the habitat where they evolved. The identification of alpha-glucuronidase isoenzymes would allow future use of genetic engineering and biocatalysis technologies aimed at specific production of the enzyme for its use in biotransformation.     

Site-directed chemically-modified magnetic enzymes: fabrication,improvements, biotechnological applications and future prospects

Numerous enzymes of biotechnological importance have been immobilized on magnetic nanoparticles (MNP) via random multipoint attachment, resulting in a heterogeneous protein population with potential reduction in activity due to restriction of substrate access to the active site. Several chemistries are now available, where the modifier can be linked to a single specific amino acid in a protein molecule away from the active-site, thus enabling free access of the substrate. However, rarely these site-selective approaches have been applied to immobilize enzymes on nanoparticles. In this review, for the first time, we illustrate how to adapt site-directed chemical modification (SDCM) methods for immobilizing enzymes on iron-based MNP. These strategies are mainly chemical but may additionally require genetic and enzymatic methods. We critically examine each method and evaluate their scope for simple, quick, efficient, mild and economical immobilization of enzymes on MNP. The improvements in the catalytic properties of few available examples of immobilized enzymes are also discussed. We conclude the review with the applications and future prospects of site-selectively modified magnetic enzymes and potential benefits of this technology in improving enzymes, including cold-adapted homologues, modular enzymes, and CO₂-sequestering, as well as non-iron based nanomaterials.     

Old pathway — new concept: control of glycolysis by metabolite- modulated dynamic enzyme associations

The presence and kinetic advantages of heterologous interactions between sequential enzymes has been established. Dynamic interactions between the sub-units of oligomeric enzymes may also affect enzymatic activity. If the interactions are specific for certain oligomeric forms of heterologous enzyme pairs, metabolic flux can be modulated by the state of association of enzymes controlled by participating alternatively in homologous and heterologous interactions. A molecular model including the regulatory role of specific metabolites is suggested for the control of glycolysis by pairwise dynamic enzyme associations.     

Application of microarrays in high-throughput enzymatic profiling

This review focuses on recent developments in microarray-based technologies for high-throughput screenings of enzymes. Novel methods of protein immobilization, detection of enzymatic activities, and inhibitions were highlighted.     

A scalable protocol for the isolation of large-sized genomic DNA within an hour from several bacteria

The available methods for assaying of protease activity of unknown or partially defined specificity utilize long peptides, mostly denatured proteins, comprehending at least all coded amino acids in cleavable positions. In contrast, here we report on an alternative approach which utilizes a small synthetic ester substrate containing only one amino acid. The approach equally detects endo- and carboxypeptidases with a wide variety of specificities including enzymes specific for basic, acidic, aromatic, and nonaromatic hydrophobic amino acid moieties. The results further revealed that most proteases could be detected in activities considerably less than 1 U. In contrast to the methods used thus far, the enzymatic hydrolysis of the small substrate can be easily and rapidly assayed by a shift in absorption resulting in a change in color of the assay mixture at visible wavelengths. Thus, no additional instrumental efforts are generally required. On the basis of these characteristics, the approach presented here could be particularly valuable for monitoring the purification of enzymes or as a rapid check for protease activity.     

Activity-based protein profiling in bacteria: Applications for identification of therapeutic targets and characterization of microbial communities

Activity-based protein profiling (ABPP) is a robust chemoproteomic technique that uses activity-based probes to globally measure endogenous enzymatic activity in complex proteomes. It has been utilized extensively to characterize human disease states and identify druggable targets in diverse disease conditions. ABPP has also recently found applications in microbiology. This includes using activity-based probes (ABPs) for functional studies of pathogenic bacteria as well as complex communities within a microbiome. This review will focus on recent advances in the use of ABPs to profile enzyme activity in disease models, screen for selective inhibitors of key enzymes, and develop imaging tools to better understand the host–bacterial interface.     

A strategy for dual inhibition of the proteasome and fatty acid synthase with belactosin C-orlistat hybrids

The proteasome, a validated cellular target for cancer, is central for maintaining cellular homeostasis, while fatty acid synthase (FAS), a novel target for numerous cancers, is responsible for palmitic acid biosynthesis. Perturbation of either enzymatic machine results in decreased proliferation and ultimately cellular apoptosis. Based on structural similarities, we hypothesized that hybrid molecules of belactosin C, a known proteasome inhibitor, and orlistat, a known inhibitor of the thioesterase domain of FAS, could inhibit both enzymes. Herein, we describe proof-of-principle studies leading to the design, synthesis and enzymatic activity of several novel, β-lactone-based, dual inhibitors of these two enzymes. Validation of dual enzyme targeting through activity-based proteome profiling with an alkyne probe modeled after the most potent inhibitor, and preliminary serum stability studies of selected derivatives are also described. These results provide proof of concept for dual targeting of the proteasome and fatty acid synthase-thioesterase (FAS-TE) enabling a new approach for the development of drug-candidates with potential to overcome resistance.     

Potential applications of enzymes immobilized on/in nano materials: A review

Several new types of carriers and technologies have been implemented in the recent past to improve traditional enzyme immobilization which aimed to enhance enzyme loading, activity and stability to decrease the enzyme biocatalyst cost in industrial biotechnology. These include cross-linked enzyme aggregates, microwave-assisted immobilization, click chemistry technology, mesoporous supports and most recently nanoparticle-based immobilization of enzymes. The union of the specific physical, chemical, optical and electrical properties of nanoparticles with the specific recognition or catalytic properties of biomolecules has led to their appearance in myriad novel biotechnological applications. They have been applied time and again for immobilization of industrially important enzymes with improved characteristics. The high surface-to-volume ratio offered by nanoparticles resulted in the concentration of the immobilized entity being considerably higher than that afforded by experimental protocols based on immobilization on planar 2-D surfaces. Enzymes immobilized on nanoparticles showed a broader working pH and temperature range and higher thermal stability than the native enzymes. Compared with the conventional immobilization methods, nanoparticle based immobilization served three important features; (i) nano-enzyme particles are easy to synthesize in high solid content without using surfactants and toxic reagents, (ii) homogeneous and well defined core-shell nanoparticles with a thick enzyme shell can be obtained, and (iii) particle size can be conveniently tailored within utility limits. In addition, with the growing attention paid to cascade enzymatic reaction and in vitro synthetic biology, it is possible that co-immobilization of multi-enzymes could be achieved on these nanoparticles.     

Activity profiling of ectomycorrhiza communities in two forest soils using multiple enzymatic tests

Data on the diversity and distribution of enzyme activities in native ectomycorrhizal (ECM) communities are inadequate. A microplate multiple enzymatic test was developed which makes it possible to measure eight enzyme activities on 14 individual, excised ECM root tips. Hydrolytic and oxidative enzymes are involved in the decomposition of lignocellulose, chitin and phosphorus-containing organic compounds. This test system was used to describe the functional diversity of ECM communities in two forest sites. This set of tests proved to be accurate and sensitive enough to reveal a high diversity of activity profiles, depending on the fungal symbiont and the soil horizon. Ectomycorrhizas can be classified into specialists and generalists, and appear to complement each other in the same horizon to collectively perform all eight activities studied. By including a higher number of different assays for more detailed analyses, ECM activity profiling will provide a valuable tool for studying the functional diversity of ECM communities.     

Enzyme genomics: Application of general enzymatic screens to discover new enzymes

In all sequenced genomes, a large fraction of predicted genes encodes proteins of unknown biochemical function and up to 15% of the genes with "known" function are mis-annotated. Several global approaches are routinely employed to predict function, including sophisticated sequence analysis, gene expression, protein interaction, and protein structure. In the first coupling of genomics and enzymology, Phizicky and colleagues undertook a screen for specific enzymes using large pools of partially purified proteins and specific enzymatic assays. Here we present an overview of the further developments of this approach, which involve the use of general enzymatic assays to screen individually purified proteins for enzymatic activity. The assays have relaxed substrate specificity and are designed to identify the subclass or sub-subclasses of enzymes (phosphatase, phosphodiesterase/nuclease, protease, esterase, dehydrogenase, and oxidase) to which the unknown protein belongs. Further biochemical characterization of proteins can be facilitated by the application of secondary screens with natural substrates (substrate profiling). We demonstrate here the feasibility and merits of this approach for hydrolases and oxidoreductases, two very broad and important classes of enzymes. Application of general enzymatic screens and substrate profiling can greatly speed up the identification of biochemical function of unknown proteins and the experimental verification of functional predictions produced by other functional genomics approaches.     

Enzyme-based antifouling coatings: a review

Abstract

A systematic overview is presented of the literature that reports the antifouling (AF) protection of underwater structures via the action of enzymes. The overall aim of this review is to assess the state of the art of enzymatic AF technology, and to highlight the obstacles that have to be overcome for successful development of enzymatic AF coatings. The approaches described in the literature are divided into direct and indirect enzymatic AF, depending on the intended action of the enzymes. Direct antifouling is used when the enzymes themselves are active antifoulants. Indirect antifouling refers to the use of enzymes to release an active biocide with AF activity. For direct AF, several patents have been granted, and a commercial product has been launched. However, the achievement of an efficient broad-spectrum AF coating based on a single or a few enzymes has not yet been achieved. An indirect AF coating is not yet available commercially. The technology is mainly limited by the instability of substrate supply, whether the substrates are found in the surrounding seawater or in the coating itself. Legislative issues regarding which part(s) of an enzyme system should be regarded as biocidal for product registration purposes are also considered. The above question currently remains unanswered for technologies utilising indirect enzymatic AF.     

Identification of a human trans-3-hydroxy-L-proline dehydratase, the first characterized member of a novel family of proline racemase-like enzymes

A family of eukaryotic proline racemase-like genes has recently been identified. Several members of this family have been well characterized and are known to catalyze the racemization of free proline or trans-4-hydroxyproline. However, the majority of eukaryotic proline racemase-like proteins, including a human protein called C14orf149, lack a specific cysteine residue that is known to be critical for racemase activity. Instead, these proteins invariably contain a threonine residue at this position. The function of these enzymes has remained unresolved until now. In this study, we demonstrate that three enzymes of this type, including human C14orf149, catalyze the dehydration of trans-3-hydroxy-L-proline to Δ(1)-pyrroline-2-carboxylate (Pyr2C). These are the first enzymes of this subclass of proline racemase-like genes for which the enzymatic activity has been resolved. C14orf149 is also the first human enzyme that acts on trans-3-hydroxy-L-proline. Interestingly, a mutant enzyme in which the threonine in the active site is mutated back into cysteine regained 3-hydroxyproline epimerase activity. This result suggests that the enzymatic activity of these enzymes is dictated by a single residue. Presumably, human C14orf149 serves to degrade trans-3-hydroxy-L-proline from the diet and originating from the degradation of proteins that contain this amino acid, such as collagen IV, which is an important structural component of basement membrane.     

Enzyme-based antifouling coatings: a review

A systematic overview is presented of the literature that reports the antifouling (AF) protection of underwater structures via the action of enzymes. The overall aim of this review is to assess the state of the art of enzymatic AF technology, and to highlight the obstacles that have to be overcome for successful development of enzymatic AF coatings. The approaches described in the literature are divided into direct and indirect enzymatic AF, depending on the intended action of the enzymes. Direct antifouling is used when the enzymes themselves are active antifoulants. Indirect antifouling refers to the use of enzymes to release an active biocide with AF activity. For direct AF, several patents have been granted, and a commercial product has been launched. However, the achievement of an efficient broad-spectrum AF coating based on a single or a few enzymes has not yet been achieved. An indirect AF coating is not yet available commercially. The technology is mainly limited by the instability of substrate supply, whether the substrates are found in the surrounding seawater or in the coating itself. Legislative issues regarding which part(s) of an enzyme system should be regarded as biocidal for product registration purposes are also considered. The above question currently remains unanswered for technologies utilising indirect enzymatic AF.     

Activity-based proteomics: enzymatic activity profiling in complex proteomes

Summary. In the postgenomic era new technologies are emerging for global analysis of protein function. The introduction of active site-directed chemical probes for enzymatic activity profiling in complex mixtures, known as activity-based proteomics has greatly accelerated functional annotation of proteins. Here we review probe design for different enzyme classes including serine hydrolases, cysteine proteases, tyrosine phosphatases, glycosidases, and others. These probes are usually detected by their fluorescent, radioactive or affinity tags and their protein targets are analyzed using established proteomics techniques. Recent developments, such as the design of probes for in vivo analysis of proteomes, as well as microarray technologies for higher throughput screenings of protein specificity and the application of activity-based probes for drug screening are highlighted. We focus on biological applications of activity-based probes for target and inhibitor discovery and discuss challenges for future development of this field.     

Conformational changes of enzymes adsorbed at liquid-solid interface: relevance to enzymatic activity

FTIR with attenuated total reflectance spectroscopy was used to study in situ adsorption of enzymes at water-solid interfaces to better understand how conformational changes may monitor enzymatic activity. Because the adsorption process depends on hydrophobic and electrostatic interactions, conformational changes were studied as a function of the nature of the adsorbing substrates, which are hydrophobic or hydrophilic in character. The adsorption kinetics of two examples of serine enzymes, alpha-chymotrypsin (alpha-chym) and Humicola lanuginosa lipase (HLL), were studied. The secondary structure and solvation of the adsorbed enzymes were both compared to the dissolved enzymes. The positively charged alpha-chym was adsorbed on a negatively charged hydrophilic support with minor structural changes, but the negatively charged lipase had no affinity for a similar support. Both enzymes were strongly retained on the hydrophobic support. The secondary and tertiary structures of the alpha-chym adsorbed on the hydrophobic support were strongly altered, which correlates to the inhibition of enzymatic hydrolysis. The specific solvation obtained for the adsorbed HLL is consistent with the existence of the open conformer in relation to the enhanced enzymatic activity at the water-hydrophobic interface.     

Harnessing the power of enzymes for environmental stewardship

Enzymes are versatile catalysts with a growing number of applications in biotechnology. Their properties render them also attractive for waste/pollutant treatment processes and their use might be advantageous over conventional treatments. This review highlights enzymes that are suitable for waste treatment, with a focus on cell-free applications or processes with extracellular and immobilized enzymes. Biological wastes are treated with hydrolases, primarily to degrade biological polymers in a pre-treatment step. Oxidoreductases and lyases are used to biotransform specific pollutants of various nature. Examples from pulp and paper, textile, food and beverage as well as water and chemical industries illustrate the state of the art of enzymatic pollution treatment. Research directions in enzyme technology and their importance for future development in environmental biotechnology are elaborated. Beside biological and biochemical approaches, i.e. enzyme prospection and the design of enzymes, the review also covers efforts in adjacent research fields such as insolubilization of enzymes, reactor design and the use of additives. The effectiveness of enzymatic processes, especially when combined with established technologies, is evident. However, only a limited number of enzymatic field applications exist. Factors like cost and stability of biocatalysts need to be addressed and the collaboration and exchange between academia and industry should be further strengthened to achieve the goal of sustainability.     

Developmental changes in the modification of lysosomal enzymes in Dictyostelium discoideum

Evidence has been found for a generalized change in the post-translational modification of lysosomal enzymes during development of Dictyostelium discoideum. The physical and antigenic properties of four developmentally regulated lysosomal enzymes, N-acetylglucosaminidase, beta-glucosidase, alpha-mannosidase, and acid phosphatase, have been examined throughout the life cycle. In vegetative cells, a single major isoelectric species is detected for each enzymatic activity on native nonequilibrium isoelectric focusing gels. Between 6 and 10 hr of development, all activities, including the preformed enzyme, become less negatively charged, resulting in a modest but reproducible shift in the isoelectric focusing pattern. This alteration is not detected by native gel electrophoresis at constant pH. As development continues, the specific activity of beta-glucosidase, alpha-mannosidase, and acid phosphatase continues to increase and coincidentally, new, less acidic isozymic bands of activity can be observed on both gel systems. Some of these new isozymes accumulate preferentially in anterior cells, while others accumulate preferentially in posterior cells of migrating slugs. N-Acetylglucosaminidase does not increase in specific activity late in development and no new isozymic species appear. Using a monoclonal antibody that reacts with sulfated N-linked oligosaccharides shared by vegetative lysosomal enzymes in D. discoideum, the antigenicity of the developmental isozymes has been characterized. All of the enzymatic activity present during vegetative growth and early development is immunoprecipitable. However, the less negatively charged isozymes that accumulate after aggregation are not recognized by the antibody. Nonantigenic acid phosphatase and alpha-mannosidase are found in both anterior and posterior cells from migrating pseudoplasmodia. Since each enzyme is coded by a single structural gene, these results suggest that the isozymes present late in development arise from the synthesis of the same polypeptides with altered post-translational modifications. The appearance of anterior and posterior specific isozymes is likely to be the result of cell type specific changes in the glycoprotein modification pathway for newly synthesized proteins.     

A general liquid chromatography/mass spectroscopy-based assay for detection and quantitation of methyltransferase activity

Methyltransferases form a large class of enzymes, most of which use S-adenosylmethionine as the methyl donor. In fact, S-adenosylmethionine is second only to ATP in the variety of reactions for which it serves as a cofactor. Several methods to measure methyltransferase activity have been described, most of which are applicable only to specific enzymes and/or substrates. In this work we describe a sensitive liquid chromatography/mass spectroscopy-based methyltransferase assay. The assay monitors the conversion of S-adenosylmethionine to S-adenosylhomocysteine and can be applied to any methyltransferase and substrate of interest. We used the well-characterized enzyme catechol O-methyltransferase to demonstrate that the assay can monitor activity with a variety of substrates, can identify new substrates, and can be used even with crude preparation of enzyme. Furthermore, we demonstrate the utility of the assay for kinetic characterization of enzymatic activity.     

Recent progress and continuing challenges in bio-fuel cells. Part I: enzymatic cells

Recent developments in bio-fuel cell technology are reviewed. A general introduction to bio-fuel cells, including their operating principles and applications, is provided. New materials and methods for the immobilisation of enzymes and mediators on electrodes, including the use of nanostructured electrodes are considered. Fuel, mediator and enzyme materials (anode and cathode), as well as cell configurations are discussed. A detailed summary of recently developed enzymatic fuel cell systems, including performance measurements, is conveniently provided in tabular form. The current scientific and engineering challenges involved in developing practical bio-fuel cell systems are described, with particular emphasis on a fundamental understanding of the reaction environment, the performance and stability requirements, modularity and scalability. In a companion review (Part II), new developments in microbial fuel cell technologies are reviewed in the context of fuel sources, electron transfer mechanisms, anode materials and enhanced O(2) reduction.