Applications of Functional Amyloids from Fungi: Surface Modification by Class I Hydrophobins

A bio-inspired approach for the synthesis of few-layer graphene using beetle defensive gland extract

Graphene exhibits remarkable properties and holds substantial promise for diverse applications. Its unique combination of thermal, chemical, physical, and biological properties makes it an appealing material for a wide range of uses. But, the lack of an economical and environmentally friendly approach to synthesize good-quality graphene represents an immense challenge for the scientific community. What makes this research unique is the utilization of the defensive gland extract from the beetle species Luprops tristis (Order: Coleoptera, Family: Tenebrionidae) to synthesize a few layers of graphene (FLG). This innovative incorporation of natural resources and exploration of biologically inspired methods provides an eco-friendly and cost-effective alternative to conventional graphene production techniques. The exfoliated graphene displayed antimicrobial effects against both Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) bacteria, with particularly potent bactericidal activity. Additionally, the cytotoxicity assay demonstrated the anti-cancer properties of biosynthesized graphene against Daltons Lymphoma Acetic (DLA) cells.

Exploring the potential of amyloids in biomedical applications: A review

Amyloid is defined as a fibrous quaternary structure formed by assembling protein or peptide monomers into intermolecularly hydrogen linked β-sheets. There is a prevalent issue with protein aggregation and the buildup of amyloid molecules, which results in human neurological illnesses including Alzheimer's and Parkinson's. But it is now evident that many organisms, like bacteria, fungi as well as humans, use the same fibrillar structure to carry out a variety of biological functions, such as structure and protection supporting interface transitions and cell-cell recognition, protein control and storage, epigenetic inheritance, and memory. Recent discoveries of self-assembling amyloidogenic peptides and proteins, based on the amyloid core structure, give rise to interesting biomaterials with potential uses in numerous industries. These functions dramatically diverge from the initial conception of amyloid fibrils as intrinsically diseased entities. Apart from the natural ability of amyloids to spontaneously arrange themselves and their exceptional material characteristics, this aspect has prompted extensive research into engineering artificial amyloids for generating various nanostructures, molecular substances, and combined materials. Here, we discuss significant developments in the artificial design of useful amyloids as well as how amyloid materials serve as examples of how function emerges from protein self-assembly at various length scales.

Assembly strategies for polyethylene-degrading microbial consortia based on the combination of omics tools and the "Plastisphere"

Numerous microorganisms and other invertebrates that are able to degrade polyethylene (PE) have been reported. However, studies on PE biodegradation are still limited due to its extreme stability and the lack of explicit insights into the mechanisms and efficient enzymes involved in its metabolism by microorganisms. In this review, current studies of PE biodegradation, including the fundamental stages, important microorganisms and enzymes, and functional microbial consortia, were examined. Considering the bottlenecks in the construction of PE-degrading consortia, a combination of top-down and bottom-up approaches is proposed to identify the mechanisms and metabolites of PE degradation, related enzymes, and efficient synthetic microbial consortia. In addition, the exploration of the plastisphere based on omics tools is proposed as a future principal research direction for the construction of synthetic microbial consortia for PE degradation. Combining chemical and biological upcycling processes for PE waste could be widely applied in various fields to promote a sustainable environment.

Comparative Study of the Solid-Liquid Interfacial Adsorption of Proteins in Their Native and Amyloid Forms

The adhesive properties of amyloid fibers are thought to play a crucial role in various negative and positive aggregation processes, the study of which might help in their understanding and control. Amyloids have been prepared from two proteins, lysozyme and β-lactoglobulin, as well as an Exendin-4 derivative miniprotein (E5). Thermal treatment was applied to form amyloids and their structure was verified by thioflavin T (ThT), 8-Anilino-1-naphthalenesulfonic acid (ANS) dye tests and electronic circular dichroism spectroscopy (ECD). Adsorption properties of the native and amyloid forms of the three proteins were investigated and compared using the mass-sensitive quartz crystal microbalance (QCM) technique. Due to the possible electrostatic and hydrophobic interactions, similar adsorbed amounts were found for the native or amyloid forms, while the structures of the adsorbed layers differed significantly. Native proteins formed smooth and dense adsorption layers. On the contrary, a viscoelastic, highly loose layer was formed in the presence of the amyloid forms, shown by increased motional resistance values determined by the QCM technique and also indicated by atomic force microscopy (AFM) and wettability measurements. The elongated structure and increased hydrophobicity of amyloids might contribute to this kind of aggregation.

Mycorrhizosphere Bacteria, Rahnella sp. HPDA25, Promotes the Growth of Armillaria gallica and Its Parasitic Host Gastrodia elata

Gastrodia elata is an entirely heterotrophic plant, the growth of which is completely reliant on Armillaria gallica, an orchid mycorrhizal fungus. To avoid damaging ecosystems, G. elata cultivation is shifting from woodland to farmland. However, whether the microbial community structure remains stable during this conversation is unknown. Here, we cultivated G. elata in woodland or farmland and found that woodland-cultivated G. elata produced a greater yield and larger tuber size. The relative abundance of Rahnella was 22.84- and 122.25-fold higher in woodland- and farmland-cultivated soil samples, respectively, than that in uncultivated soil samples. To investigate how Rahnella impacts the growth of G. elata and establishes symbiosis with Armillaria gallica, three Rahnella spp. strains (HPDA25, SBD3, and SBD11) were isolated from mycorrhizosphere soil samples. It was found that these strains, especially HPDA25, promoted the growth of A. gallica. Ultra-performance liquid chromatography coupled to a triple quadrupole mass spectrometry analysis detected the indole-3-acetic acid with 16.24 ng/ml in HPDA25 fermentation solution. Co-culturing with the strain HPDA25 or exogenous indole-3-acetic acid increased the branching and fresh weight of rhizomorphs and the growth rate and extracellular laccase activity of A. gallica, compared with A. gallica cultured alone. The results of RNA-seq and quantitative real-time polymerase chain reaction analysis showed that co-culturing A. gallica with HPDA25 increased the expression level of the genes including hydrophobin, SUR7/PalI family, and pectin methylesterase, whereas decreased the expression levels of glycolysis-related genes. Furthermore, co-culturing with the strain HPDA25, A. gallica promotes the growth of G. elata and enhances the tuber size of G. elata. These results provide new insights into an orchid mycorrhizal symbiosis and the cultivation of G. elata.

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.

Soluble Expression and Efficient Purification of Recombinant Class I Hydrophobin DewA

Hydrophobins are small proteins (<20 kDa) with an amphipathic tertiary structure that are secreted by various filamentous fungi. Their amphipathic properties provide surfactant-like activity, leading to the formation of robust amphipathic layers at hydrophilic–hydrophobic interfaces, which make them useful for a wide variety of industrial fields spanning protein immobilization to surface functionalization. However, the industrial use of recombinant hydrophobins has been hampered due to low yield from inclusion bodies owing to the complicated process, including an auxiliary refolding step. Herein, we report the soluble expression of a recombinant class I hydrophobin DewA originating from Aspergillus nidulans, and its efficient purification from recombinant Escherichia coli. Soluble expression of the recombinant hydrophobin DewA was achieved by a tagging strategy using a systematically designed expression tag (ramp tag) that was fused to the N-terminus of DewA lacking the innate signal sequence. Highly expressed recombinant hydrophobin DewA in a soluble form was efficiently purified by a modified aqueous two-phase separation technique using isopropyl alcohol. Our approach for expression and purification of the recombinant hydrophobin DewA in E. coli shed light on the industrial production of hydrophobins from prokaryotic hosts.

Graphene oxide biohybrid layer enhances sensitivity and anticorrosive properties in refractive index sensor

Graphene-based materials are capable of enhancing the refractometric response of prism- and optical fiber-based surface plasmon resonance (SPR) sensors; however, complicated multistep and time-consuming attaching processes could limit their practical applications. Herein, for the first time, we demonstrate the immobilization of graphene oxide (GO) submicrometric sheets onto the surface of a gold-coated single-mode fiber using a coating of fungal self-assembling proteins, the hydrophobins (HFBs), as an adhesive nanolayer. Hetero-core fiber tip SPR structures used in this study, consisting of a mirrored multimode–single-mode fiber structure coated with different thin layers (a chromium layer of 3 nm and a gold layer of 30 nm on top) exhibited a refractive index sensitivity (SRI) of 1842 nm RIU−1 (RIU: refractive index unit) at a refractive index (RI) of 1.36. Self-assembly of GO over the SPR fiber tip via HFB, offered an enhancement of up to 20% in the SRI. Moreover, this HFB-GO coating prevented degradation of the Al thin film mirror caused by corrosive salt-water solutions. The process is very simple, harmless, rapid (around 15 min) and scalable, as it is mostly based on one plasma treatment, which can be performed in large chambers and two dip coating steps, in liquid baths. All these features make the use of self-assembled bio/non-bio hybrid coating a green industrial method to improve the performance of SPR fiber biosensors, if compared with traditional chemical methods. Materials applied in this technology, fungal proteins and derivatives of graphite, are sustainable and largely available.

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.

Fungal potential for the degradation of petroleum-based polymers: An overview of macro- and microplastics biodegradation

Petroleum-based plastic materials as pollutants raise concerns because of their impact on the global ecosystem and on animal and human health. There is an urgent need to remove plastic waste from the environment to overcome the environmental crisis of plastic pollution. This review describes the natural and unique ability of fungi to invade substrates by using enzymes that have the capacity to detoxify pollutants and are able to act on nonspecific substrates, the fungal ability to produce hydrophobins for surface coating to attach hyphae to hydrophobic substrates, and hyphal ability to penetrate three dimensional substrates. Fungal studies on macro- and microplastics biodegradation have shown that fungi are able to use these materials as the sole carbon and energy source. Further research is required on novel isolates from plastisphere ecosystems, on the use of molecular techniques to characterize plastic-degrading fungi and enhance enzymatic activity levels, and on the use of omics-based technologies to accelerate plastic waste biodegradation processes. The addition of pro-oxidants species (photosensitizers) and the reduction of biocides and antioxidant stabilizers used in the plastic manufacturing process should also be considered to promote biodegradation. Interdisciplinary research and innovative fungal strategies for plastic waste biodegradation, as well as ecofriendly manufacturing of petroleum-based plastics, may help to reduce the negative impacts of plastic waste pollution in the biosphere.

Denatured lysozyme-coated carbon nanotubes: a versatile biohybrid material

Carbon nanotubes (CNTs) are among the most versatile nanomaterials, but their exploitation is hindered by limited dispersibility, especially in aqueous solvents. Here, we show that AP-LYS, a highly cationic soluble derivative of denatured hen egg lysozyme, is a very effective tool for the unbundling and solubilisation of CNTs. AP-LYS proved to mediate the complete and stable dispersion of CNTs at protein: CNT ratios ≥1: 3 (w:w) in very mild conditions (10–20 minutes sonication in ammonium acetate buffer, pH 5.0). Electrophoretic mobility and ζ-potential measurements confirmed that dispersed CNTs were coated by the protein, whereas molecular docking was used to study the interactions between AP-LYS and CNTs. AP-LYS-coated CNTs proved to be a very effective microbial cell-flocculating agent with an efficiency similar to that of chitosan, one of the best available flocculating agents, thus suggesting that this hybrid could find industrial applications in the treatment of wastewaters contaminated by microbial cells, or to remove microbial cells after fermentation processes. Moreover, we exploited the low stability of AP-LYS-coated CNT dispersions in eukaryotic cell culture media to prepare scaffolds with an extracellular matrix-like rough surface for the cultivation of eukaryotic cells.

Targeting Antitumoral Proteins to Breast Cancer by Local Administration of Functional Inclusion Bodies

Two structurally and functionally unrelated proteins, namely Omomyc and p31, are engineered as CD44-targeted inclusion bodies produced in recombinant bacteria. In this unusual particulate form, both types of protein materials selectively penetrate and kill CD44+ tumor cells in culture, and upon local administration, promote destruction of tumoral tissue in orthotropic mouse models of human breast cancer. These findings support the concept of bacterial inclusion bodies as versatile protein materials suitable for application in chronic diseases that, like cancer, can benefit from a local slow release of therapeutic proteins.

Versatile biomimetic medical device surface: hydrophobin coated, nitric oxide-releasing polymer for antimicrobial and hemocompatible applications

In medical device design, there is a vital need for a coating that promotes treatment of the patient and simultaneously prevents fouling by biomacromolecules which in turn can progress to infections, thrombosis, and other device-related complications. In this work, hydrophobin SC3 (SC3), a self-assembling amphiphilic protein, was coated on a nitric oxide (NO) releasing medical grade polymer to provide an antifouling layer to work synergistically with NO's bactericidal and antiplatelet activity (SC3-NO). The contact angle of SC3 samples were ∼30% lesser than uncoated control samples and was maintained for a month in physiological conditions, demonstrating a stable, hydrophilic coating. NO release characteristics were not adversely affected by the SC3 coating and samples with SC3 coating maintained NO release. Fibrinogen adsorption was reduced over tenfold on SC3 coated samples when compared to non-SC3 coated samples. The viable cell count of adhered bacteria (Staphylococcus aureus) on SC3-NO was 79.097 ± 7.529% lesser than control samples and 49.533 ± 18.18% lesser than NO samples. Platelet adherence on SC3-NO was reduced by 73.407 ± 14.59% when compared to control samples and 53.202 ± 25.67 when compared to NO samples. Finally, the cytocompatibility of SC3-NO was tested and proved to be safe and not trigger a cytotoxic response. The overall favorable results from the physical, chemical and biological characterization analyses demonstrate the novelty and importance of a naturally-produced antifouling layer coated on a bactericidal and antiplatelet polymer, and thus will prove to be advantageous in a multitude of medical device applications.

Assembly and disassembly of Aspergillus fumigatus conidial rodlets

The rodlet structure present on the Aspergillus fumigatus conidial surface hides conidia from immune recognition. In spite of the essential biological role of the rodlets, the molecular basis for their self-assembly and disaggregation is not known. Analysis of the soluble forms of conidia-extracted and recombinant RodA by NMR spectroscopy has indicated the importance of disulfide bonds and identified two dynamic regions as likely candidates for conformational change and intermolecular interactions during conversion of RodA into the amyloid rodlet structure. Point mutations introduced into the RODA sequence confirmed that (1) mutation of a single cysteine was sufficient to block rodlet formation on the conidial surface and (2) both presumed amyloidogenic regions were needed for proper rodlet assembly. Mutations in the two putative amyloidogenic regions retarded and disturbed, but did not completely inhibit, the formation of the rodlets in vitro and on the conidial surface. Even in a disturbed form, the presence of rodlets on the surface of the conidia was sufficient to immunosilence the conidium. However, in contrast to the parental conidia, long exposure of mutant conidia lacking disulfide bridges within RodA or expressing RodA carrying the double (I115S/I146G) mutation activated dendritic cells with the subsequent secretion of proinflammatory cytokines. The immune reactivity of the RodA mutant conidia was not due to a modification in the RodA structure, but to the exposure of different pathogen-associated molecular patterns on the surface as a result of the modification of the rodlet surface layer. The full degradation of the rodlet layer, which occurs during early germination, is due to a complex array of cell wall bound proteases. As reported earlier, this loss of the rodlet layer lead to a strong anti-fumigatus host immune response in mouse lungs.

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

A simple and stable immobilization of a laccase from Pleurotus ostreatus was obtained through genetic fusion with a self-assembling and adhesive class I hydrophobin. The chimera protein was expressed in Pichia pastoris and secreted into the culture medium. The crude culture supernatant was directly used for coatings of polystyrene multi-well plates without additional treatments, a procedure that resulted in a less time-consuming and chemicals reduction. Furthermore, the gene fusion yielded a positive effect with respect to the wild-type recombinant enzyme in terms of both immobilization and stability. The multi-well plate with the immobilized chimera was used to develop an optical biosensor to monitor two phenolic compounds: L-DOPA ((S)-2-amino-3-(3,4-dihydroxyphenyl) propanoic acid) and caffeic acid (3-(3,4-dihydroxyphenyl)-2-propenoic acid); the estimation of which is a matter of interest in the pharmaceutics and food field. The method was based on the use of the analytes as competing inhibitors of the laccase-mediated ABTS oxidation. The main advantages of the developed biosensor are the ease of preparation, the use of small sample volumes, and the simultaneous analysis of multiple samples on a single platform.

Bacterial inclusion bodies are industrially exploitable amyloids

Understanding the structure, functionalities and biology of functional amyloids is an issue of emerging interest. Inclusion bodies, namely protein clusters formed in recombinant bacteria during protein production processes, have emerged as unanticipated, highly tunable models for the scrutiny of the physiology and architecture of functional amyloids. Based on an amyloidal skeleton combined with varying amounts of native or native-like protein forms, bacterial inclusion bodies exhibit an unusual arrangement that confers mechanical stability, biological activity and conditional protein release, being thus exploitable as versatile biomaterials. The applicability of inclusion bodies in biotechnology as enriched sources of protein and reusable catalysts, and in biomedicine as biocompatible topographies, nanopills or mimetics of endocrine secretory granules has been largely validated. Beyond these uses, the dissection of how recombinant bacteria manage the aggregation of functional protein species into structures of highly variable complexity offers insights about unsuspected connections between protein quality (conformational status compatible with functionality) and cell physiology.

Self-Assembling Protein-Polymer Bioconjugates for Surfaces with Antifouling Features and Low Nonspecific Binding

A new method is demonstrated for preparing antifouling and low nonspecific adsorption surfaces on poorly reactive hydrophobic substrates, without the need for energy-intensive or environmentally aggressive pretreatments. The surface-active protein hydrophobin was covalently modified with a controlled radical polymerization initiator and allowed to self-assemble as a monolayer on hydrophobic surfaces, followed by the preparation of antifouling surfaces by Cu(0)-mediated living radical polymerization of poly(ethylene glycol) methyl ether acrylate (PEGA) performed in situ. By taking advantage of hydrophobins to achieve at the same time the immobilization of protein A, this approach allowed to prepare surfaces for IgG1 binding featuring greatly reduced nonspecific adsorption. The success of the surface modification strategy was investigated by contact angle, XPS, and AFM characterization, while the antifouling performance and the reduction of nonspecific binding were confirmed by QCM-D measurements.

Environmentally friendly covalent coupling of proteins onto oxidized cellulosic materials

Cellulose is a biodegradable and renewable material that is one of the most abundant biopolymers with many different applications from low value newsprint products to high value biomedical sensor devices.

Insights into Stabilizing Forces in Amyloid Fibrils of Differing Sizes from Polarizable Molecular Dynamics Simulations

Pathological aggregation of amyloid-forming proteins is a hallmark of a number of human diseases, including Alzheimer's, type 2 diabetes, Parkinson's, and more. Despite having very different primary amino acid sequences, these amyloid proteins form similar supramolecular, fibril structures that are highly resilient to physical and chemical denaturation. To better understand the structural stability of disease-related amyloids and to gain a greater understanding of factors that stabilize functional amyloid assemblies, insights into tertiary and quaternary interactions are needed. We performed molecular dynamics simulations on human tau, amyloid-β, and islet amyloid polypeptide fibrils to determine key physicochemical properties that give rise to their unique characteristics and fibril structures. These simulations are the first of their kind in employing a polarizable force field to explore properties of local electric fields on dipole properties and other electrostatic forces that contribute to amyloid stability. Across these different amyloid fibrils, we focused on how the underlying forces stabilize fibrils to elucidate the driving forces behind the protein aggregation. The polarizable model allows for an investigation of how side-chain dipole moments, properties of structured water molecules in the fibril core, and the local environment around salt bridges contribute to the formation of interfaces essential for fibril stability. By systematically studying three amyloidogenic proteins of various fibril sizes for key structural properties and stabilizing forces, we shed light on properties of amyloid structures related to both diseased and functional states at the atomistic level.

Pichia pastoris is a Suitable Host for the Heterologous Expression of Predicted Class I and Class II Hydrophobins for Discovery, Study, and Application in Biotechnology

The heterologous expression of proteins is often a crucial first step in not only investigating their function, but also in their industrial application. The functional assembly and aggregation of hydrophobins offers intriguing biotechnological applications from surface modification to drug delivery, yet make developing systems for their heterologous expression challenging. In this article, we describe the development of Pichia pastoris KM71H strains capable of solubly producing the full set of predicted Cordyceps militaris hydrophobins CMil1 (Class IA), CMil2 (Class II), and CMil3 (IM) at mg/L yields with the use of 6His-tags not only for purification but for their detection. This result further demonstrates the feasibility of using P. pastoris as a host organism for the production of hydrophobins from all Ascomycota Class I subdivisions (a classification our previous work defined) as well as Class II. We highlight the specific challenges related to the production of hydrophobins, notably the challenge in detecting the protein that will be described, in particular during the screening of transformants. Together with the literature, our results continue to show that P. pastoris is a suitable host for the soluble heterologous expression of hydrophobins with a wide range of properties.

Evaluating the potential of natural surfactants in the petroleum industry: the case of hydrophobins

Enhancing oil recovery from currently available reservoirs is a major issue for petroleum companies. Among the possible strategies towards this, chemical flooding through injection of surfactants into the wells seems to be particularly promising, thanks to their ability to reduce oil/water interfacial tension that promotes oil mobilization. Environmental concerns about the use of synthetic surfactants led to a growing interest in their replacement with surfactants of biological origin, such as lipopeptides and glycolipids produced by several microorganisms. Hydrophobins are small amphiphilic proteins produced by filamentous fungi with high surface activity and good emulsification properties, and may represent a novel sustainable tool for this purpose. We report here a thorough study of their stability and emulsifying performance towards a model hydrocarbon mixture, in conditions that mimic those of real oil reservoirs (high salinity and high temperature). Due to the moderate interfacial tension reduction induced in such conditions, the application of hydrophobins in enhanced oil recovery techniques does not appear feasible at the moment, at least in absence of co-surfactants. On the other hand, the obtained results showed the potential of hydrophobins in promoting the formation of a gel-like emulsion ‘barrier’ at the oil/water interface.