Development of a biosensing platform based on a laccase-hydrophobin chimera

Multidomain chimeric enzymes as a promising alternative for biocatalysts improvement: a minireview

Searching for new and better biocatalysts is an area of study in constant development. In nature, mechanisms generally occurring in evolution, such as genetic duplication, recombination, and natural selection processes, produce various enzymes with different architectures and properties. The recombination of genes that code proteins produces multidomain chimeric enzymes that contain two or more domains that sometimes enhance their catalytic properties. Protein engineering has mimicked this process to enhance catalytic activity and the global stability of enzymes, searching for new and better biocatalysts. Here, we present and discuss examples from both natural and synthetic multidomain chimeric enzymes and how additional domains heighten their stability and catalytic activity. Moreover, we also describe progress in developing new biocatalysts using synthetic fusion enzymes and revise some methodological strategies to improve their biological fitness.

Recent Advances in the Development of Oxidoreductase-Based Biosensors for Detection of Phenolic Antioxidants in Food and Beverages

Antioxidants are known to exhibit a protective effect against reactive oxygen species (ROS)-related oxidative damage. As a result, inclusion of exogenous antioxidants in the diet has greatly increased. In this sense, detection and quantification of such antioxidants in various food and beverage items are of eminent importance. Monophenols and polyphenols are among the most prominent natural antioxidants. In this regard, biosensors have emerged as a simple, fast, and economical method for determination of such antioxidants. Owing to the fact that majority of the phenolic antioxidants are electroactive, oxidoreductase enzymes are the most extensively availed bioreceptors for their detection. Herein, the different types of oxidoreductases that have been utilized in biosensors for the biorecognition and quantification of natural phenolic compounds commonly present in foods and beverages are discussed. Apart from the most accustomed electrochemical biosensors, this review sheds light on the alternative transduction systems for the detection of phenolic antioxidants. Recent advances in the strategies involved in enzyme immobilization and surface modification of the biosensing platform are analyzed. This review aims to provide a brief overview of the latest developments in biosensor technology for phenolic antioxidant analysis in foodstuffs and future directions in this field.

Synthetic Biology: Bottom-Up Assembly of Molecular Systems

The bottom-up assembly of biological and chemical components opens exciting opportunities to engineer artificial vesicular systems for applications with previously unmet requirements. The modular combination of scaffolds and functional building blocks enables the engineering of complex systems with biomimetic or new-to-nature functionalities. Inspired by the compartmentalized organization of cells and organelles, lipid or polymer vesicles are widely used as model membrane systems to investigate the translocation of solutes and the transduction of signals by membrane proteins. The bottom-up assembly and functionalization of such artificial compartments enables full control over their composition and can thus provide specifically optimized environments for synthetic biological processes. This review aims to inspire future endeavors by providing a diverse toolbox of molecular modules, engineering methodologies, and different approaches to assemble artificial vesicular systems. Important technical and practical aspects are addressed and selected applications are presented, highlighting particular achievements and limitations of the bottom-up approach. Complementing the cutting-edge technological achievements, fundamental aspects are also discussed to cater to the inherently diverse background of the target audience, which results from the interdisciplinary nature of synthetic biology. The engineering of proteins as functional modules and the use of lipids and block copolymers as scaffold modules for the assembly of functionalized vesicular systems are explored in detail. Particular emphasis is placed on ensuring the controlled assembly of these components into increasingly complex vesicular systems. Finally, all descriptions are presented in the greater context of engineering valuable synthetic biological systems for applications in biocatalysis, biosensing, bioremediation, or targeted drug delivery.

Innovative surface bio-functionalization by fungal hydrophobins and their engineered variants

Research on innovative surface functionalization strategies to develop materials with high added value is particularly challenging since this process is a crucial step in a wide range of fields (i.e., biomedical, biosensing, and food packaging). Up to now, the main applied derivatization methods require hazardous and poorly biocompatible reagents, harsh conditions of temperature and pressure, and are time consuming and cost effective. The discovery of biomolecules able to adhere by non-covalent bonds on several surfaces paves the way for their employment as a replacement of chemical processes. A simple, fast, and environment-friendly method of achieving modification of chemically inert surfaces is offered by hydrophobins, small amphiphilic proteins produced by filamentous fungi. Due to their structural characteristics, they form stable protein layers at interfaces, serving as anchoring points that can strongly bind molecules of interest. In addition, genetic engineering techniques allow the production of hydrophobins fused to a wide spectrum of relevant proteins, providing further benefits in term of time and ease of the process. In fact, it is possible to bio-functionalize materials by simply dip-casting, or by direct deposition, rendering them exploitable, for example, in the development of biomedical and biosensing platforms.

A New Strategy for As(V) Biosensing Based on the Inhibition of the Phosphatase Activity of the Arsenate Reductase from Thermus thermophilus

Arsenic (As) pollution is a widespread problem worldwide. In recent years, biosensors based on enzymatic inhibition have been developed for arsenic detection, making the study of the effect of inhibitors on the selected enzymatic activity crucial for their setup. The arsenate reductase of Thermus thermophilus HB27, TtArsC, reduces As(V) into As(III), but is also endowed with phosphatase activity. This work investigates the inhibitory effects of As(V) and As(III) on phosphatase activity by taking advantage of a simple colorimetric assay; the results show that both of them are non-competitive inhibitors affecting the Vmax but not the K_M of the reaction. However, their Ki values are different from each other (15.2 ± 1.6 μM for As(V) and 394.4 ± 40.3 µm with As(III)), indicating a higher inhibitory effect by As(V). Moreover, the inhibition-based biosystem results to be selective for As(V) since several other metal ions and salts do not affect TtArsC phosphatase activity; it exhibits a sensitivity of 0.53 ± 0.03 mU/mg/μM and a limit of detection (LOD) of 0.28 ± 0.02 μM. The good sensitivity and specificity for As(V) point to consider inhibition of TtArsC phosphatase activity for the setup of a novel biosensor for the detection of As(V).

Engineering multifunctional enzymes for agro-biomass utilization

Lignocellulosic biomass is a plentiful renewable resource that can be converted into a wide range of high-value-added industrial products. However, the complexity of its structural integrity is one of the major constraints and requires combinations of different fibrolytic enzymes for the cost-effective, industrially and environmentally feasible transformation. An interesting approach is constructing multifunctional enzymes, either in a single polypeptide or by joining multiple domains with linkers and performing diverse reactions simultaneously, in a single host. The production of such chimera proteins multiplies the advantages of different enzymatic reactions in a single setup, in lesser time, at lower production cost and with desirable and improved catalytic activities. This review embodies the various domain-tailoring and extracellular secretion strategies, possible solutions to their challenges, and efforts to experimentally connect different catalytic activities in a single host, as well as their applications.

The laccase mediator system at carbon nanotubes for anthracene oxidation and femtomolar electrochemical biosensing

We investigated the use of POXA1b laccase from Pleurotus ostreatus for the oxidation of anthracene into anthraquinone. We show that different pathways can occur depending on the nature of the redox mediator combined to laccase, leading to different structural isomers. The laccase combined with 2,2'-azine-bis(3-ethylbenzothiazoline-6-sulfonic acid (ABTS) leads to the formation of 1,4-anthraquinone and/or 1,2-anthraquinone. The unprecedented role of carbon nanotubes (CNTs) as redox mediators for oxidation of anthracene into 9,10-anthraquinone is shown and corroborated by density-functional theory (DFT) calculations. Owing to the efficient adsorption of anthraquinones at CNT electrodes, anthracene can be detected with low limit-of-detection using either laccase in solution, CNT-supported laccase or laccase immobilized at magnetic beads exploiting the adhesive property of a chimeric hydrophobin-laccase.

A machine learning-enhanced biosensor for mercury detection based on an hydrophobin chimera

Marine waters are becoming contaminated by diverse pollutants at a fast rate, and detection of these water pollutants has become a major concern in recent years. Among these, mercury is considered the most toxic element for human health. At present, despite the commonly used methods for its detection are accurate, they often require sophisticated equipments, have relatively high costs, are demanding and time-consuming. Herein a novel solution to detect mercury (II) pollution in sea water is proposed, and an easy and portable detection method has been developed. Indeed, a hydrophobin based chimera able to both adhere to polystyrene multiwell plates and bind mercury (II) with a consequent fluorescent decrease was designed. The chimera was the recognition element in a fluorescence-based biosensor able to detect mercury (II) in the nM range. Indeed, this biosensor specifically measure Hg²⁺ concentration also in the presence of other metals, reaching a limit of detection of 0.4 nM in tap water and 0.3 nM in sea water. Moreover, the developed biosensor was coupled to machine learning methodologies with the big advantage of predicting mercury concentration levels without the use of classical reader devices, thus allowing in situ monitoring of sea pollution by non-skilled personnel.

A Comprehensive Insight into Fungal Enzymes: Structure, Classification, and Their Role in Mankind's Challenges

Enzymes have played a crucial role in mankind's challenges to use different types of biological systems for a diversity of applications. They are proteins that break down and convert complicated compounds to produce simple products. Fungal enzymes are compatible, efficient, and proper products for many uses in medicinal requests, industrial processing, bioremediation purposes, and agricultural applications. Fungal enzymes have appropriate stability to give manufactured products suitable shelf life, affordable cost, and approved demands. Fungal enzymes have been used from ancient times to today in many industries, including baking, brewing, cheese making, antibiotics production, and commodities manufacturing, such as linen and leather. Furthermore, they also are used in other fields such as paper production, detergent, the textile industry, and in drinks and food technology in products manufacturing ranging from tea and coffee to fruit juice and wine. Recently, fungi have been used for the production of more than 50% of the needed enzymes. Fungi can produce different types of enzymes extracellularly, which gives a great chance for producing in large amounts with low cost and easy viability in purified forms using simple purification methods. In the present review, a comprehensive trial has been advanced to elaborate on the different types and structures of fungal enzymes as well as the current status of the uses of fungal enzymes in various applications.

Immobilization of Antibodies by Genetic Fusion to a Fungal Self-Assembling Adhesive Protein

Although antibody immobilization on solid surfaces is extensively used in several applications, including immunoassays, biosensors, and affinity chromatography, some issues are still challenging. Self-assembling protein layers can be used to coat easily different surfaces by direct deposition. A specific biofunctional layer can be formed using genetic engineering techniques to express fused proteins acting as self-immobilizing antibodies. In this study, fusion proteins combining the self-assembling adhesive properties of a fungal hydrophobin and the functionality of the single chain fragment variables (ScFvs) of two antibodies were produced. The chosen ScFvs are able to recognize marine toxins associated with algal blooms, saxitoxin, and domoic acid, which can bioaccumulate in shellfish and herbivorous fish causing food poisoning. ScFvs fused to hydrophobin Vmh2 from Pleurotus ostreatus were produced in Escherichia coli and recovered from the inclusion bodies. The two fusion proteins retained the functionality of both moieties, being able to adhere on magnetic beads and to recognize and bind the two neurotoxins, even with different performances. Our immobilization procedure is innovative and very easy to implement because it allows the direct functionalization of magnetic beads with ScFvs, without any surface modification. Two different detection principles, electrochemical and optical, were adopted, thus achieving a versatile platform suitable for different antigen detection methods. The sensitivity of the saxitoxin optical biosensor [limit of detection (LOD) 1.7 pg/ml] is comparable to the most sensitive saxitoxin immunosensors developed until now.

Research progress and the biotechnological applications of multienzyme complex

The multienzyme complex system has become a research focus in synthetic biology due to its highly efficient overall catalytic ability and has been applied to various fields. Multienzyme complexes are formed by cascading complexes, which are multiple functionally related enzymes that continuously and efficiently catalyze the production of substrates. Compared with current mainstream microbial cell catalytic systems, in vitro multienzyme molecular machines have many advantages, such as fewer side reactions, a high product yield, a fast reaction speed, easy product separation, a tolerable toxic environment, and robust system operability, showing increasing competitiveness in the field of biomanufacturing. In this review, the research progress of multienzyme complexes in nature and multienzyme cascades in vivo or in vitro will be introduced, and the discovered enzyme cascades concerning scaffolding proteins will also be discussed. This review is expected to provide a more theoretical basis for the modification of multienzyme complexes and broaden their application in the field of synthetic biology. KEY POINTS: • The cascade reactions of some natural multienzyme complexes are reviewed. • The main approaches of constructing artificial multienzyme complexes are summarized. • The structure and application of cellulosomes are discussed and prospected.

Self-assembling thermostable chimeras as new platform for arsenic biosensing

The correct immobilization and orientation of enzymes on nanosurfaces is a crucial step either for the realization of biosensors, as well as to guarantee the efficacy of the developed biomaterials. In this work we produced two versions of a chimeric protein, namely ArsC-Vmh2 and Vmh2-ArsC, which combined the self-assembling properties of Vmh2, a hydrophobin from Pleurotus ostreatus, with that of TtArsC, a thermophilic arsenate reductase from Thermus thermophilus; both chimeras were heterologously expressed in Escherichia coli and purified from inclusion bodies. They were characterized for their enzymatic capability to reduce As(V) into As(III), as well as for their immobilization properties on polystyrene and gold in comparison to the native TtArsC. The chimeric proteins immobilized on polystyrene can be reused up to three times and stored for 15 days with 50% of activity loss. Immobilization on gold electrodes showed that both chimeras follow a classic Langmuir isotherm model towards As(III) recognition, with an association constant (KAsIII) between As(III) and the immobilized enzyme, equal to 650 (± 100) L mol-1 for ArsC-Vmh2 and to 1200 (± 300) L mol-1 for Vmh2-ArsC. The results demonstrate that gold-immobilized ArsC-Vmh2 and Vmh2-ArsC can be exploited as electrochemical biosensors to detect As(III).

Development of anti-bacterial surfaces using a hydrophobin chimeric protein

The search for new approaches for developing antimicrobial surfaces is a challenge of great urgency to prevent and control microbial growth on surfaces. The strategy herein proposed relies on the design of a new, simple and general tool for creating antimicrobial surfaces, based on a hydrophobin chimeric protein which fuses the adhesive self-assembling class I hydrophobin Vmh2 from Pleurotus ostreatus to the human antimicrobial peptide LL-37. The recombinant LL37-Vmh2 protein displayed both the adhesive and the antimicrobic properties of its members, and when deposited on polystyrene surface, a positive effect due to the fusion was observed in terms of both efficacy and versatility of the coating. Indeed, the chimeric protein significantly enlarges the range of pathogens affected by Vmh2 layer rendering it able to inhibit three Gram-positive and two Gram-negative pathogens, selected among the renowned biofilm producer bacteria. Confocal Laser Scanning Microscopy analysis performed on Staphylococcus epidermidis biofilms formed on coated surfaces proved that, besides inhibiting biofilm formation, the LL37-Vmh2 coating also displayed biocidal activity, since dead cells were present in the biofilm layer. The reported results open new perspectives in various fields of application of LL37, and of antimicrobial peptides in general. LL37-Vmh2 increases the inventory of chimeric hydrophobins, further proving their effectiveness and versatility in surface functionalization.

Tree bark scrape fungus: A potential source of laccase for application in bioremediation of non-textile dyes

Although laccase has been recognized as a wonder molecule and green enzyme, the use of low yielding fungal strains, poor production, purification, and low enzyme kinetics have hampered its large-scale application. Thus,this study aims to select high yielding fungal strains and optimize the production, purification, and kinetics of laccase of Aspergillus sp. HB_RZ4. The results obtained indicated that Aspergillus sp. HB_RZ4 produced a significantly large amount of laccase under meso-acidophilic shaking conditions in a medium containing glucose and yeast extract. A 25 μM CuSO4 was observed to enhance the enzyme yield. The enzyme was best purified on a Sephadex G-100 column. The purified enzyme resembled laccase of A. flavus. The kinetics of the purified enzyme revealed high substrate specificity and good velocity of reaction,using ABTS as a substrate. The enzyme was observed to be stable over various pH values and temperatures. The peptide structure of the purified enzyme was found to resemble laccase of A. kawachii IFO 4308. The fungus was observed to decolorize various dyes independent of the requirement of a laccase mediator system.Aspergillus sp. HB_RZ4 was observed to be a potent natural producer of laccase, and it decolorized the dyes even in the absence of a laccase mediator system. Thus, it can be used for bioremediation of effluent that contains non-textile dyes.

From Graphite to Laccase Biofunctionalized Few-Layer Graphene: A "One Pot" Approach Using a Chimeric Enzyme

A chimeric enzyme based on the genetic fusion of a laccase with a hydrophobin domain was employed to functionalize few-layer graphene, previously exfoliated from graphite in the presence of the hydrophobin. The as-produced, biofunctionalized few-layer graphene was characterized by electrochemistry and Raman spectroscopy, and finally employed in the biosensing of phenols such as catechol and dopamine. This strategy paves the way for the functionalization of nanomaterials by hydrophobin domains of chimeric enzymes and their use in a variety of electrochemical applications.